10 references - inflibnetshodhganga.inflibnet.ac.in/bitstream/10603/6271/15/15_chapter 10.pdf ·...

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References References Abdalla AM, Reddy OUK, El-Zik KM, Pepper AE (2001) Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP.Theor Appl Genet 102: 222-229 Adin A, Weber JC, Sotelo Montes C, Vidaurre H, Vosman B, Smulders MJ (2004) Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management. Theor Appl Genet 2004 Feb 18 [Epub ahead of print] Alberola TM, Frutos R (1996) Molecular structure of a gypsy element of Drosophila subobscura (gypsyDs) constituting a degenerate form of insect retroviruses Nucleic Acids Res. 24: 914-923 Allaby RG, Brown TA (2000) Identification of a 5S rDNA spacer type specific to Triticum urartu and wheats containing the T. urartu genome. Genome 43: 250-254 Alonso-Blanco C, Peeters AJ, Koorneef M, Lister C, Dean C, van den Bosch N, Pot J, Kuiper MT (1998) Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J 14: 259-71 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410 Alvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phyl Evol 29: 417–434 Al-Zahim MA, Ford-Lloyd BV, Newbury HJ (1999) Detection of somaclonal variation in garlic (Allium sativum L.) using RAPD and cytological analysis. Plant Cell Rep 18: 473-477 Amarasinghe V, Carlson J (1998) Physical mapping and characterization of 5S rRNA genes in Douglas-fir. Journal of Heredity 89: 495-500 Andrade LB, Echeverrigaray S, Fracaro F, Pauletti GF, Rota L (1999) The effect of growth regulators on shoot propagation and rooting of common lavender (Lavandula vera DC). Pl Cell Tiss Org Cult 8: 235-242 Appels R, Dvorak J (1982) The wheat ribosomal DNA spacer region: its structure and variation in populations and among species. Theor. Appl. Genet. 63: 337-348 Appels R, Honeycutt RL (1986) rDNA evolution over a billion years. In: Dutta SK (ed) DNA systematics, vol II, CRC Press, Boca Raton, FL, 81-55 Appels R, Driscoll C, Peacock WJ (1978) Heterochromatin and highly repeated DNA sequences in rye (Secale cereale). Chromosoma 70: 67-89 Appels R, Reddy P, McIntyre CL, Moran LB, Frankel OH, Clarke BC (1989). The molecular-cytogenetic analysis of grasses and its applications to studying relationships among species of the Triticeae. Genome 31: 122-133. Appels R, Baum BR, Clarke BC (1992) The 5S DNA units of bread wheat ( Triticum aestivum). Pl Syst Evol 183: 183-194 10

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References

References

Abdalla AM, Reddy OUK, El-Zik KM, Pepper AE (2001) Genetic diversity and

relationships of diploid and tetraploid cottons revealed using AFLP.Theor Appl

Genet 102: 222-229

Adin A, Weber JC, Sotelo Montes C, Vidaurre H, Vosman B, Smulders MJ (2004)

Genetic differentiation and trade among populations of peach palm (Bactris

gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource

management. Theor Appl Genet 2004 Feb 18 [Epub ahead of print]

Alberola TM, Frutos R (1996) Molecular structure of a gypsy element of Drosophila

subobscura (gypsyDs) constituting a degenerate form of insect retroviruses Nucleic

Acids Res. 24: 914-923

Allaby RG, Brown TA (2000) Identification of a 5S rDNA spacer type specific to

Triticum urartu and wheats containing the T. urartu genome. Genome 43: 250-254

Alonso-Blanco C, Peeters AJ, Koorneef M, Lister C, Dean C, van den Bosch N, Pot J,

Kuiper MT (1998) Development of an AFLP based linkage map of Ler, Col and Cvi

Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred

line population. Plant J 14: 259-71

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment

search tool. J Mol Biol 215: 403-410

Alvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic

inference. Mol Phyl Evol 29: 417–434

Al-Zahim MA, Ford-Lloyd BV, Newbury HJ (1999) Detection of somaclonal

variation in garlic (Allium sativum L.) using RAPD and cytological analysis. Plant

Cell Rep 18: 473-477

Amarasinghe V, Carlson J (1998) Physical mapping and characterization of 5S rRNA

genes in Douglas-fir. Journal of Heredity 89: 495-500

Andrade LB, Echeverrigaray S, Fracaro F, Pauletti GF, Rota L (1999) The effect of

growth regulators on shoot propagation and rooting of common lavender

(Lavandula vera DC). Pl Cell Tiss Org Cult 8: 235-242

Appels R, Dvorak J (1982) The wheat ribosomal DNA spacer region: its structure

and variation in populations and among species. Theor. Appl. Genet. 63: 337-348

Appels R, Honeycutt RL (1986) rDNA evolution over a billion years. In: Dutta SK

(ed) DNA systematics, vol II, CRC Press, Boca Raton, FL, 81-55

Appels R, Driscoll C, Peacock WJ (1978) Heterochromatin and highly repeated DNA

sequences in rye (Secale cereale). Chromosoma 70: 67-89

Appels R, Reddy P, McIntyre CL, Moran LB, Frankel OH, Clarke BC (1989). The

molecular-cytogenetic analysis of grasses and its applications to studying

relationships among species of the Triticeae. Genome 31: 122-133.

Appels R, Baum BR, Clarke BC (1992) The 5S DNA units of bread wheat (Triticum

aestivum). Pl Syst Evol 183: 183-194

10

References

Arcade A, Anselin F, Rampant P F, Lesage M C, Paques L E, Prat D (2000)

Application of AFLP, RAPD and ISSR markers to genetic mapping of European and

Japanese larch. Theor Appl Genet 100: 299-307

Archak S, Gaikwad AB, Gautam D, Rao EV, Swamy KR, Karihaloo JL (2003)

Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP)

for genetic analysis of cashew (Anacardium occidentale L.) accessions of India.

Genome. 46:362-9.

Arnheim N (1983) Concerted evolution of multigene families. In: Nei M, Koehn RK

(eds) Evolution of genes and proteins. Sinauer Associates, Sunderland, MA, USA.

Pp 38-61

Arumuganathan K, Earle ED (1991) Estimation of nuclear DNA content of plants by

flow cytometry. Plant Mol Biol Rep 9: 229-241

Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau JY, Telismart H, Girard JC, Raboin

LM, Risterucci AM, Grivet L, D'Hont A (2004) Targeted mapping of a sugarcane

rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers.

Theor Appl Genet 108: 759-764

Awasthi AK, GM Nagaraja, GV Naik, Kanginakudru S, Thangavelu K, Nagaraju J

(2004) Genetic diversity and relationships in mulberry (genus Morus) as revealed

by RAPD and ISSR marker assays. BMC Genet. 5: 1

Baker WJ, Hedderson TA, Dransfield J (2000) Molecular phylogenetics of Calamus

(Palmae) and related rattan genera based on 5S nrDNA spacer sequence data. Mol

Phyl Evol 14: 218-231

Barciszewska MZ, Mashkova TD, Kisselev LL, Barciszewski J (1987) The nucleotide

sequence of 5S ribosomal RNAs from two plants: rape and white beet. Nucl Acids

Res 15: 363-364

Barker JH, Matthes M, Arnold GM, Edwards KJ, Ahman I, Larsson S, Karp A (1999)

Characterisation of genetic diversity in potential biomass willows (Salix spp.) by

RAPD and AFLP analyses. Genome 42: 173–183

Barrett JW, Rajora OP, Yeh FCH, Dancik BP, Strobeck C (1993) Mitochondrial DNA

variation and genetic relationships of Populus species. Genome 36:87-93

Basten CJ, Ohta T (1992) Simulation study of a multigene family, with special

reference to the evolution of compensatory advantageous mutations. Genetics 132:

247-252

Baum BR, Johnson DA (1994) The molecular diversity of the 5S rRNA gene in barley

(Hordeum vulgare). Genome 37: 992-998

Baum BR, Johnson DA (1996) The 5S rRNA gene units in ancestral two-row barley

(Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence

analysis and phylogenetic relationship with the 5S rDNA units in cultivated barley

(H. vulgare L.). Genome 39: 140-149.

Baum BR, Appels R (1992) Evolutionary change at the 5S DNA loci of species in the

Triticeae. Pl Syst Evol 183: 195-208

Becerra JX (2003) Evolution of Mexican Bursera (Burseraceae) inferred from ITS,

ETS, and 5S nuclear ribosomal DNA sequences. Mol Phylogenet Evol. 26: 300-309

Beck SL, Dunlop R, van Staden J (1998) Micropropagation of Acacia mearnsii from

ex-vitro material. Plant Growth Regulation 26: 143-148

References

Becker J, Vos P, Kuiper M, Salamini F, Heun M (1995) Combined mapping of AFLP

and RFLP markers in barley. Mol Gen Genet 249: 65-73

Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics

12: 627-631

Bedbrook JR, Jones J, O‘dell M, Thompson RD, Flavell RB (1980) A molecular

description of telomeric heterochromatin of Secale species. Cell 19: 545-560

Bell CJ, Ecker JR (1994). Assignment of 30 microsatellite loci to the linkage map of

Arabidopsis. Genomics 19: 137-144

Bennet MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Phil Trans R

Soc Lond B 274: 227-274

Bennett MD, Smith JB, Heslop-Harrison JS (1982) Nuclear DNA amounts in

angiosperms. Philos Trans R Soc Lond B 216:179-182

Bennetzen JL (1996) The contribution of retroelements to plant genome

organization, function and evolution. Trend Micro-biol 4: 347-353

Bennetzen JL (2000). Transposable elements contributions to plant gene and

genome evolution. Plant Mol. Biol. 42:351-369

Berenyi M, Gichuki S, Schmidt J, Burg K (2003) Ty1-copia retrotransposon-based S-

SAP (sequence-specific amplified polymorphism) for genetic analysis of

sweetpotato. Theor Appl Genet 105: 862 - 869

Bernard G, Baradat P, Chevalier D, Tagmount A, Berville A (2001) Genetic

differentiation in the olive complex (Olea europea) revealed by RAPDs and RFLPs in

the rRNA genes. Genet Res Crop Evol 48: 165-182

Bhatia S, Singh K, Jagannathan V, Lakshmikumaran M (1993) Organization and

sequence analysis of the 5S rRNA genes in Brassica campestris. Plant Sci 92: 47-55

Bhatia S, Das S, Jain A, Lakshmikumaran M (1995) DNA fingerprinting of Brassica

juncea cultivars using microsatellite probes. Electrophoresis 16: 1750-1754

Bhojwani SS, Dhawan V, Cocking EC (1986) Plant tissue culture: a classified

bibliography. Elsevier, Amsterdam, pp 399-432

Binelli G, Bucci G (1994) A genetic linkage map of Picea abies Karst based on RAPD

markers as a tool in population genetics. Theor Appl Genet 88: 283-288

Blusch JH, Haltmeier M, Frech K, Sander I, Leib-Mosch C, Brack-Werner R, Werner

T (1997) Identification of endogenous retroviral sequences based on modular

organization: proviral structure at the SSAV1 locus. Genomics 43: 52-61.

Bodenes C, Joandet S, Laigret F, Kremer A (1997) Detection of genomic regions

differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and

Q. rubur L. Heredity 78: 433-444

Boeke JD, Corces VG (1989) Transcription and reverse transcription of

retrotransposons. Annu Rev Microbiol 43: 403-434

Bogenhagen DF, Sakonju S, Brown DD (1980) A control region in the center of the

5S RNA gene directs specific initiation of transcription: II. The 3' border of the

region. Cell 19: 27-35

Bohanec B, Jakse M, Ihan A, Jvornik B (1995) studies of gynogenesis in onion

(Allium cepa). Plant Sci 104:215-224

Boyko E, Kalendar R, Korzun V, Schulman A, Gill B S (2000) An additional 177 new

loci for the Aegilops tauschii high-density genetix map, including defense-response

References

genes, microsatellite, REMAP and IRAP markers. Wheat Genet Resource centre.

Abstracts 2000

Bradeen JM, Simon PW (1998) Conversion of an AFLP fragment linked to the carrot

Y2 locus to a simple, codominant, PCR based marker form. Theor Appl Genet 97:

960-967

Bradshaw HD, Villar M, Watson BD, Otto KG, Stewart S, Stettler RF (1994)

Molecular genetics of growth and development in Populus. III A genetic linkage map

of a hybrid poplar composed of RFLP, STS, and RAPD markers. Theor Appl Genet

89: 167-178

Bradshaw HD, Stettler RF (1995) Molecular genetics of growth and development in

Populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits

in a forest tree. Genetics 139: 963-973.

Bradshaw HD, Ceulemans R, Davis J, Stettler RF (2000) Emerging model systems:

Poplar (Populus) as a model forest tree. Journal of Plant Growth Regulators 19:

306-313.

Breiman A, Felsenburg T, Galun E (1987) Nor loci analysis in progenies of plants

regenerated from scutellar callus of bread wheat: a molecular approach to evaluate

somaclonal variation. Theor Appl Genet 73:827-831

Breyne P, Boerjan W, Gerats T, van Montagu M, van Gysel A (1997) Application of

AFLP in plant breeding, molecular biology and genetics. Belg Journ Bot 129: 107-117

Broeck van den D, Maes T, Sauer M, Zethof J, Keukeleire PD, D‘Hauw M, Mantagu

MV, Gerats T (1998) Transposon display identifies individual transposable elements

in high copy number lines. Plant J 13:121-129

Broekhulzen JTM (1964) The identification of poplar clones in the nursery. Ned.

Bosb Tijdschr. 36: 105–117

Brown PTH, Gobel E, Lorz H (1991) RFLP analysis of Zea mays callus culture and

their regenerated plants. Theor Appl Genet 81: 227-232

Brown PTH, Lange FD, Kranz E, Lorz H (1993) Analysis of single protoplasts and

regenerated plants by PCR and RAPD technology. Mol Gen Genet 237: 311–317

Brunner AM, Busov VB, Strauss SH (2004) Poplar genome sequence: functional

genomics in an ecologically dominant plant species. Trends Plant Sci 9: 49-56

Bureau TE, Wessler SR (1994) Stowaway: anew family of inverted repeat elements

associated with the genes of both monocotyledonous dicotyled plants. Plant Cell 6:

907-916

Busch W, Martin R, Herrmann RG, Hohmann U (1995) Repeated DNA sequences

isolated by microdissection .1. Karyotyping of barley (Hordeum vulgare L.).

Genome 38: 1082-1090.

Caetano-Anolles G, Bassam BJ, Gresshoff PM (1991a) DNA amplification

fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology 9:

553-557

Caetano-Anolles G, Bassam BJ, Gresshoff PM (1991b) DNA amplification

fingerprinting : A strategy for genome analysis. Plant Mol Bio Rep 9: 294-307

Caetano-Anolles G, Bassam BJ, Gresshoff PM (1992) DNA fingerprinting and

MAAPing out a RAPD definition. Biotechnology 10: 937-937

References

Caicedo AL, Gaitan E, Duque MC, Chica OT, Debouck DG, Tohme J (1999) AFLP

fingerprinting of Phaseolus lunatus L. and related wild species from South America.

Crop Sci 39: 1497-1507

Campell BR, Song Y, Posch TE, Cullis CA, Town CD (1992) Sequence and

organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana. Gene

112: 225-228

Capesius I (1991) Sequence of the 5S ribosomal RNA gene from Sinapis alba. Plant

Mol Biol 17: 169-170

Capesius I (1993) Sequences of 5S rRNA gene from B. nigra and its relation to other

5S r RNA genes from Brassicaceae. J Plant Physiol 142: 112-114

Capo-chichi LJA, Weaver DB, Morton CM (2001) AFLP assessment of genetic

variability among velvetbean (Mucuna sp.) accessions. Theor Appl Genet 103: 1180-

1188

Caporali E, Portaluppi P, Spada A, Marziani G, Falavigna A, Restivo F, Tassi F

(1999) Construction of a linkage map of Asparagus officinalis through different

molecular markers. Acta Hort. (ISHS) 479: 75-76

Caranta C, Thabuis A, Palloix A (1999) Development of a CAPS marker for the Pvr4

locus: A tool for pyramiding potyvirus resistance genes in pepper. Genome 42: 1111-

1116

Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SW (2000)

The MITE family Heartbreaker (Hbr): Molecular markers in maize. Proc Natl Acad

Sci USA 97 : 10083-10089.

Casacuberta JM, Vernhettes S, Audeon C, Grandbastien AM (1997). Quasispecies in

retrotransposon : a role for sequence variability in Tnt1 evolution. Genetica 100:

109-117

Castiglione S, Wang G, Damiani G, Bandi C, Bisoffi S, Sala F (1993) RAPD

fingerprints for identification and for taxonomic studies of elite poplar (Populus

spp.) clones. Theor Appl Genet 87: 54-59

Castilho A, Heslop-Harrison (1995) Physical mapping of 5S and 18S-25S rDNA and

repetitive DNA sequences in Aegilops umbellulata. Genome 38:91-96

Castillo CO, Chalmers KJ, Waugh R, Powell W (1994) Detection of genetic diversity

and selective gene introgression in coffee using RAPD markers. Theor Appl Genet

87: 934-940

Catalan P, Kellogg EA, Olmstead RG (1997) Phylogeny of Poaceae subfamily

Pooideae based on chloroplast ndhF genesequences. Mol Phyl Evol. 8, 150–166.

Cecchini E, Natali L, Cavallini A, Durante M (1992) DNA variations in regenerated

plants of pea (Pisum sativum L.) Theor Appl Genet 84: 874-879

Cervera MT, Gusmao J, Steenackers M, Peleman J, Storme V, Van den Broeck A,

Van Montagu M, Boerjan W (1996) Identification of AFLP molecular markers for

resistance against Melampsora larici-populina in Populus. Theor Appl Genet 93:

733–737.

Cervera MT, Villar M, Faivre-Rampant P, Goue MC, Van Montagu M, Boerjan W

(1997) Applications of molecular marker technologies in Populus breeding. pp 101-

115. In: Micropropagation, genetic engineering, and molecular biology of Populus.

Klopfenstein NB, Chun YW, Kim MS, Ahuja MR Eds. Rocky Mountain Forest and

Range Experiment Station, Fort Collins, Colorado. 326 pp

References

Cervera MT, Cabezas JA, Sancha JC, Martinez de Toda F, Martinez-Zapater JM

(1998) Applications of AFLPs to the characterization of grapevine Vitis vinifera L.

genetic resources. A case with accessions from Rioja (Spain). Theor Appl Genet 97:

51-59

Cervera MT, Remington D, Frigerio M-M, Storme, Ivens B, Boerjan W, Plomion C

(2000) Improved AFLP analysis of tree species. Can J For Res 1608–1616

Cervera MT, Storme V, Ivens B, Gusmao J, Liu BH, Hostyn V, Van Slycken J, Van

Montagu M, Boerjan W (2001) Dense genetic linkage maps of three Populus species

(Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite

markers. Genetics 158: 787-809

Chalmers KJ, Newton AC, Waugh R, Wilson J, Powell W (1994) Evaluation of the

extent of genetic variation in mahoganies (Meliaceae) using RAPD markers. Theor

Appl Genet 89: 504-508

Chang R-Y, O‘Donoughue LS, Bureau TE (2001) Inter-MITE polymorphisms (IMP):

a high throughput transposon-based genome mapping and fingerprinting approach.

Theor Appl Genet 102: 773-781

Chardenon J, Semizoglu MA (1965) Remarks on Populus euphratica Oliv.

Document, 12th Session of the International Poplar Commission, Teheran.

FAO/IPC-166.

Charrier B, Foucher F, Kondorsi E, d‘Aubenton-Carafa Y, Thermes C, Rater P (1999)

Bigfoot, a new family of MITE elements characterised from the Medicago genus.

Plant J. 18: 431-441

Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler, BD, Duvall MR,

Price RA, Hills HG, Qiu Y-L,Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR,

Sytsma KJ et al. (1993) Phylogenetics of seed plants: An analysis of nucleotide

sequences from the plastid gene rbcL. Ann Missouri Bot Gard 80: 528–580.

Chaturvedi AN, Rawat BS (1994) Poplar tree improvement programme. Indian

Forester 120: 97–124

Chauhan N, Negi MS, Sabharwal V, Khurana DK, Lakshmikumaran M (2004)

Screening interspecific hybrids of Populus (P. ciliata × maximowiczii) using AFLP

markers. Theor Appl Genet 108: 951-957

Cheghamirza K, Koveza O, Konovalov F, Gostimsky S (2002) Identification of RAPD

markers and their use for molecular mapping in pea (Pisum sativum L.). Cell Mol

Biol Lett 7:649-655

Cheliak WM, Dancik BP (1982) Genetic diversity of natural populations of a clone-

forming tree, Populus tremuloides. Canadian Journal of Genetic Cytology 24: 611-

616

Cheliak WM, Pitel JA (1985) Inheritance and linkage of allozymes in Larix larcina.

Silvae Genetica. 34: 142-148

Chen CX, Wang ZL, Yang DE, Ye CJ, Zhao YB, Jin DM, Weng ML, Wang B (2004)

Molecular tagging and genetic mapping of the disease resistance gene RppQ to

southern corn rust. Theor Appl Genet 108: 945-950

Chen JJ, Devanand PS, Norman DJ, Henny RJ, Chao CT (2004) Genetic

relationships of Aglaonema species and cultivars inferred from AFLP markers.

Annals of Botany 93: 157-166

References

Chong DKX, Yang RC, Yeh FC (1994) Nucleotide divergence between populations of

trembling aspen (Populus tremuloides) estimated with RAPDs. Curr Genet 26: 374-

376.

Chowdhury MKU, Vasil V, Vasil IK (1994) molecular analysis of plants regenerated

from embryogenic cultures of wheat (Triticum aesativum L.). Theor Appl Genet 87:

821-828

Chowdhury MKU, Vasil JK (1993) Molecular analysis of plants regenerated from

embryogenic cultures of hybrid sugarcane cultivars (Saccharum spp.). Theor Appl

Genet 86: 181-188

Clegg MT (1993) Chloroplast gene sequences and the study of plant evolution. Proc

Natl Acad Sci USA 90: 363–367.

Collevatti RG, Grattapaglia D, Hay JD (2001) High resolution microsatellite based

analysis of the mating system allows the detection of significant bi-parental

inbreeding in Caryocar brasiliense, an endangered tropical tree species. Heredity

86: 60-67

Colombani VS, Causse M, Gervais L, Philouze J (2000) Efficiency of RFLP, RAPD

and AFLP markers for the construction of an intraspecific map of the tomato

genome. Genome 43: 29-40

Conkle MT (1981) Isozyme variation and linkage in six conifer species. In:

Proceedings of the symposium on isozymes of North American forest trees and

insects. 1979 July 27, Berkeley, CA, USA., U S Dept. of Agriculture, Forest Service :

11-17

Costa P, Pot D, Dubos C, Frigerio JM, Pionneau C, Bodenes C, Bertocchi E, Cervera

MT, Remington DL, Plomion C (2000) A genetic map of maritime pine based on

AFLP, RAPD and protein markers. Theor Appl Genet 100: 39-48

Cox AV, Bennett MD, Dyer TA (1992) Use of the polymerase chain reaction to detect

spacer size heterogeneity in plant 5S rRNA gene clusters and to locate such clusters

in wheat (Triticum aestivum L.). Theor Appl Genet 83: 684-690

Cregan P B, Akkaya M S, Bhagwat A A, Lavi U, Rogwen J (1994) Length

polymorphisms of simple sequence repeat (SSR) DNA as molecular markers. In:

Gresshoff P M (ed) Plant Genome Analysis. CRC Press, London, pp 47-56

Cronn RC, Cedroni M, Haselkorn T, Grover C, Wendel JF (2002) PCR-mediated

recombination in amplification products derived from polyploid cotton. Theor Appl

Genet 104: 482–489

Cronn RC, Zhao X, Paterson AH, Wendel JF (1996) Polymorphism and concerted

evolution in a tandemly repeated gene family: 5S Ribosomal DNA in Diploid and

Allopolyploid Cottons. J Mol Evol 42: 685-705

Cuenca S, Amo-Marco JB (2000) In-vitro propagation of Centaurea spachii from

inflorescence stems. Plant Growth Reg 26: 143-148

Cullis CA, Creisen GP, Gorman SW, Teasdale RD (1988) The 25S, 18s, and 5S

ribosomal RNA genes from Pinus radiata D. Don, In: Cheliak WM, Yapa AC (eds)

Molecular genetics of forest trees, Petawa Natl For Inst Rep, Chalk River, Ontario,

Canada, pp 24-40

Dallas JF (1988) Detection of DNA "fingerprints" of cultivated rice by hybridization

with a human minisatellite probe, Proc Natl Acad Sci USA 85: 6831-6835

References

Damasco OP, Graham GC, Henry RJ, Adkins SW, Smith MK (1996) Random

amplifed polymorphic DNA (RAPD) detection of dwarf off-types in micropropagated

Cavendish (Musa spp.) bananas. Plant Cell Rep 16: 118-123

D'Amto F (1985) Cytogenetics of plant cell and tissue cultures and their regenerants.

CRC Crit Rev Plant Sci 3: 73-112

Das S, Rajagopal J, Bhatia S, Srivastava PS, Lakshmikumaran M (1999) Assessment

of genetic variation within Brassica campestris cultivars using AFLP and RAPD

markers. J Biosci (Bangalore) 24: 433-440

DeKoeyer DL, Tinker NA, Wight CP, Deyl J, Burrows VD, O'Donoughue LS, Lybaert

A, Molnar SJ, Armstrong KC, Fedak G, Wesenberg DM, Rossnagel BG, McElroy AR

(2004) A molecular linkage map with associated QTLs from a hulless x covered

spring oat population. Theor Appl Genet. 108: 1285-1298

Dean C, Schmidt R (1995) Plant genomes: A current molecular description. Annu

Rev Plant Mol Biol 46: 395-418

Delourme R, Bouchereau A, Hubert N, Renard M, Landry BS (1994) Identification of

RAPD markers linked to a fertility restorer gene for the Ogura radish cytoplasmic

male sterility of rapeseed (Brassica napus L.). Theor Appl Genet 88: 741-748

Deng Z, Huang s, Xiao S, Gmitter Jr.FG (1997) Development and characterization of

SCAR markers linked to the Citrus tristeza. Genome 40: 697-740

DeVerno LL, Park YS, Bonga JM, Barrett JD, Simpson C (1999) Somaclonal

variation in cryopreserved embryonic clones of white spurce [Picea glauca

(Moench) Voss.]. Plant Cell Rep 18: 948-953

Devey ME, Sewell MM, Uren TL, Neale DB (1999) Comparitive mapping in loblolly

and radiata pine using RFLP and microsatellite markers. Theor Appl Genet 99: 656-

662

Dickmann DI, Isebrands JG (2001) Poplar clones: an introduction and caution. In:

Poplar Culture in North America (Eds.) DI Dickmann, JG Isebrands, JE

Eckenwalder, J Richardson. NRC Research Press, Ottawa, Canada pp. 309–324

Dickmann DI, Stuart KW (1983) The culture of Poplars in Eastern North America.

MSU, East Lansing, Michigan, USA pp. 168

Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome

evolution. Nature 284: 601-603

Doolittle WF, McGrath JM, This P, Chevre AM, Quiros CF (1990) Ribosomal RNA

genes in diploid and amphidiploid Brassica and related species: organization,

polymorphism and evolution. Genome 33:733-744

Dover G (1982) Molecular Drive: A cohesive mode of species evolution. Nature 299:

111-117

Dover GA (1994) Concerted evolution, molecular drive and natural selection. Curr

Biol 4: 1165.

D'Ovidio R, Mugnozza GS, Tanzarella OA (1991) rDNA cloning and rapid hybrid

identification in Populus spp. (Salicaceae) Pl Syst Evol 177: 165-74.

Doyle JJ, Doyle JL (1990) Isolation of plants DNA from fresh tissue. Focus 12: 13-15

Drossou A, Katsiotis A, Leggett JM, Loukas M, Tsakas S (2004) Genome and species

relationships in genus Avena based on RAPD and AFLP molecular markers. Theor

Appl Genet. 2004 Mar 10 [Epub ahead of print]

References

Dubcovsky J, Dvorak J (1995) Ribosomal RNA multigene loci: Nomads of Triticeae

genomes. Genetics 134: 277-292

Duran Y, Fratini R, Garcia P, Perez de la Vega M (2004) An intersubspecific genetic

map of Lens. Theor Appl Genet 108: 1265-1273

Durante M, Geri C, Grisvard J, Guille E, Parenti R, Buiatti M (1983) Variation in

DNA complexity in Nicotiana glauca tissue cultures. I. Pith tissue de-differentiation

in-vitro. Protoplasma 114: 114-118

Durbin ML, Denton A, Clegg MT (2001) Dynamics of Mobile Element Activity in

Chalcone Synthase Loci in the Common Morning Glory (Ipomoea Purpurea). Proc

Natl Acad Sci USA 98: 5084-5089

Dvorak J, Zhang HB, Kota RS, Lassner M (1989) Organization and evolution of the

5S ribosomal RNA gene family in wheat and related species. Genome 32: 1003-1016

Earle ED, Demarly Y (1982) Variability in plants regenerated from tissue culture.

Praeger, NY

Eckenwalder JE (1977) North American cottonwoods (Populus, Salicaceae) of

sections Abaso and Aigeros. J. Arnold Arbor. 58:193-207

Eckenwalder JE (1984) Natural intersectional hybridization between North

American species of Populus (Salicaceae) in sections Aigeiros and Tacamahaca. I.

Population studies of P. × parryi. Can. J. Bot. 62:317-324.

Eckenwalder JE (1996) Systematics and evolution of Populus. In Biology of Populus

and its Implications for Management and Conservation. Edited by RF Stettler, HD

Bradshaw Jr, Heilman PE, Hinckley TM. NCR Research Press, Ottawa, ON, pp 7-32

Eiadthong W, Yonemori K, Kanzaki S, Sugiura A (2000) Amplified fragment length

polymorphism analysis for studying the genetic relationships among Mangifera

species in Thailand. J Amer Soc Hort Sci 125: 160-164

Ellis THN, Davies DR, Castleton JA, Bedford ID (1984) The organization and

genetics of rDNA length variants in peas. Chromosoma (Berl) 91: 74-81

Ellis THN, Lee D, Thomas CM, Simpson PR, Cleary WG, Newman MA, Burcham

KWG (1988) 5S rRNA genes in Pisum: Sequence, long range and chromosomal

organisation. Mol Gen Genet 214: 333-342

Ellis RP, McNicol JW, Baird E, Booth A, Lawrence P, Thomas B, Powell W (1997)

The use of AFLPs to examine genetic relatedness in Barley. Mol Breed 3: 359-369

Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Ty1-copia class

retrotransposon insertion site polymorphism for linkage and diversity analysis in

pea. Mol Gen Genet 260: 9-19

EMBL Database Website. [Online.] http://www.ebi.ac.uk. [30 March 2004, last date

accessed]

Ennequin TML, Panaud O, Toupance B, Sarr A (2000) Assessment of genetic

relationships between Setaria italica and its wild relative S. virdis using AFLP

markers. Theor Appl Genet 100: 1061-1066

Erschadi S, Haberer G, Schoniger M, Torres Ruiz RA (2000) Estimating genetic

diversity of Arabidopsis thaliana ecotypes with amplified fragment length

polymorphisms (AFLP). Theor Appl Genet 100: 633-640

References

Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IE (1999) Early nuclear

events in plant defence signalling: rapid gene activation by WRKY transcription

factors. EMBO J. 18: 4689-99.

Faivre-Rampant P, Castiglione S, Le Guerroue B, Bisoffi S, Lefevre F, Villar M

(1995a) Molecular approaches to the study of poplar systematics. Proceeding of the

international poplar symposium; 1995 August 20-25, Seattle, WA, USA: University

of Washington: 45. Abstract.

Faivre-Rampant P, Prado-Vivant E, Le Guerroue B, Scheider C, Darmency M

(1995b) Fluorescence in situ hybridization detects a variable number of ribosomal

DNA loci in poplar species. In: Plant genome meeting III; 1995 january 15-19, San

Diego, CA, USA

FAO (1958) Poplars in forestry and land use. FAO forestry and Forest products

studies, No. 12.

FAO (1979) Poplars and Willows. FAO Forestry Series Rome

Feinberg AP, Vogelstein B (1983) A technique for radio-labeling DNA restriction

endonuclease fragments to high specific activity. Anal Biochem 132: 6-13

Felsenstein J (1985) Confidence limits on phylogenies: An approach using

bootstrap, Evolution 39: 783-791

Finnegan DJ, Rubin GM, Young MW, Hogness DS. (1978) Repeated gene families in

Drosophila melanogaster. Cold Spring Harb Symp Quant Biol. 42 : 1053-63.

Flathman PE, Lanza GR (1998) Phytoremediation: Current views on an emergent

green technology. J. Soil Contamination 7: 415-432.

Flavell RB (1986) Repetitive DNA and chromosome evolution inplants. Philos Trans

R Soc Lond B 312: 227-242.

Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992a). Ty1-

copia group retrotransposons are ubiquitous and heterogeneous in higher-plants.

Nuc Acids Res 20: 3639-3644

Flavell AJ, Smith DB, Kumar A (1992b). Extreme heterogeneity of Ty1-copia group

retrotransposons in plants. Mol Gen Genet 231:233-242

Flavell AJ, Pearce SR, Heslop-Harrison JS, and Kumar A (1997) The evolution of

Ty1-copia group retrotransposons in eukaryote genomes. Genetica 100: 185-195

Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion

polymorphisms (RBIP) for high throughput marker analysis. Plant J 16: 643-650

Frasch M, Wenzel W, Hess D (1989) The nucleotide sequences of nuclear 5S rRNA

genes and spacer regions of Petunia hybrida. Nucleic Acids Res. 17: 2857

Fregene M, Bernal A, Duque M, Dixon A, Tohme J (2000) AFLP analysis of African

cassava (Manihot esculenta Crantz.) germaplasm resistant to cassava mosaic disease

(CMD). Theor Appl Genet 100: 678-685

Fry DJ, Douglas GC, Saieed NT (1997) Somaclonal variation in Populus: an

evaluation. In: Klopfenstein NB, Chun YW, Kim M-S, Ahuja MR (eds)

Micropropagation, genetic engineering and molecular biology of Populus. USDA For

Serv Rocky Mount Res Stn, Gen Tech Rep RM-GTR-297, Fort Collins,Colo., pp 33–

43

Fulnecek J, Matyasek R, Kovarik A, Bezdek M (1998) Mapping of 5-methylcytosine

residues in Nicotiana tabacum 5S rRNA genes by genomic sequencing. Mol Gen

Genet 259: 133–141

References

Furini A, Wunder J (2004) Analysis of eggplant (Solanum melongena)-related

germplasm: morphological and AFLP data contribute to phylogenetic

interpretations and germplasm utilization. Theor Appl Genet 108:197-208

Gaiotto FA, Bramucci M, Grattapaglia D (1997) Estimation of out-crossing rate in a

breeding population of Eucalyptus urophylla with dominant RAPD and AFLP

markers. Theor Appl Genet 95: 842-849

Galindo LM, Gaitan-Solis E, Baccam P, Tohme J (2004) Isolation and

characterization of RNase LTR sequences of Ty1-copia retrotransposons in common

bean (Phaseolus vulgaris L). Genome 47: 84-95

Gallois A, Audran JC, Burrus M (1998) Assessment of genetic relationships and

population discrimination among Fagus sylvetica l by RAPD. Theor Appl Genet 97:

211-219

Galvan MZ, Aulicino MB, Garcia-Medina S, Balatti PA (2001) Genetic diversity

among Northwestern Argentinian cultivars of common bean (Phaseolus vulgaris) as

revealed by RAPD markers. Genet Res Crop Evol 48: 251-260

Garber K, Bilic I, Pusch O, Tohme J, Bachmair A, Schweizer D, Jantsch V (1999)

The Tpv2 family of retrotransposons of Phaseolus vulgaris: structure, integration

characteristics, and use for genotype classification. Plant Mol Biol 39: 797-807

Garcia-Martinez J, Martinez-Izquierdo JA (2003) Study on the Evolution of the

Grande Retrotransposon in the Zea Genus. Mol Biol Evol 20: 831 -841

Garcia-Mas J, Oliver M, Gomez-Paniagua H, de Vicente MC (2000) Comparing

AFLP, RAPD, and RFLP markers for measuring genetic diversity in melon. Theor

Appl Genet 101: 860-864

Gaudel M, Taberlet P, Till-Bottraud I (2000) Genetic diversity in an endangered

alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment

length polymorphism markers. Mol Ecol 9: 1625-1637

George (1993) Plant Propagation by Tissue Culture, 2nd Ed, Exegetics Ltd. Part 1.

The Technology, pp. 574,

Gerbi SA (1985) Evolution of ribosomal DNA. In: McIntyre RJ (ed) Molecular

evolutionary genetics. Plenum, NY, pp 419-490

Gerlach WL, Appels R, Dennis ES, Peacock WJ (1978) Evolution and analysis of

wheat genomes using highly repeated DNA sequences. In Proceedings of the 5th

International Wheat Genetics Symposium, New Delhi. Ed. S. Ramanujam. pp. 81-91

Gerlach WL, Dyer TA (1980) Sequence organisation of the repeating units in the

nucleus of wheat which contains 5S r RNA genes. Nucl Acids Res 8: 4851-4865

Gilbert (nee Stoker) KG, Garton S, Karam MA, Arnold GM, Karp, Edwards KJ,

Cooke DT, Barker JHA (2002) A high degree of genetic diversity is revealed in Isatis

spp. (dyer's woad) by amplified fragment length polymorphism (AFLP). Theor Appl

Genet 104: 1150-1156

Godwin ID, Sangduen N, Kunanuvatchaidach R, Piperidis G, Adkins SW (1997)

RAPD polymorphism among variant and phenotypically normal rice (Oryza sativa

var. indica) somaclonal progenies. Plant Cell Rep 16: 320-324

Goldsbrough PB, Ellis THN, Lomonosoff GP (1982) Sequence variation and

methylation of the flax 5S rRNA genes. Nucl Acids Res 10: 4501-4514

References

Gorman SW, Teasdale RD, Cullis CA (1992) Structure and organization of the 5S

rRNA genes (5S DNA) in Pinus radiata (Pinaceae). Pl Syst Evol 183: 223-234

Goto S, Thakur RC, Ishii K (1998) Determination of genetic stability in long-term

micropropagated shoots of Pinus thunbergii Parl. using RAPD markers. Plant Cell

Rep 18: 193-197

Gottlob-McHugh SG, Levesque M, McKenzie K, Olson M, Yarosh O, Johnson DA

(1990) Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill

and conservation of the 5S rDNA repeat structure in higher plants. Genome 33: 486-

494

Goulao L, Cabrita L, Oliveira CM, Leitao JM (2001) Comparing RAPD and AFLP

analysis in discrimination of genetic similarities among apple (Malus domestica)

cultivars. Euphytica 119: 259-270

Grandbastien MA (1992) Retroelements in higher plants. Trends Genet. 8, 103-108

Grandbastien MA, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like

transposable element of tobacco isolated by plant cell genetics. Nature 337:376-380

Grandbastien MA, Lucas H, More J-B, Mhiri C, Vernhettes S, Casacuberta JM

(1997) The expression of tobacco Tnt1 retrotransposon is linked to plant defence

responses. Genetica 100:241-252

Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and

Eucalyptus urophylla using a pseudo-testcross: Mapping strategy and RAPD

markers Genetics 137: 1121-1137

Greef JM, Deuter M, Jung C, Schondelmaier J (1997) Genetic diversity of European

Miscanthus species revealed by AFLP fingerprinting. Genetic Resources and Crop

Evolution 44: 185-195

Grellet F, Penen P (1984) Chromatin organization and methylation patterns of

wheat 5S RNA genes (Triticum aestivum var Hardi). Plant Sci Lett 37: 129-136

Gruendler P, Unfried I, Pascher K, Schweizer D (1991) rDNA intergenic region from

Arabidopsis thaliana: structural analysis, infraspecific variation and functional

implications. J Mol Biol 221: 1209-1222

Gu WK, Weeden NF, Yu J, Wallace DH (1995) Large scale, cost-effective screening

of PCR products in marker-assisted selection application. Theor Appl Genet 91: 9-14

Guohao H, Prakash CS, Jarret RL (1995) Analysis of genetic diversity in sweet potato

(Ipomoea batatas) germplasm collection using DNA amplification fingerprinting.

Genome 38: 938-945

Gupta V, Lakshmisita G, Shaila MS, Jagannath V, Lakshmikumaran M (1992).

Characterization of species-specific repeated DNA sequences from Brassica nigra.

Theor Appl Genet 84: 397-402.

Hake S, Walbot V (1980) The genome of Zea mays, its organization, and homology

to related grasses. Chromosoma 79: 251-270

Halanych KM (1991) 5S ribosomal RNA sequence inappropriate for phylogenetic

reconstruction. Mol Biol Evol 8: 249-253.

Hanley S, Barker A, Van Ooijen W, Aldam C, Harris L, Ahman I, Larsson S, Karp A

(2002) A genetic linkage map of willow (Salix viminalis) based on AFLP and

microsatellite markers. Theor Appl Genet 105: 1087-1096

References

Hansen LJ, Chalker DL, Sandmeyer SB (1988) Ty3, a yeast retrotransposon

associated with tRNA genes, has homology to animal retroviruses. Mol Cell Biol 8:

5245-5256

Hanson RE, Islam-Faridi NM, Crane CF, Zwick MS, Czeschin DG, Wendel JF,

McKnight TD, Price HJ, Stelly DM (2000) Ty1-copia-retrotransposon Behavior in a

Polyploid Cotton. Chrom Res 8: 73 - 76

Harbinder S, Lakshmikumaran M (1990) A repetitive sequence from Diplotaxis

erucoides is highly homologous to that of Brassica campestris and B. oleracea. Pl

Mol Biol 15: 155-156

Hartl L, Seefelder S (1998) Diversity of selected hop cultivars detected by fluorescent

AFLPs. Theor Appl Genet 96: 112-116

Hartmann C, Recipin H, Jubier M, Valor C, Delcher B, Henry Y, de Buyser J,

Lejeune B, Rode A (1994) Mitochondrial DNA variability in a single wheat

regenerant involves a rare recombination event across a short repeat. Curr Genet

25:456–464

Harvengt L, Trontin J, Reymond I, Canlet F, Paques M (2001) Molecular evidence of

true-to-type propagation of a 3-year-old Norway spruce through somatic

embryogenesis. Planta 213: 828-832

Hashmi G, Huettel R, Meyer R, Krusberg L, Hammerschlag F (1997) RAPD analysis

of somaclonal variants derived from embryo callus cultures of peach. Plant Cell Rep

16: 624-627

Hayashi E, Kondo T, Terada K, Kuramoto N, Kawasaki S (2004). Identification of

AFLP markers linked to a resistance gene against pine needle gall midge in Japanese

black pine. Theor Appl Genet 108: 1177 - 1181

Hayden MJ, Sharp PJ (2001) Targeted development of informative microsatellite

(SSR) markers. Nucl Acid Res 29: 1-6

Hemleben V, Grierson D (1978) Evidence that in higher plants the 25S and 18s

rRNA genes are not interspersed with genes for 5S rRNA. Chromosoma (Berl) 65:

353-358

Hemleben V, Werts D (1988) Sequence organization and putative regulatory

elements in the 5SrRNA genes of two higher plants (Vigna radiata and Matthiola

incana). Gene 62: 165-169

Hemleben V (1990) Molekularbiologie der Pflanzen. Stuttgart: Gustav Fischer

Verlag

Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG,

Kamm A, Doudrick RL, Schwarzacher T, Katsiotis A, Kubis S, Kumar A, Pearce SR,

Flavell AJ, Harrison GE (1997). The chromosomal distributions of Ty1-copia group

retrotransposable elements in higher plants and their implications for genome

evolution. Genetica 100: 197-204

Heslop-Harrison JS, Schwarzacher T (1996) Genomic Southern and in situ

hybridization for plant genome analysis. In: Jauhar PP, ed. Methods of Genome

Analysis in Plants. Boca Raton: CRC, 163-179.

Heusden AW, Ooijen JW, Ginkel RV, Verbeek WHJ, Wietsma WA, Kik C (2000a) A

genetic map of an interspecific cross in Allium based on amplified fragment length

polymorphism (AFLP) markers. Theor Appl Genet 100: 118-126

References

Heusden AW, Shigyo M, Tashiro Y, Ginkel RV, Kik C (2000b) AFLP linkage group

assignment to the chromosomes of Allium cepa L. monosomic addition lines. Theor

Appl Genet 100: 480-486

Higashiyama T, Noutoshi Y, Fujie M, Yamada T (1997) Zepp, a LINE-like

retrotransposon accumulated in the Chlorella telomeric region. EMBO J. 16, 3715-

3723

Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture.

EMBO J 12: 2521-2528

Hirochika H, Otsuki H, Yoshikawa M, Otsuki Y, Sugimoto K, Takeda S (1996a)

Autonomous transposition of the tobacco retrotransposon in rice. Plant Cell 8: 725-

734

Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996b) Retrotransposons

of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci 93: 7783-

7788

Ho CY, McMaugh SJ, Wilton AN, McFarlane IJ, Mackinlay AG (1997) DNA

amplification variation within cultivars of turf-type Couch grass (Cynodon spp.).

Plant Cell Rep 16: 797-801

Holme IB, Torp AM, Hansen LN, Andersen SB (2004) Quantitative trait loci

affecting plant regeneration from protoplasts of Brassica oleracea. Theor Appl

Genet 108: 1513 – 1520

Hongtrakul V, Gordan MH, Knapp SJ (1997) Amplified fragment length

polymorphism as a tool for DNA fingerprinting sunflower germplasm: genetic

diversity among oilseed inbred lines. Theor Appl Genet 95: 400-407

Hu C, Crovello TJ, Sokal RR (1985) The numerical taxonomy of some species of

Populus based only on vegetative characters. Taxon 34: 197–205

Hua J, Leslie LD, Shen X, Kolb FL (2000) Combined AFLP and RFLP mapping in

two hexaploid oat recombinant inbred populations. Genome 43: 94-101

Hughes SL, Hunter PJ, Sharpe AG, Kearsey MJ, Lydiate DJ, Walsh JA (2003)

Genetic mapping of the novel Turnip mosaic virus resistance gene TuRB03 in

Brassica napus. Theor Appl Genet 107: 1169-1173

Hull R, Covey SN (1996) Retroelements: Propagation and adaptation. Virus Genes

11, 105-118.

Hunter RL, Marckert CL (1957) Histochemical demonstration of enzymes separated

by zone electrophoresis in starch gels. Science 125: 1294-1295

Hyun OJ, Rajora OP, Zsuffa L (1987) Genetic variation in trembling aspen in

Ontario based on isozyme studies. Canadian Journal of Forest Research, 17: 1134-

1138

Incirli A, Akkaya MS (2001) Assessment of genetic relationships in durum wheat

cultivars using AFLP markers. Genet Res Crop Evol 48: 233-238

Isabel N, Tremblay L, Michaud M, Tremblay FM, Bousquet J (1993) RAPDs as an

aid to evaluate the genetic integrity of somatic embryogenesis derived populations of

Picea mariana. Theor Appl Genet 86: 81-87

Isidore E, van Os H, Andrzejewski S, Bakker J, Barrena I, Bryan GJ, Caromel B, van

Eck H, Ghareeb B, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van

der Voort JR, Rousselle-Bourgeois F, van Vliet J, Waugh R (2003) Toward a

References

marker-dense meiotic map of the potato genome: lessons from linkage group I.

Genetics 165: 2107-2116

Ivandic V, Thomas WTB, Nevo E, Zhang Z, Forster BP (2003) Associations of simple

sequence repeats with quantitative trait variation including biotic and abiotic stress

tolerance in Hordeum spontaneum. Plant Breed 122: 300-304

Jaccard P (1908) Nouvelles researches sur la distribution florale. Bull Soc Vaud Sci

Nat 44: 223-270

Jain A, Bhatia S, Banga SS, Prapash S, Lakshmikumaran M (1994) Potential use of

random amplified polymorphic DNA (RAPD) technique to study the genetic

diversity in Indian mustard (Brassica juncea) and its relationship to heterosis.

Theor Appl Genet 88: 116-122

Jain A, Apparanda C, Bhalla PL (1999) Evaluation of genetic diversity and genome

fingerprinting of Pandorea spp. (Bignoniaceae) by RAPD and inter-SSR PCR.

Genome 42: 714-719

Jaligot, E, Rival A, Beulé T, Dussert S, Verdeil JL (2000) Somaclonal variation in oil

palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep 19:

684-690

Jaligot E, Beule T, Baurens FC, Billotte N, Rival A (2004) Search for methylation-

sensitive amplication polymorphisms associated with the mantled variant

phenotype in oil palm (Elaeis guineensis Jacq.). Genome 47: 224-228

Jamsari A, Nitz I, Reamon-Büttner SM, Jung C (2004) BAC-derived diagnostic

markers for sex determination in Asparagus. Theor Appl Genet 108:1140-1146

Jeffreys AJ, Wilson V, Thein SL (1985) Individual specific fingerprints of human

DNA, Nature, 316:76-79.

Jepsen E (1994) Ozone and acid deposition gradients and biomonitoring site

selection in Wisconsin. In: Proc 16th Intl Meeting Air Pollution Effects on Forest

Ecosystems, Fredericton, NB. p. 23

Jin YK, Bennetzen JL (1989) Structure and coding properties of Bs1, a maize

retrovirus-like transposon. Proc Natl Acad Sci USA 86, 6235–6239 (1989).

John B, Miklos GLG (1979) Functional aspects of satellite DNA and

heterochromatin. Int. Rev. Cytol. 58: l-114

Johnson DA, Chan CCY, Gottlobmchugh SG, Mackenzie K, Marengere L,

Prudhomme MC (1992) Structure of the 5S ribosomal-rna genes in birch (Betula

papyrifera) and alder (Alnus incana). Genome, 35(2), 337-341

Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C,

Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti

M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert, Rueda J, Linacero R,

Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers

in plants by a network of European laboratories. Mol Breed 3: 381-390

Julier B, Flajoulot S, Barre P, Cardinet G, Santoni S, Huguet T, Huyghe C (2003)

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago

sativa) using microsatellite and AFLP markers. BMC Plant Biology 3:9

Kalendar R, Grob T, Regina M, Suoneimi A, Schulman A (1999) IRAP and REMAP:

two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet

98: 704-711

References

Kamm A, Galasso I, Schmidt T, Heslop-Harrison JS (1995) Analysis of a repetitive

DNA family from Arabidopsis arenosa and relationships between Arabidopsis

species. Plant Mol Biol 27: 853-862

Kanazin V, Ananiev E, Blake T (1993) The genetics of 5S rRNA encoding multigene

families in barley. Genome 36: 1023-1028

Karp A (1995) Somaclonal variation as a tool for crop improvement. Euphytica

85:295–302

Karp A (1998) Molecular tools for screening biodiversity. p xxiv. Karp A, Isaac PG,

Ingram DS. Eds. Chapman & Hall, London. 498 pp

Karp A, Edwards K (1998) DNA markers: a global overview. In G Caetano-Annoles &

PM Gresshoff (Eds.) DNA markers: Protocols, Applications and Overviews. Wiley-

VCH, New York. pp. 1–14

Kathiravan K, Ignacimuthu S (1999) Micropropagation of Canavalia virosa (Roxb.)

Wight and Arn: a medicinal plant. Phytomorphology 49: 61-66

Kato A, Iida Y, Yakura K, Tanifuji S (1985). Sequence analysis of Vicia faba highly

repeated DNA: the Bam HI repeated sequence. Plant Mol Biol 5: 411-415.

Kato H, Sriprasertsak P, Seki H, Ichinose Y, Shiraishi T, Yamada T (1999)

Functional analysis of retrotransposons in pea. Plant Cell Physiol. 40: 933–941

Kawata M, Ohmiya A, Shimamoto Y, Oono K, Takaiwa F (1995) Structural changes

in the plastid DNA of rice (Oryza sativa L.) during tissue culture. Theor Appl Genet

90: 364-371

Keil M, Griffin AR (1994) Use of random amplified polymorphic DAN (RAPD)

markers in the discrimination and verification of genotypes in Eucalyptus. Theor

Appl Genet 89:442-450

Keim P, Paige KN, Whitham, Lark KG (1989) Genetic Analysis of an Interspecific

Hybrid Swarm of Populus: Occurrence of Unidirectional Introgression.Genetics 123:

557-565

Kellogg EA, Appels R (1995) Intraspecific and interspecific variation in 5S RNA

genes are decoupled in diploid wheat relatives. Genetics 140: 325-343

Kellogg EA, Appels R, Mason-Gamer RJ (1996) When genes tell diff erent stories:

the diploid genera of Triticeae (Gramineae). Syst Bot 21:321–347

Khosla PK, Khurana DK (1982) Evolution of the genus Populus L. and systematic

placement of P. ciliata Wall. ex. Royle. J. Tree. Sci. 1:81-87

Khurana DK (1989) Crossability pattern of Populus ciliata Wall. Ex Royle. In:

IUFRO Proc. Recent Developments in Poplar Selection and Propagation Techniques.

IFTB, Hann. Munden, germany: 159-166

Khurana DK (2002) Genetic diversity in poplars for sustainable development. In: Vij

SP, Kondu K, Sharma ML, Gupta A Eds. Plant genetic diversity: Exploration,

evaluation, conservation. Affliated East-West Press, New Delhi pp 181-187

Khurana DK, Bhanwara RK (1982) Ontogeny of catkin drop and embryology of

Populus ciliata and its crosses with P. deltoides. In: Improvement of Forest

Biomass. Khosla PK. Editor. ISTS, Solan, India pp 413-418

Khurana DK, Mohanty TL (2000) Identification of selected clones of Populus

deltoides Marsh. by qualitative morphological traits. Environment and Ecology 18:

958–961

References

Khurana DK, Narkhede S (1995) Poplar improvement in Himachal Pradesh (India).

In: DK Khurana (Ed.) Poplars in India: recent research trends. UHF, Solan. pp. 7–

40

Khurana DK, Thakur S (1995) P. ciliata X maximowiczii : preliminary report on a

potential hybrid for mid west Himalayan Zone. The Indian Forester 121 : 802-806

Kidwell KK, Osborn TC (1993) Variation among alfalfa somaclones in copy number

of repeated DNA sequences. Genome 36: 906-912

Kiers AM, Mes THM, van der Meijden R, Bachmann K (2000) A search for

diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory

cultivar groups. Genome 43: 470-476

Kim A, Terzian C, Santamaria P, Pelisson A, Purd‘Homme N, Bucheton A (1994)

Retroviruses in invertebrate: the gypsy retrotransposon is apparently an infectious

retrovirus of Drosophila melanogaster. Proc Natl Acad Sci USA 91:1285-1289

Kim DH, Heber D, Still DW (2004) Genetic diversity of Echinacea species based

upon amplified fragment length polymorphism markers. Genome 47:102-11

Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge University

Press, Cambridge, Massachusetts.

Knoop V, Unseld M, Marienfeld J, Brandt P, Sünkel S, Ullrich H, Brennicke A (1996)

copia-, gypsy- and LINE-like Retrotransposon fragments in the mitochondrial

genome of Arabidopsis thaliana Genetics 142: 579-585

Konieczny A, Ausubel M (1993) A procedure for mapping Arabidopsis mutations

using codominant ecotype-specific PCR-based markers. Plant J 4: 403-410

Konieczny A, Voytas DF, Cummings MP, Ausubel FM (1991) A superfamily of

Arabidopsis thaliana retrotransposons. Genetics 127:801-809

Kopp RF, Smart LB, Maynard CA, Tuskan GA, Abrahamson LP (2002) Predicting

within-family variability in juvenile height growth of Salix based upon similarity

among parental AFLP fingerprints. Theor Appt Genet 105:106-112

Kossack DS, Kinlaw CS (1999) IFG, a gypsy-like retrotransposon in Pinus

(Pinaceae), has an extensive history in pines. Plant Mol Biol 39: 417-426.

Krauss SL (2000) patterns of mating in Persoonia mollis (Proteaceae) revealed by

an analysis of paternity using AFLP: implications for conservation. Aust J Bot 48:

349-356

Kubis S, Schmidt T, Seymour J, Harrison H (1998) Repetitive DNA elements as a

major components of plant genomes. Jour of Bot 82:45-55

Kumar A (1998) The evolution of plant retroviruses: moving to green pastures.

Trends Plant Sci 3: 371-374.

Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 1-78

Kumar S, Tamura K, Nei M (1994). MEGA: Molecular Evolutionary Genetics

Analysis software for microcomputers. Comput. Applic. Biosci. 10: 189-191.

Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R, Flavell

AJ (1997) The Ty1-copia group retrotransposons of plants: genomic organisation,

evolution and use as molecular markers. Genetica 100: 205-217

Kunze R, Saedler H, LoÈnnig W-E (1997) Plant transposable elements. Adv Bot Res

27:331-470

References

Lagoda PJL, Noyer JL, Dambier D, Baurens FC, Grapin A, Lanaud C (1998)

Sequence tagged microsatellite site (STMS) markers in the Musaceae. Molecular

Ecology 7:657-666

Lakshmikumaran M, D‘ Ambrosio E, Laimins LA, Lin DT, Furano AV (1985) Long

interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus.

Mol Cell Biol 5: 2197-2203

Lakshmikumaran M, Negi MS (1994) Structural analysis of two length variants of

the rDNA intergenic spacer from Eruca sativa. Pl Mol Biol 24: 915-927

Lall IP, Maneesha, Upadhyaya KC (2002) Panzee, a copia-like retrotransposon from

the grain legume, pigeonpea (Cajanus cajan L.). Mol Genet Gen 267: 271-80

Lance Gn, Williams WT (1967) A general theory of classifactory sorting strategies. 1.

Hierarchical systems. Computer J 9: 373-380

Lanteri S, Saba E, Cadinu M, Mallica GM, Baghino L, Portis E (2004) Amplified

fragment length polymorphism for genetic diversity assessment in globe artichoke.

Theor Appl Genet. 2004 Feb 14 [Epub ahead of print]

Lapitan NLV, Ganal MW, Tanksley SD (1991) Oganization of the 5S ribosomal RNA

genes in the genome of tomato. Genome 34: 509-514

Larkin PJ, Scowcroft WR (1981) Somaclonal variations: A novel source of variability

from cell cultures for plant improvement. Theor Appl Genet 60: 197-214

Larson SR, Cartier E, Mc Cracken CL, Dyer D (2001) Mode of reproduction and

amplified length polymorphism variation in purple needle grass (Nassella pulchra):

utilization of natural germplasm resources. Mol Ecol 10: 1165-1177

Lawton MA, Dean SM, Dron M, Kooter JM, Kragh KM, Harrison MJ, Yu L, Tanguay

L, Dixon RA, Lamb CJ (1991) Silencer region of a chalcone synthase promoter

contains multiple binding sites for a factor, SBF-1, closely related to GT-1. Plant Mol

Biol 16: 235-49.

Ledbetter SA, Nelson DL, Warren St, Ledbetter DH (1990) Rapid isolation of DNA

probes within specific chromosome regions by interspersed repetitive sequence

polymerase chain reaction. Genomics 6: 475-481

Leitch IJ, Heslop-Harrison JS (1993) Physical mapping of four sites of 5S rDNA

sequences and one site of alpha-amylase-2 gene in barley (Hordeum vulgare)

Genome 36:517-523

Lee D, Ellis THN, Turner L, Hellens RP, Cleary WG (1990) A copia-like element in

Pisum demonstrates the uses of dispersed repeated sequences in genetic analysis.

Plant Mol Biol 15: 707–722

Leroy XJ, Leon K, Charles G, Branchard M (2000) Cauliflower somatic

embryogenesis and analysis of regenerant stability by ISSRs. Plant Cell Rep 19:

1102-1107

Lespinasse D, Rodier-Goud M, Grivet L, Leconte A, Legante H, Seguin M (2000) A

saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP,

microsatellite, and isozyme markers. Theor Appl Genet 100: 127-138

Leutwiler LS, Hough-Evans BR, Meyerowitz EM (1984) The DNA of Arabidopsis

thaliana. Mol Gen Genet 194: 15-23

Lewin R (1982) Repeated DNA in search of a function. Science 217: 621-623

Li W, Sun G, Liu J, Masilamany P, Taylor JH, Yan W, Kasha KJ, Pauls KP (2004)

Inheritance of plant regeneration from maize (Zea mays L.) shoot meristem cultures

References

derived from germinated seeds and the identification of associated RAPD and SSR

markers. Theor Appl Genet 108: 681-687

Li X, Guo R, Pedersen C, Hayman D, Langridge P (1997) Physical localization of

rRNA genes by two-colour fluorescent in-situ hybridization and sequence analysis of

the 5S rRNA gene in Phalaris coerulescens. Hereditas 126:289-294

Lima MLA, Garcia AAF, Oliveira KM, Matsuoka S, Arizono H, de Souza Jr. CL, de

Souza AP (2002) Analysis of genetic similarity detected by AFLP and coefficient of

parentage among genotypes of sugar cane (Saccharum spp.) Theor Appl Genet 104:

30-38

Lin D, Hubbes M, Zsuffa L (1994) Differentiation of poplar and willow clones using

RAPD fingerprints. Tree Physiol 14:1097-1105

Linares AR, Bowen T, Diver GA (1994) Aspects of nonrandom turnover involved in

the concerted evolution of intergenic spacers within the ribosomal DNA of

Drosophila melanogaster. J Mol Evol 39: 151-159

Lisowska K, Wysokinska H (2000) In-vitro propagation of Catalpa ovata G. Don. Pl

Cell Tiss Org Cult 60: 171-176

Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in-vitro

amplification of a di-nucleotide repeat within the cardiac muscle action gene. Am J

Hum Genet 44: 397-401

Liu Z, Furnier GR (1993a) Comparison of allozyme, RFLP and RAPD markers for

revealing genetic variation within and between trembling aspen and bigtooth aspen.

Theor Appl Genet 87: 97-105

Liu Z, Furnier GR (1993b) Inheritance and linkage of allozymes and restriction

fragment length polymorphisms in trembling aspen. Journal of Heredity 84: 419-

424

Loh JP, Kiew R, Set O, Gan LH, Gan YY (2000) A study of genetic variation and

relationships within the Bamboo subtribe Bambusinae using amplified fragment

length polymorphism. Annals Bot 85: 607-612

Long EO, Dawid IB (1980) Repeated genes in eukaryotes. Annu Rev Biochem 49:

727-764

Lubberstedt T, Melchinger E, Duble C, Vuylsteke M, Kuiper M (2000) Relationships

among early European maize inbreds: IV. Genetic diversity revealed with AFLP

markers and comparison with RFLP, RAPD and Pedigree data. Crop Sci 40: 783-791

Lund S T, Furnier GR, Mohn CA (1992) Isozyme variation in quaking aspen in

Minnesota. Can J For Res 22: 521-524

Lynch M, Crease TJ (1990) The analysis of population survey data on DNA sequence

variation. Mol Biol Evol 7: 377-394.

Mandel M, Higa A (1970) Calcium dependent bacteriophage DNA infection. J Mol

Biol 53: 159

Manninen I, Schulman A (1993) BARE-1, a copia -like retroelement in barley

(Hordeum vulgare L.) Plant Mol Biol: 22: 829–846

Mantel NA (1967) The detection of disease clustering and a generalized regression

approach. Cancer Res 27: 209-220

Mao C, Yi K, Yang L, Zheng B, Wu Y, Liu F, Wu P (2004) Identification of

aluminium-regulated genes by cDNA-AFLP in rice (Oryza sativa L.): aluminium-

regulated genes for the metabolism of cell wall components. J Exp Bot 55: 137-143

References

Marczewski W, Hennig J, Gebhardt C. (2002) The Potato virus S resistance gene Ns

maps to potato chromosome VIII. Theor Appl Genet 105: 564-567

Marques CM, Araujo JA, Ferreira JG, Whetten R, O‘Malley, Liu BH, Sederoff R

(1998) AFLP genetic maps of Eucalyptus globulus and E. tereticornis. Theor Appl

Genet 96: 727-737

Martins M, Tenreiro R, Oliveira MM (2003) Genetic relatedness of Portuguese

almond cultivars assessed by RAPD and ISSR markers. Plant Cell Rep. 22: 71-78

Mascia PH, Rubenstein I, Phillips RL,Wang AS, Xiang LZ (1981) Localization of the

5S rRNA genes and evidence for diversity in the 5S rDNA region of maize. Gene

15:7-20

Mathur RS, Sharma KK (1983) Poplars in India. Indian Forester 109: 591–631

Matsumoto S, Fukui H (1996) Identification of rose cultivars and clonal plants by

random amplified polymorphic DNA. Sci Hortic 67: 49-54

Matsuoka Y, Tsunewaki K (1997) Presence of wheat retrotransposons in Gramineae

species and the origin of wheat retrotransposon families. Genes Genet Systems

72:335–343

Mattson WJ, Hart EA, Volney WJA (2001) Poplar Culture in North America (Eds.)

DI Dickmann, JG Isebrands, JE Eckenwalder, J Richardson. NRC Research Press,

Ottawa, Canada pp 219-245

Matyasek R, Fulnecek J, Lim KY, Leitch AR, Kovarik A (2002) Evolution of 5S rDNA

unit arrays in the plant genus Nicotiana (Solanaceae). Genome 45: 556-562

Maughan PJ, Saghai Maroof MA, Buss GR, Huestis GM (1996) Amplified fragment

length polymorphism (AFLP) in soybean: species diversity, inheritance and near-

isogenic lines. Theor Appl Genet 93: 392-401

McClintock B (1951) Chromosome organization and genic expression. Cold Spring

Harbor Symp. Quant. Biol. 16: 13-47

McClintock B (1984) The significance of responses of the genome to challenge.

Science 226: 792-801

McGregor CE, Lambert CA, Greyling MM, Louw JH, Warnich L (2000) A

comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and

SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113: 135-

144

McIntyre CL, Winberg B, Houchins K, Appels R, Baum B (1992) Relationships

between Oryza (Poaceae) species based on 5S DNA sequences. Pl Syst Evol 183: 249-

264

Meacham, CA (1984) The role of hypothesized direction of characters in the

estimation of evolutionary history. Taxon 33:26-38

Mehlenbacher SA, Brown RN, Davis JW, Chen H, Bassil NV, Smith DC, Kubisiak TL

(2004) RAPD markers linked to eastern filbert blight resistance in Corylus avellana.

Theor Appl Genet 108: 651-656

Mehta AK, Chauhan SK, Khurana DK (1995) Finding suitable clones of poplar for

Himachal Pradesh In: DK Khurana (Ed.) Poplars in India: recent research trends.

UHF, Solan. pp. 113–119

Menkir A, Melake-Berhan A, The C, Ingelbrecht I, Adepoju A (2004) Grouping of

tropical mid-altitude maize inbred lines on the basis of yield data and molecular

markers. Theor Appl Genet. 2004 Feb 20 [Epub ahead of print]

References

Messing J, Carlson J, Hagen G, Rubensteini K, Oleson A (1984) Cloning and

sequencing of the ribosomal RNA genes in maize, 17s region. DNA 3: 31-40

Meyer W, Mitchell TG, Freedman EZ, Vilgalys R (1993) Hybridization probes for

conventional DNA fingerprinting can be used as single primers in the PCR to

distinguish strains of Cryptococcus neoformans. J Clin Microbiol 31: 2274-2280

Meyers BC, Shen KA, Rohani P, Gaut BS, Michelmore RW (1998) Receptor-like

Genes in the Major Resistance Locus of Lettuce Are Subject to Divergent Selection

Plant Cell 10: 1833-1846

Mhiri C, Morel JB, Verbhettes S, Casacuberta JM, Lucas H, Grandbastien MA (1997)

The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by

abiotic stress. Plant Mol Biol 33: 257-266

Michaels SD, Amasino RM (1998) A robust method for detecting single-nucleotide

changes as polymorphic markers by PCR. Plant J 14: 381-385

Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to

disease-resistance genes by bulked segregant analysis: A rapid method to detect

markers in specific genomic regions by using segregating populations. Proc Natl

Acad Sci USA 88: 9828-9831

Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, Powell W, Waugh

R (1997) Comparison of PCR based marker systems for the analysis of genetic

relationships in cultivated potato. Mol breed 3: 127-136

Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998)

Isolation and characterisation and mapping of simple sequence repeat loci in potato.

In: A Karp, PG Isaac and DS Igram (eds), Molecular Tools for Screening

Biodiversity, 371—381. Chapman & Hall, London.

Mohan M, Nair S, Bhagwat A, Krishna TG, Yano M, Bhatia CR, Sasakai T (1997)

Genome mapping, molecular markers and marker assisted selection in crop plants.

Mol Breed 3: 87-103

Moran GF, Bell JC (1983) Eucalyptus. In: Tanksley, S D, Orton T J (eds) Isozyme in

plant genetics and breeding. Amsterdam: Elsevier: 423-441

Moran GF, Smith D, Bell JC, Appels R (1992). The 5S RNA genes in Pinus radiata

and the spacer region as a probe for relationships between Pinus species. Plant Syst.

Evol. 183: 209-221.

Morgante M, Olivierri AM (1993) PCR-amplified microsatellites as markers in plant

genetics. Plant J 3: 175-182

Morgante M, Vogel J (1994) Compound microsatellite primers for the detection of

genetic polymorphisms. US Patent Appl 08/326456

Moury B, Pflieger S, Blattes A, Lefebvre A, Palloix A (2000) A CAPS marker to assist

selection of tomato spotted wilt virus (TSWV) resistance in pepper. Genome 43: 137-

142

Mukai Y, Endo TR, Gill BS (1990) Physical mapping of the 5S rRNA multigene

family in common wheat. J Heredity 81: 290-295

Muller E, Brown PTH, Hartke S, Lorz H (1990) DNA variation in tissue-culture-

derived rice plants. Theor Appl Genet 80:673–679

Mullis K, Faloona S, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic

amplification of DNA in-vitro, the polymerase chain reaction. Cold Spring Harbor

Symp Quant Biol, 51: 263-273

References

Muluvi G M, Sprent J I, Soranzo N, Provan J, Odee D, Folkard G, McNicol JW,

Powell W (1999) Amplified Fragment Length Polymorphism (AFLP) analysis of

genetic variation in Moringa oleifera Lam. Mol Ecol 8: 463-470

Munthali MT, Newbury HJ, Ford-Lloyd BV (1996) The detection of somaclonal

variants of beet using RAPD. Plant Cell Rep 15: 474-478

Nagaki K, Tsujimoto H, Isono K, Sasakuma T (1995) Molecular charachterization of

a tandem repeat, Afa family, and its distribution among Triticaceae. Genome 38:

479-486

Nagy ED, Lelley T (2003) Genetic and physical mapping of sequence-specific

amplified polymorphic (SSAP) markers on the 1RS chromosome arm of rye in a

wheat background. Theor Appl Genet 107: 1271 - 1277

Nagylaki T (1990) Gene conversion, linkage, and the evolution of repeated genes

among multiple chromosomes. Genetics 126: 261-276

Nance WL, Tuskan GA, Nelson CD, Doudrick RL (1992) Potential application of

molecular markers for genetic analysis of host-pathogen systems in forest trees. Can

J For Res 22: 1036-1043

Nebauer SG, del Castillo-Agudo L, Segura J (1999) RAPD variation within and

among natural populations of outcrossing willow-leaved foxglove (Digitalis obscura

L.). Theor Appl Genet 98: 985-994

Negi MS, Devic M, Delseny M, Lakshmikumaran M (2000a). Identification of AFLP

fragments linked to seed coat colour in Brassica juncea and conversion to SCAR

marker for rapid selection. Theor Appl. Genet 101: 146-152

Negi MS, Singh A, Lakshmikumaran M (2000b) Genetic variation and relationship

among and within Withania species as revealed by AFLP markers. Genome 43: 975-

980

Nei M (1987) Molecular Evolutionary Genetics. Columbia Univ. Press, New York.

Nei M, Li W (1979) Mathematical model for studying genetic variation in terms of

restriction endonucleases. Proc Nat Acad Sci USA 79: 5269-5273

Nelke M, Nowak J, Wright JM, McClean NL (1993) DNA fingerprinting of red clover

(Trifolium pratense L.) with Jeffreys probes: detection of somaclonal variation and

other applications. Plant Cell Rep 13: 72-78

Newcombe G (2001) Poplar Culture in North America (Eds.) DI Dickmann, JG

Isebrands, JE Eckenwalder, J Richardson. NRC Research Press, Ottawa, Canada, pp

223-246

Nikaido AM, Ujino T, Iwata H, Yoshimura K, Yoshimura K, Suyama Y, Murali M,

Nagasaka K, Tsumura Y (2000) AFLP and CAPS linkage maps of Cryptomeria

japonica. 100: 825-831

Nobre J, Santos C, Romano A (2000) Micropropagation of the Mediterranean

species Viiburnum tinus. Pl Cell Tiss Org Cult 60: 75-78

Noma K, Ohtsubo H, Ohtsubo E (1998) Non-LTR retrotransposons (LINEs) as

ubiquitous components among plant kingdom. Plant and Animal Genome VI, San

Diego, Abstracts guide, 103

Nybom H, Rogstad SH, Schaal BA (1990) Genetic variation detected by use of M13

―DNA fingerprint‖ probe in Malus, Prunus and Rubus (Rosaceae). Theor Appl Genet

79: 153-156

Ohta T (1983) On the evolution of multigene families. Theor Popul Biol 37: 213-219

References

Ohta T (1990) How gene families evolve. Theor Popul Biol 37: 213-219

Ohta T, Dover GA (1983) Population genetics of multigene families that are

dispersed into two or more chromosomes. Proc Natl Acad Sci, USA 80: 4079-4083

Okada N, Hamada M (1997) The 3‘ ends of tRNA-derived SINEs originated from

3‘ends of LINEs: a new example from the bovine genome. J Mol Evol 44: S52-S56

Olmstead RG, Palmer JD (1994) Chloroplast DNA systematics: A review of methods

and data analysis. Am J Bot 81: 1205–1224

Olmstead RG, Reeves PA (1995) Evidence for the polyphyly of the Scrophulariaceae

based on chloroplast rbcL and ndhF sequences. Ann Missouri Bot Garden 82: 176–

193

Ostrander E A, Jong P M, Rine J, Duyk G (1992) Construction of small-insert

genomic libraries highly enriched for microsatellite repeat sequences. Proc Natl

Acad Sci USA 89: 3419-3423

Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on

personal computers. Computer Applications in the Biosciences 12: 357-358.

Paglia G, Morgante M (1998) PCR-based multiplex DNA fingerprinting techniques

for the analysis of conifer genomes. Mol Breed 4: 173-177

Paglia GP, Olivieri AM, Morgante M (1998) Towards second generation STS

(sequence-tagged sites) linkage maps in conifers: a genetic map of Norway spruce

(Picea abies K). Mol Gen Genet 258:466-478

Pakniyat H, Powell W, Baird E, Handley LL, Robinson D, Scrimgeour CM, Nevo E,

Hackett CA, Caligari PDS, Forster BP (1997) AFLP variation in wild barley

(Hordeum spontaneum C. Koch) with reference to salt tolerance and associated

ecogeography. Genome 40: 332-341

Palombi M, Damiano C (2002) Comparison between RAPD and SSR molecular

markers in detecting genetic variation in kiwifruit (Actinidia deliciosa A. Chev) pp.

Plant Cell Reports 20: 1061 - 1066

Pan YB, Burner DM, Legendre BL (2000) An assessment of the phylogenetic

relationship among sugarcane and related taxa based on the nucleotide sequence of

5S rRNA intergenic spacers. Genetica 108: 285-95

Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and

characterization of simple sequence length polymorphism (SSLP) in rice (Oryza

sativa L.). Mol Gen Genet 252: 597-607

Pandian A, Ford R, Taylor PWJ (2000) Transferability of Sequence Tagged

Microsatellite Site (STMS) Primers across four major pulses. Plant Mol Biol Rep 18:

395a-395h

Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked

to downy mildew resistance genes in lettuce. Theor Appl Genet 85: 985-993

Paran I, Aftergoot E, Shifriss D (1998) Variation in Capsicum annuum revealed by

RAPD and AFLP markers. Euphytica 99: 167-173

Pardue ML, Brown DD, Birnstiel ML (1973) Location of the genes for 5S ribosomal

RNA in Xenopus laevis. Chromosoma 42: 191-203

Parsons BJ, Newbury HJ, Jackson MT, Ford-Lloyd BV (1997) Contrasting genetic

diversity relationships are revealed in rice (Oryza sativa). Mol Breed 3: 115-125

References

Paul S, Wachira FN, Powell W, Waugh R (1997) Diversity and genetic differentiation

among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze)

revealed by AFLP markers. Theor Appl Genet 94: 255-263.

Peacock WJ, Dennis ES, Rhoades MM, Pryor AJ (1981) Highly repeated DNA

sequence limited to knob heterochromatin in maize. Proc Natl Acad Sci USA

78:4490-4494

Peakall R, Smouse PE, Huff DR (1995) Evolutionary implications of allozyme and

RAPD variation in diploid populations of dioecious buffalograss Buchloe

dactyloides. Mol Ecol 4:135–147

Pearce SR, Harrison G Li D, Heslop-Harrison JS, Kumar A and Flavell AJ (1996a)

The Ty1-copia group retrotransposons in Vicia species: copy number, sequence

heterogeneity and chromosomal localisation. Mol Gen Genet 250: 305-315

Pearce SR, Pich U, Harrison G, Flavell AJ, Heslop-Harrison JS, Schubert I, Kumar A

(1996b) The Ty1-copia group retrotransposons of Allium cepa are distributed

throughout the chromosomes but are enriched in the terminal heterochromatin.

Chromosome Res 4: 257-364.

Pearce SR, Harrison G, Heslop-Harrison JS, Flavell AJ, Kumar A (1997)

Characterisation and genomic organisation of Ty1-copia group retrotransposons in

rye (Secale cereale). Genome 40: 617-625

Pearce SR, Stuart-Rogers C, Kumar A, Flavell AJ (1999) Rapid isolation of plant Ty1-

copia group retrotransposon LTR sequences for molecular marker studies. Plant J.

19: 711-717.

Pearce SR, Knox MR, Ellis THN, Flavell AJ, Kumar A (2000) Pea Ty1-copia group

retrotransposons: Transpositional activity and use as markers to study genetic

diversity in Pisum. Mol Gen Genet 263: 898-907

Pearl HM, Nagai C, Moore PH, Steiger DL, Osgood RV, Ming R (2004) Construction

of a genetic map for arabica coffee. Theor Appl Genet108: 829-835

Pech M, Streeck RE, Zachau HG (1979) Patchwork structure of a bovine satellite

DNA. Cell 18, 883-893

Pehu E, Thomas M, Poutala T, Karp A, Jones MGK (1990) Species specific

sequences in the genus Solanum : identification, charachterization, and application

to study somatic hybrids of S. brevidens and S. tuberosum. Theor Appl Genet 80:

693-698

Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G,

Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines

detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97: 1248-1255

Perera L, Russell JR, Provan J, Mc Nicol JW, Powell W (1998) Evaluating genetic

relationships between indigenous coconut (Cocos nucifera L.) accessions from Sri

Lanka by means of AFLP profiling. Theor Appl Genet 96: 545-550

Perera L, Russell JR, Provan J, Powell W (2000) Use of microsatellite DNA markers

to investigate the level of genetic diversity and population genetic structure of

coconut (Cocos nucifera L.). Genome 43: 15-21

Peschke VM, Philips RL (1992) Genetic implications of somaclonal variation in

plants. Adv Genet 30: 41-75

Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic stability of plant tissue cultures:

breakdown of normal controls. Proc Natl Acad Sci USA 91: 5222-5226

References

Pillay M, Myers G O (1999) Genetic diversity in cotton assessed by variation in

ribosomal RNA genes and AFLP markers. Crop Sci 39: 1881-1886

Piller KJ, Baerson SR, Polans NO, Kaufman LS (1990) Structural analysis of the

short length ribosomal DNA variant from Pisum sativum L. cv. Alaska. Nuc Acids

Res 18: 3135-3145

Pinon J, Teissier du Cros E, (1976) Sensibilite aux rouilles de differentes especes de

peupliers Melamspora alli-populina Kleb. Annales des Sciences Forestieres 33: 49-

59

Playford J, Appels R, Baum BR (1992) The 5S DNA units of Acacia species

(Fabaceae). Pl Syst Evol 183: 235-247

Porceddu A, Albertini E, Barcaccia G, Falistocco E, Falcinelli M (2002) Linkage

mapping in apomictic and sexual Kentucky bluegrass (Poa pratensis L.) genotypes

using a two way pseudo- testcross strategy based on AFLP and SAMPL markers.

Theor Appl Genet 104: 273-280

Poulsen GB, Kahl G, Weising K (1993) Abundance and polymorphism in simple

reprtitive DNA sequences in Brassica napus. Theor Appl Genet 85: 994-1000

Poulsen GB, Kahl G, Weising K (1994) Differential abundance of simple repetitive

sequences in species of Brassica and related Brassiceae. Plant Syst Evol 190: 21-30

Pouteau S, Grandbastien M-A, Boccara M (1994). Microbial elicitors of plant defense

responses activate transcription of a retrotransposon. Plant J 5: 535 542

Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996)

The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for

germplasm analysis. Mol Breed 2: 225-238

Prado EA, Faivre-Rampant P, Schneider C, Darmency MA (1996) Detection of a

variable number of ribosomal DNA loci by fluorescent in-situ hybridization in

Populus species. Genome, 39: 1020-1026.

Prakash S, Hinata K (1980) Taxonomy, cytogenetics and origin of crop brassicas – a

review. Opera Botanica 55: 1-57

Price AH, Steele KA, Moore BJ, Barraclough PB, Clark LJ (2000a) A combined

RFLP and AFLP linkage map of upland rice (Oryza sativa L.) used to identify QTLs

for root penetration ability. Theor Appl Genet 100: 49-56

Price Z, Dumortier F, Mayes S (2000b) Development and application of IRAP (Inter

retrotransposon amplified polymorphism) based on copia like retrotransposons in

African oil palm (Elaeis guineensis jacq.), Wheat Genetics Resource Centre.

Abstracts 2000

Prioul S, Frankewitz A, Deniot G, Morin G, Baranger A (2004) Mapping of

quantitative trait loci for partial resistance to Mycosphaerella pinodes in pea (Pisum

sativum L.), at the seedling and adult plant stages. Theor Appl Genet. 108:1322-

1334

Promnitz LC, Wray PH (1976) Rapid selection techniques for identifying superior

clones. USDA For Serv North Cent Res Stn Gen Tech Rep NC-21:25-31

Purba AR, Noyer JL, Baudouin L, Perrier X, Hamon S, Lagoda PJL (2000) A new

aspect of genetic diversity of Indonesian oil palm (Elaeis guineensis Jacq.) revealed

by isoenzyme and AFLP markers and its consequence in breeding. Theor Appl Genet

101: 956-961

References

Purugganan MD, Wessler SR (1995) Transposon signatures: species-specific

molecular markers that utilize a class of multiple-copy nuclear DNA. Mol Ecol

4:265-269

Qi J, Zhou D, Wu W, Lin L, Wu J, Fang P (2003) Application of ISSR technology in

genetic diversity detection of jute. Ying Yong Sheng Tai Xue Bao. 14: 1473-7

Quagliaro G, Vischi M, Tyrka M, Olivieri AM (2001) Identification of wild and

cultivated sunflower for breeding purposes by AFLP markers. The Amer genet Asso

92: 38-42

Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based

molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet

Gen 271: 91–97

Quiros CF, This P, Laudie M, Benet A, Chevre AM, Delseny M (1991) Analysis of a

set of RAPD markers by hybridization and sequencing in Brassica: A note of

caution. Plant Cell Rep 14: 630-634

Rafalski JA, Wiewiorowski M, Soll D (1982) Organization and di-nucleotide

sequence of nuclear 5S rRNA genes in yellow lupin (Lupinus luteus). Nucl Acids Res

10: 7635-7642

Rahman MH, Dayanandan S, Rajora OP (2000) Microsatellite DNA markers in

Populus tremuloides. Genome 43: 293-297

Rahman MH, Rajora OP (2002) Microsatellite DNA fingerprinting, differentiation,

and genetic relationships of clones, cultivars, and varieties of six poplar species from

three sections of the genus Populus. Genome 45: 1083-1094

Rajagopal J, Bashyam L, Bhatia S, Khurana DK, Srivastava PS, Lakshmikumaran M

(2000) Evaluation of genetic diversity in the Himalayan Poplar using RAPD

markers. Silvae Genetica 49: 60-66

Rajesh PN, Tullu A, Gil J, Gupta V, Ranjekar PK and Muehlbauer FJ (in press).

Identification of an STMS marker for the double-podding gene in chickpea. Theor

Appl Genet

Rajora OP (1988) Allozymes as aids for identification and differentiation of some

Populus maximowiczii Henry clonal varieties. Biochemical Systematics and Ecology

16 635-640

Rajora OP (1989) Characterization of 43 Populus nigra L. clones representing

selection, cultivars and botanical varieties based on their allozyme genotypes.

Euphytica. 43 197-206

Rajora OP, Dancik BP (1995a) Chloroplast DNA variation in Populus I. Interspecific

restriction fragment diversity within Populus deltoides, P. nigra and

P. maximowiczii. Theor Appl Genet 90: 317-323

Rajora OP, Dancik BP (1995b) Chloroplast DNA variation in Populus II.

Interspecific restriction fragment polymorphisms and genetic relationships among

Populus deltoides, P. nigra, P. maximowiczii and P. x canadensis. Theor Appl

Genet 90: 324-330

Rajora OP, Rahman MH (2003) Microsatellite DNA and RAPD fingerprinting,

identification and genetic relationships of hybrid poplar (Populus x canadensis)

cultivars. Theor Appl Genet 106: 470-477

Rajora OP, Zsuffa L (1991) Screening Populus deltoides Marsh. selections by

allozymes to assure species identity. Scand J For Res 6: 471–478

References

Rani V, Parida A, Raina SN (1995) Random amplified polymorphic DNA (RAPD)

markers for genetic analysis in micropropagated plants of Populus deltoides Marsh.

Plant Cell Rep 14: 459-462

Rani V, Raina SN (1998) Genetic analysis of enhanced axillary branching derived

Eucalyptus tereticornis and E. camaldulensis. Plant Cell Rep 17: 236-242

Rani V, Raina SN (2000) Genetic fidelity of organized meristem-derived

micropropagated plants: a critical appraisal. In Vitro Cell Dev Biol-Plant 36: 319-

330

Rani V, Singh KP, Shiran B, Nandy S, Goel S, Devarumath RM, Sreenath HL, Raina

SN (2000) Evidence for new nuclear and mitochondrial genome organizations

among high-frequency somatic embryogenesis-derived plants of allotetraploid

Coffea arabica L. (Rubiaceae). Plant Cell Rep 19: 1013-1020

Rani V, Raina S N, Parida A (2001) Chromosome number dependent genome size

and rapd fingerprinting diagnostics for genetic integrity of enhanced axillary

branching-derived plants of ten forest tree species. Acta Hort. (ISHS) 560:534-534

Razin A, Riggs AD (1980) DNA methylation and gene function. Science 210: 604-

610

Reamon-Buttner ST, Schmidt T, Jung C (1999) AFLPs represent highly repetitive

sequences in Asparagus officinalis L. Chromosome Research 7: 297-304

Reddy P, Appels R (1989) Organisation and evolution of the 5S ribosomal RNA gene

family in wheat and related species. Genome 32: 1003-1005

Remington DL, Whetten RW, Liu BH, O‘Malley DM (1999) Construction of an AFLP

genetic linkage map with nearly complete genome coverage in Pinus taeda. Theor

Appl Genet 98: 1279-1292

Renganayaki K, Read J, Fritz AK (2001) Genetic diversity among Texas bluegrass

genotypes (Poa arachnifera Torr.) revealed by AFLP and RAPD markers. 102: 1037-

1045

Rieseberg LH, Soltis DE, (1991) Phylogenetic consequences of cytoplasmic gene .ow

in plants. Evol. Trends Plant 5: 65–84.

Rieseberg LH, Wendel JF (1993) Introgression and its consequences in plants. In:

Harrison, R. (Ed.), Hybrid Zones and the Evolutionary Process. Oxford University

Press, Oxford, pp. 70–109

Rivera R, Edwards KJ, Barker JHA, Arnold GM, Ayad G, Hodgkin T, Karp A (1999)

Isolation and characterisation of polymorphic microsatellites in Cocos nucifera L.

Genome 42: 668–675

Roder MS, Sorrells ME, Tanksley SD (1992) 5S ribosomal gene clusters in wheat:

pulsed field gel electrophoresis reveals a high degree of polymorphism. Mol Gen

Genet 232: 215-220

Roder MS, Korzun V, Wendehake K, Plaschke J, Tixer MH, Leroy P, Ganal MW

(1998) A microsatellite map of wheat. Genetics 149: 2007-2023

Rogers SA, Pauls KP (2000) Ty1-copia-like retrotransposons of tomato

(Lycopersicon esculentum Mill.). Genome 43: 887-94

Rogers SO, Benedich AJ (1987) Ribosomal RNA genes in plants, variability in copy

number and in the intergenic spacer. Plant Mol Biol 9: 509-520

Rohlf FJ (1998) NTSYS-pc. Numerical taxonomy and multivariate analysis system.

Version 2.0. Exeter Publications, NY

References

Roldan-Ruiz I, Dendauw J, Bockstaele EV, Depicker A, de Loose M (2000) AFLP

markers reveal high polymorphic rates in rye grasses (Lolium spp.). Mol Breed 6:

125-134

Ronald WG (1982) Intersectional hybridization of Populus sections Leuce-Aigeiros

and Leuce-Tacamahaca. Silvae Genet 31: 94-99

Rose MR, Doolittle WF (1983) Molecular Biological mechanisms of speciation.

Science 220: 157-162

Rostiana O, Niwa M, Marubashi W (1999) Efficiency of Inter-Simple sequence

repeat PCR for detecting somaclonal variation among leaf culture regenerated plants

of horseradish. Breed Sci 49: 245-250

Rottenberg A, Nevo E, Zohary D (2000) Genetic variability in sexually dimorphic

and monomorphic populations of Populus euphratica (Salicaceae) Can. J. For. Res.

30(3): 482-486

Roy JK, Balyan HS, Prasad M, Gupta PK (2002) Use of SAMPL for study of DNA

polymorphism, genetic diversity and possible gene tagging in bread wheat. Theor

Appl Genet 104: 465-472

Roy JK, Lakshmikumaran MS, Balyan HS, Gupta PK (2004) AFLP-based genetic

diversity and its comparision with diversity based on SSR, SAMPL, and phenotypic

traits in bread wheat. Biochemical genetics 42: 43-59

Rozas J, Sanchez-delbarrio J, Messeguer XC, Rozas R (2003) DnaSP, DNA

polymorphism analyses by the coalescent and other methods. Bioinformatics 19:

2496-2497

Rus-Kortekaas W, Smulders MJM, Arens P, Vosman B (1994) Direct comparison of

levels of genetic variation in tomato detected by a GACA-containing microsatellite

probe and by random amplified polymorphic DNA. Genome 37: 375-381

Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997)

Direct comparison of the levels of genetic variation among barley accessions

detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95: 714-722

Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A laboratory

manual.: Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

Sanchez de la Hoz MP, Davila JP, Loarce Y, Ferrer E (1996) Simple sequence repeat

primers used in polymerase chain reaction amplifications to study genetic diversity

in barley. Genome 39: 112-117.

Sanchez G, Restrepo S, Duque M C, Fregene M, Bonierbale M, Verdier V (1999)

AFLP assessment of genetic variability in cassava accessions (Manihot esculenta)

resistant and susceptible to the cassava bacterial blight (CBB). Genome 42: 163-172

Sandmeyer SB, Hansen LJ, Chalker DL (1990) Integration specificity of

retrotransposons and retroviruses. Annu Rev Genet 24: 491-518

Sanger F, Nicklen S, Coulsen AR (1977) DNA sequencing with chain terminating

inhibitors. Proc natl Acad Sci USA 74: 5463-5467

SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome

size was caused by the massive amplification of intergene retrotransposons. Ann of

Bot 82:37-44 Suppl A

SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, ZakharovD, Melake-Berhan A,

Springer PS, Edwards KJ, Lee M, Avra-mova Z, Bennetzen JL (1996) Nested

References

retrotransposons in the intergenic regions of the maize genome. Science 274:765-

768

SanMiguel P, Gaut BS, Tikhonov A, Nakijama Y and Bennetzen JL (1998) The

paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45

Saraswat CV, Khurana DK, Thakur S (1993) Poplar improvement in Himachal

Pradesh (India). Farm Forestry Training course meet, Beijing China, Paper

presentation Sept 14-28, 1993

Sastri DC, Hilu K, Appels R, Lagudah ES, Playford J, Baum BR (1992) An overview

of evolution in plant 5S DNA. Plant Syst Evol 183: 169-181

Scalfi M, Troggio M, Piovani P, Leonardi S, Magnaschi G, Vendramin GG, Menozzi P

(2004) A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech

(Fagus sylvatica L.). Theor Appl Genet 108: 433-441

Scheepers D, Eloy MC, Briquet M (1997) Use of RAPD patterns for clone verification

and in studying provenance relationships in Norway spruce (Picea abies). Theor

Appl Genet 94: 480-485

Schlotterer C, Tautz D (1992) Silppage synthesis of simple sequence DNA. Nuc Acid

Res 20: 211-215

Schlotterer C, Tautz D (1994) Chromosomal homogeneity of Drosophila ribosomal

DNA arrays suggests intrachromosomal exchanges drive concerted evolution. Curr

Biol 4: 777-783

Schmidt T, Boblenz K, Metzlaff M, Kaemmer D, Weising K, Kahl G (1993) DNA

fingerprinting in sugarbeet (Beta vulgaris) –identification of double haploid

breeding lines. Theor Appl Genet 85: 653-657

Schmidt M, Walz C, Hesemann CV (1996) Somaclonal variation of mitochondrial

ATPase subunit 6 gene region in regenerated triticale shoot and full-grown plants.

Theor Appl Genet 93: 355-360

Schmidt T, Heslop-Harrison JS (1998). Genes, genomes and junk: a model of the

large scale organization of plant chromosomes. Trends Plant Sci 3:195-199.

Schmidt K, Jensen K (2000) Genetic structure and AFLP variation of remnant

populations in the rare plant Pedicularis palustris (Scrophulariaceae) and its

relation to population size and reproductive components. Am J Bot 87: 678-689

Schneeberger RG, Creissen GP, Cullis CA (1989) Chromosomal and molecular

analysis of 5S RNA gene organization in the flax, Linum usitatissimum. Gene 83: 75-

84

Schneeberger RS, Cullis CA (1991) Specific DNA alterations associated and the

environmental induction of heritable changes in flax. Genetics 128: 619-630

Schnell RJ, Ronning CM, Knight RJ (1995). Identification of cultivars and

validation of genetic relationships in Mangifera indica L. using RAPD markers.

Theor Appl Genet 90: 269-274

Schondelmaier T, Smith T, Heslop-Harrison JS, Jung C (1997) Genetic and

chromosomal localization of 5S rDNA locus in Sugarbeet (Beta vulgaris L.) Genome

40:171-175

Schwarz-Sommer Z, Gierl A, Cuypers H, Peterson PA, Saedler H (1985) Plant

transposable elements generate the DNA sequence diversity needed in evolution.

EMBO J 4: 591 - 597

References

Schwarzacher T, Anamthawat-Jónsson K, Harrison GE, Islam AKMR, Jia JZ, King

IP, Leitch AR, Miller TE, Reader SM, Rogers WJ, Shi M, Heslop-Harrison JS (1992)

Genomic in situ hybridization to identify alien chromosomes and chromosome

segments in wheat. Theor Appl Genet 84: 778-786

Schwarzacher T, Heslop-Harrison JS (1991) In situ hybridization to plant telomeres

using synthetic oligomers. Genome 34: 317-333

Scoles GJ, Gill BS, Xin ZY, Clarke BC, McIntyre CL, Chapman C, Appels R (1988)

Frequent duplication and deletion events in the 5S RNA genes and the associated

spacer regions of the Triticeae. Plant Syst Evol 160: 105-122

Scotti I, Soranzo N, Ferrario G, Binelli G (1998) Genetic variation in Norway spruce

as revealed by mapped PCR-based markers. Acta Horticolturae 457: 363–370

Scotti I, Magni F, Fink R, Powell W, Binelli G, Hedley PE (2000) Microsatellite

repeats are not randomly distributed within Norway spruce (Picea abies K.)

expressed sequences. Genome 43 : 41-46

Sebastian RL, Howell EC, King GJ, Marshall DF, Kearsey MJ (2000) An integrated

AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct

doubled haploid mapping populations. Theor Appl Genet 100: 75-81

Seefelder S, Ehrmaier H, Schweizer G, Seigner E (2000) Genetic diversity and

phylogenetic relationships among accessions of hop, Humulus lupulus, as

determined by amplified fragment length polymorphism fingerprinting compared

with pedigree data. Plant Breed 119: 257-263

Sellmer JC, McCown BH, Haissig BE (1989) Shoot culture dynamics of six Populus

clones. Tree Physiol 5:219-227

Serret MD, Udupa SM, Weigand F (1997) Assessment of genetic diversity of

cultivated chickpea using microsatellite derived RFLP markers: Implications for

origin. Plant Breed 116: 573-578

Shan X, Blabe TK, Talbert LE (1999) Conversion of AFLP markers to sequence

specific PCR markers in barley and wheat. Theor Appl Genet 98: 1072-1078

Sharma A, Sharma R, Machii S (2000) Assessment of genetic diversity in a Morus

germplasm collection using fluorescence-based AFLP markers. Theor Appl Genet

101: 1049-1055

Sharma SK, Knox MR, Ellis THN (1996) AFLP analysis of the diversity and

phylogeny of Lens and its comparison with RAPD analysis. Theor Appl Genet 93:

751-758

Shchukin A, Ben-Bassat D, Israeli Y (1997) Plant regeneration via somatic

embryogenesis in Grand Naine banana and its effect on somaclonal variation

Acta Hort 447: 317

Shenoy VB, Vasil IK (1992) Biochemical and molecular analysis of plants derived

from embryogenic tissue cultures of napier grass (Pennisetum purpureum K.

Schum). Theor Appl Genet 83: 947-955

Shim SI, Jorgensen RB (2000) Genetic structure in cultivated and wild carrots

(Daucus carota L.) revealed by AFLP analysis. Theor Appl Genet 100: 227-233

Shimron-Abarbanell D, Breiman A (1991) Comprehensive molecular

characterization of tissue-culture-derived Hordeum marinum plants. Theor Appl

Genet 83:71–80

References

Shirasu K, Schulman AS, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb

barley DNA sequence provides evidence for reversible genome expansion. Genome

Res 10:908–915

Shirzadegan M, Palmer JD, Christey M, Earle ED (1991) Patterns of Mitochondrial

DNA instability in Brassica compestris cultured plants. Pant Mol Biol 16: 21-37

Shoyama Y, Xuan Xuan Z, Nakai R, Shiraishi S, Kohda H (1997) Micropropagation

of Panax notoginseng by somatic embryogenesis and RAPD analysis of regenerated

plantlets. Plant Cell Rep 16: 450-453

Siebert PD, Chenchik A, Kellog DE, Lukyanov KA and Lukyanov SA (1995) An

improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23:

1087-1088

Silvio-May (1978) Silvics and Ecology of Populus ciliata Wall. Early results with

breeding and growing of it. Instituto di Sperimentazione per la Pioppiocoltura,

Casale Monferrato, Italy.

Simons KJ, Gehlhar SB, Maan SS, Kianian SF (2003) Detailed mapping of the

species cytoplasm-specific (scs) gene in durum wheat. Genetics 165: 2129-2136.

Singh D, Singh M (2001) Organization of 5S ribosomal RNA genes in tea (Camellia

sinensis). Genome 44: 143-146

Singh K, Bhatia S, Lakshmikumaran S (1994) Novel variants of 5S rRNA genes in

Eruca sativa. Genome 88: 116-122

Singh A, Negi MS, Rajagopal J, Bhatia S, Tomar UK, Srivastava PS,

Lakshmikumaran M (1999) Assessment of genetic diversity in Azadirachta indica

using AFLP markers. Theor Appl Genet 99: 272-279

Singh A, Chaudhury A, Srivastava PS, Lakshmikumaran M (2002) Comparision of

AFLP and SAMPL markers for assessment of intra-population genetic variation in

Azadirachta indica A. Juss. Plant Sci 162: 17-25

Smith GP (1976) Evolution of repeated DNA sequences by unequal crossover.

Science 191: 528-535

Smith RL, Sytsma KJ (1990) Evolution of P. nigra (Sect. Aigeiros): Introgressive

hybridization and the chloroplast contribution of P. alba (Sect. Leuce). Am J Bot 77:

1176-1187

Sneath PHA, Sokal RR (1973) Numerical taxonomy. W H Freeman, San Francisco,

California

Sokal RR, Michener CD (1958) A statistical method for evaluating systematic

relationships. Univ Kansas Sci Bull 38: 1409-1438

Soleimani VD, Baum BR, Johnson DA (2002) AFLP and pedigree-based genetic

diversity estimates in modern cultivars of durum wheat [Triticum turgidum L.

subsp. durum (Desf.) Husn.] Theor Appl Genet 104: 350-357

Sollner-Webb B, Tower J (1986) Transcription of cloned eukaryotic ribosomal RNA

genes. Ann Rev Biochem 55: 801-830

Soltis DE, Soltis PS, Doyle JJ (Eds.) (1998) Molecular systematics of plants II: DNA

sequencing. Kluwer Academic, Boston.

Song K M, Osborn T C, Williams P H (1988a) Brassica taxonomy based on nuclear

restriction fragment length polymorphisms (RFLPs). 1. Genome evolution of diploid

and amphidiploid species. Theor Appl Genet 75: 784-794

References

Song K M, Osborn T C, Williams P H (1988b) Brassica taxonomy based on nuclear

restriction fragment length polymorhisms (RFLPs). 2. Preliminary analysis of

subspecies within B. rapa (syn. campestris) and B. oleracea. Theor Appl Genet 76:

593-600

Song K M, Osborn T C, Williams P H (1990) Brassica taxonomy based on nuclear

restriction fragment length polymorphisms (RFLPs). 3. Genome relationships in

Brassica and related genera and the origin of B. oleracea and B. rapa (syn.

campestris). Theor Appl Genet 79: 497-506

Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai

WX, Zhu LH, et al. (1995) A receptor kinase-like protein encoded by the rice disease

resistance gene, Xa21. Science 270:1804-1806

Spooner DM, Ugarte ML, Skroch PW (1997) Species boundaries and

interrelationships of two closely sympatric diploid wild potato species Solanum

astleyi and S. boliviense, based on RAPDs. Theor Appl Genet 95: 764-771

Stallings RL, Ford AF, Nelson D, Torney DC, Hildebrand CE, Moyzis R K (1991)

Evolution and distribution of (GT)n repetitive sequences in mammalian genomes.

Genomics 10: 807-815

Steele KP, Holsinger KE, Jansen RK, Taylor DW (1991) Assessing the reliability of 5S

rRNA sequence data for phylogenetic analysis in green plants. Mol Biol Evol 8: 240-

248

Stehlik I, Blattner FR (2004) Sex-specific SCAR markers in the dioecious plant

Rumex nivalis (Polygonaceae) and implications for the evolution of sex

chromosomes. Theor Appl Genet 108: 238-42

Steiger DL, Nagai C, Moore PH, Morden CW, Osgood RV, Ming R (2002) AFLP

analysis of genetic diversity within and among Coffea arabica cultivars. Theor Appl

Genet 105: 209-215

Stein L (2001) Genome Annotation: From Sequence to Biology. Nature Reviews

Genetics 493-503.

Stettler RF, Bradshaw HD, Heilman PE, Hinckley TM (Eds.) (1996) Biology of

Populus and its implications for management and conservation. Ottawa, Ontario,

Canada : NRC Research Press, 539 p

Stiles JI, Lemme C, Sondur S, Morshidi MB, Manshardt R (1993) Using randomly

amplified polymorphic DNA for evaluating genetic relationships among papaya

cultivars. Theor Appl Genet 85: 697-701

Storme V, Vanden Broeck A, Ivens B, Halfmaerten D, Van Slycken J, Castiglione S,

Grassi F, Fossati T, Cottrell JE, Tabbener HE, Lefèvre F, Saintagne C, Fluch S,

Krystufek V, Burg K, Bordács S, Borovics A, Gebhardt K, Vornam B, Pohl A, Alba N,

Agúndez D, Maestro C, Notivol E, Bovenschen J, van Dam BC, van der Schoot J,

Vosman B, Boerjan W, Smulders MJM (2004) Ex-situ conservation of Black poplar

in Europe: genetic diversity in nine gene bank collections and their value for nature

development. Theor Appl Genet 108: 969-981

Sudupak MA, Akkaya MS, Kence A (2004) Genetic relationships among perennial

and annual Cicer species growing in Turkey assessed by AFLP fingerprinting. Theor

Appl Genet 108:937-944

References

Suoniemi A, Anamthawat-Jónsson K, Arna T, Schulman AH (1996) The BARE-1

retrotransposon is a major, dispersed component of the barley (Hordeum vulgare

L.) genome. Plant Mol Biol 30: 1321-1339

Suoniemi A, Schmidt D, Schulman AH (1997) BARE-1 insertion site preferences and

evolutionary conservation of RNA and cDNA processing sites. Genetica 100: 219-

230

Suoniemi A, Tanskanen J, Pentikainen O, Johnson M, Schulman AH (1998) The

core domain of retrotransposon integrase in Hordeum: Predicted structure and

evolution. Mol Biol Evol 15: 1135-1144

Svitashev S, Bryngelsson T, Vershinin A, Pedersen C, Sall T, Bothmer R von (1994)

Phylogenetic analysis of genus Hordeum using repetitive DNA sequences. Theor

Appl Genet 89: 801-810

Swofford DL (1991) PAUP: phylogenetic analysis using parsimony, version 3.0.

Illinois Natural History Survey, Champaign

Takaiwa F, Oono K, Sugiura M (1984) The complete nucleotide sequence of a rice

17S rRNA gene. Nucl Acids Res 12: 5369-5379

Tang W (2001) In-vitro regeneration of loblolly pine and random amplified

polymorphic DNA analyses of regenerated plantlets. Plant Cell Rep 20: 163-168

Tanhuanpaa PK, Vikki JP, Vikki HJ (1996) Mapping of QTL for oleic acid

concentration in spring turnip rape (Brassica rapa ssp oleifera). Theor Appl Genet

92: 952-956

Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in

plant breeding: new tools for old sciences. Biotechnology 7: 257-264

Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for

map-based gene cloning in plants with large genomes. Trends Genet 11:63-68

Taran B, Warkentin T, Somers DJ, Miranda D, Vandenberg A, Blade S, Woods S,

Bing D, Xue A, DeKoeyer D, Penner G (2003) Quantitative trait loci for lodging

resistance, plant height and partial resistance to mycosphaerella blight in field pea

(Pisum sativum L.). Theor Appl Genet 107: 1482-1491

The Angiosperm Phylogeny Group (1998) An ordinal classification for the families of

flowering plants. Annals Of The Missouri Botanical Garden 85: 531-553

Tautz D (1989) Hypervariability of simple sequences as a general source for

polymorphic DNA markers. Nucl Acids Res 17: 6463-6467

Taylor G (2002) Populus: Arabidopsis for forestry. Do we need a model tree? Ann

Bot 90: 681-689

Teulat B, Aldam C, Trehin R, Lebrun P, Barker JHA, Arnold GM, Karp, Baudouin L,

Rognon F (2000) An analysis of genetic diversity in coconut (Cocos nucifera)

populations from across the geographic range using sequence-tagged

microsatellites (SSRs) and AFLPs. Theor Appl Genet 100: 764-771

Thomas CM, Vos P, Zabeau M, Jones DA, Norcott KA, Chadwich BP, Jones JDG

(1995) Identification of amplified restriction fragment length polymorphism (AFLP)

markers tightly linked to the tomato Cf-9 gene for resistance to Cladosporium

fulvum. Plant J 8: 785-794

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: Improving the

sensitivity of progressive multiple sequence alignment through sequence weighting,

References

position-specific gap penalties and weight matrix choice. Nucl Acids Res 22: 4673-

4680

Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES

(2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet

28: 286-289

Tomkins JP, Wood TC, Barnes LS, Westman A, Wing RA (2001) Evaluation of

genetic variation in the daylily (Hemerocallis spp.) using AFLP markers. Theor Appl

Genet 102: 489-496

Torjek O, Kiss E, Kiss J, Kondrak M, Gyulai G, Gergacz J, Heszky L (2001)

Evaluation of genetic diversity of poplar genotypes by RAPD and AP-PCR analysis.

Acta Biol Hung 52: 345-54.

Travis SE, Maschinski J, Keim P (1996) An analysis of genetic variation in

Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using

AFLP markers. Mol Ecol 5: 735-745

Trontin J, Grandemange C, favre J (1999) Two highly divergent 5S rDNA unit size

classes occur in composite tandem array in European larch (Larix decidua Mill.)

and Japanese larch (Larix kaempferi (Lamb.) Carr.). Genome 42: 837-848

Tsarouhas V, Gullberg U, Lagercrantz U. (2002) An AFLP and RFLP linkage map

and quantitative trait locus (QTL) analysis of growth traits in Salix.Theor Appl

Genet 105:277-288

Tsarouhas V, Gullberg U, Lagercrantz U (2004) Mapping of quantitative trait loci

(QTLs) affecting autumn freezing resistance and phenology in Salix. Theor Appl

Genet 108: 1335-1342

Udovicic R, McFadden GI, Ladiges PY (1995) Phylogeny of Eucalyptus and

Angophora based on 5S rDNA spacer sequence data. Mol Phyl Evol 4: 247-256

Valles MP, Wang ZY, Montavon P, Portrykus I, Spangenberg G (1993) Analysis of

genetic stability of plants regenerated from suspension cultures and protoplasts of

meadow fescue (Festuca pratensis Huds.). Plant Cell Rep 12: 101-106

Van Droogenbroeck B, Breyne P, Goetghebeur P, Romeijen-Peeteers, Kyndt T,

Gheysen G (2002) AFLP analysis of the genetic relationships among papaya and its

wild relatives (Caricaceae) from Ecuador. Theor Appl Genet 105: 289-297

Vandenberghe A, Chen MW, Dams E, de Baere R de Roeck E, Huysmans E, de

Watcher R (1984) The corrected nucleotide sequences of 5S RNAs from six

angiosperms. FEBS Lett 171: 17-23

Vanderwiel PL, Voytas D, Wendel JF (1993) Copia-like retrotransposable element

evolution in diploid and polyploid cotton (Gossypium L.). J Mol Evol 36:429-447

VanToai TT, Peng J, St. Martin S (1996) Using AFLP markers to determine the

contribution of parental genomes during recurrent selection. Soybean genetics

newsletter 23: 214-216

Varmus H (1982) Form and function of retroviral proviruses. Science 216: 812-820.

Varshney A, Lakshmikumaran M, Srivastava PS, Dhawan V (2000) Establishment of

genetic fidelity of in-vitro raised Lilium bulblets through RAPD markers. In Vitro

Cell Dev Biol-Plant 36: 383-391

Varshney A, Mohapatra T, Sharma RP (2004) Development and validation of CAPS

and AFLP markers for white rust resistance gene in Brassica juncea. Theor Appl

Genet. Mar 2 [Epub ahead of print]

References

Varshney RK, Kumar A, Balyan HS, Roy JK, Prasad M, and Gupta PK (2000)

Characterization of microsatellites and development of chromosome specific STMS

markers in bread wheat. Plant Mol Biol Rep 18:5-16.

Vega KG, Chavira MG, Vega OM, Simpson J (2001) Analysis of genetic diversity in

Agave tequilana var. Azul using RAPD markers. Euphytica 119: 335-341

Vershinin AV, Heslop-Harrison JS (1998) Comparative analysis of the nucleosomal

structure of rye, wheat and their relatives. Plant Mol Biol 36: 149-161

Vershinin AV, Allnutt TR, Knox MR, Ambrose MJ, Ellis TH (2003) Transposable

elements reveal the impact of introgression, rather than transposition, in Pisum

diversity, evolution, and domestication. Mol Biol Evol 20: 2067-2075

Viart M (1977) Silviculture of temperate and semi-temperate forests. A technical

account of a study tour made in India (Oct. 5th to Nov. 18th, 1976). Report submitted

to the Government of India.

Vijverberg K, Van Der Hulst RG, Lindhout P, Van Dijk PJ (2004) A genetic linkage

map of the diplosporous chromosomal region in Taraxacum officinale (common

dandelion; Asteraceae). Theor Appl Genet 108: 725-732

Villar M, Lefevre F, Bradshaw HD, Teissier du Cros E (1996) Molecular genetics of

rust resistance in poplars (Melampsora larici-populina Kleb./Populus sp.) by

bulked segregant analysis in a 2 x 2 factorial mating design. Genetics 143: 531-536

Virk, PS, Ford-LLoyd, BV, Jackson, MT, Pooni, HS, Clemeno, TP and Newbury, HJ

(1996) Predicting quantitative variation within rice germplasm using molecular

markers. Heredity 76: 296-304

Vivek BS, Simon PW (1999). Linkae relationships among molcular markers and

storage root traits of carrot (Daucus carota L. ssp. sativus). Theor Appl Genet 99:

58-64

Vogel JM, Scolnik PA (1998) Direct Amplification from micro-satellites: detection of

simple repeat-based polymorphisms without cloning. In: Caetano-Anolles G,

Gresshoff PM (eds) DNA Markers; Protocols, Applications, and Overviews. Wiley-

Liss, Inc, NY, pp 133-150

Voorrips RE, Jongerius MC, Kanne HJ (1997) Mapping of two genes for resistance

to clubroot (Plasmodiophora brassicae) in a population of doubled haploid lines of

Brassica oleracea by means of RFLP and AFLP markers. Theor Appl Genet 94: 75-

82

Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Plot J,

Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA

fingerprinting. Nucl Acids Res 23: 4407-4414

Vosman B, Arens P, Rus-Kortekaas W, Smulders MJM (1992) Identification of

highly polymorphic DNA regions in tomato. Theor Appl Genet 85: 239-244

Voytas DF, Cummings MP, Konieczny AK, Ausubel FM, Rodermel SR (1992) Copia-

like retrotransposons are ubiquitous among plants. Proc Natl Acad Sc USA 89: 7124-

7128

Vuylsteke M, Mank R, Brugmans B, Stam P, Kuiper M (2000) Further

characterization of AFLP data as a toolin genetic diversity assessments among maize

(Zea mays L.) inbred lines. Mol Breed 6: 2665-276

Wachira FN, Waugh R, Hackett CA, Powell W (1995) Detection of genetic diversity

in tea (Camellia sinensis) using RAPD markers. Genome 38: 201-210

References

Walbot V (1992) Strategies for mutagenesis and gene cloning using transposon

tagging and T-DNA insertional mutagenesis. Ann Rev Plant Physiol 43: 49-82

Wallner E, Weising K, Rompf R, Kahl G, Kopp B (1996) Oligonucleotide

fingerprinting and RAPD analysis of Achillea species: Characterization and long-

term monitoring of micropropagated clones. Plant Cell Rep 15: 647-652

Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant tandem repeats.

Theor Appl Genet 88: 1-6

Wang G, Castiglione S, Chen Y, Li L, Han Y, Tian Y, Gabriel DW, Han Y, Mang K,

Sala F (1996) Poplar (Populus nigra L.) plants transformed with a Bacillus

thuringiensis toxin gene: insecticidal activity and genomic analysis. Transgenic Res

5:289–301

Wang YH, Thomas CE, Dean RA (1997) A genetic map of melon (Cucumis melo L.)

based on amplified fragment length polymorphism (AFLP) markers. Theor Appl

Genet 95: 791-798

Watanabe A, Araki S, Kobari S, Sudo H, Tsuchida T, Uno T, Kosaka N, Shimomura

K, Yamazaki M, Saito K (1998) In-vitro propagation, restriction fragment length

polymorphism, and random amplified polymorphic DNA analyses of Angelica

plants. Plant Cell Rep 18: 187-192

Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W

(1997) Genetic distribution of BARE-1-like retrotransposable elements in the barley

genome revealed by sequence-specific amplification polymorphisms (S-SAP) Mol

Gen Gen 253: 687-694

Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can

be typed using the polymerase chain reaction. Am J Hum Genet 44: 388-396

Weigel R, Wolf R, Hesemann CV (1995) Mitochondrial DNA variation in plants

regenerated from embryogenic callus cultures of cms triticale. Theor Appl Genet 91:

1237-1241

Weining S, Langridge (1991) Identification and mapping of polymorphisms in

cereals based on polymerase chain reaction. Theor Appl Genet 82: 209-216

Weising K, Nybom H, Wolff K, Meyer W (1995) DNA fingerprinting in plants and

fungi. CRC Press, Boca Raton, Florida

Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary

primers. Nucl Acids Res 18: 7213-7218

Welsh J, McClelland M (1991) Genomic fingerprinting using arbitrarily primed PCR

and a matrix of pairwise combinations of primers. Nucl Acids Res 19: 5277-5279

Wendel JF, Schnabel A, Seelanan T (1995) Bidirectional interlocus concerted

evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad

Sci USA 92: 280-284

Weng C, Kubisiak TL, Stine M (1998) SCAR markers in a longleaf pine x slash pine

F1 family. For genet 5(4): 239-247

Wendel JF, Wessler S R (2000). Retrotransposon-mediated genome evolution on a

local ecological scale. Proc Natl Acad Sci USA 6 : 6250-6252

Wessler S, Bereau TE, White SE (1995) LTR-retrotransposons and MITEs:

important players in the evolution of plant genomes. Current opinion Genet Dev

5:814-821

References

Wheeler WC, Honeycutt RL (1988) Paired sequence differences in ribosomal RNAs:

evolutinary and phylogenetic implications. Mol Biol Evol 5: 90-96

White SE, Habera LF, Wessler SR (1994) Retrotransposons in the flanking regions

of normal plant genes: a role for copia-like elements in the evolution of gene

structure and expression. Proc Natl Acad Sci 91 (25): 11792–11796

Wiesner I, Wiesnerova D (2003) Insertion of a reamplification round into the ISSR-

PCR protocol gives new flax fingerprinting patterns. Cell Mol Biol Lett. 8: 743-48

Wilde J, Waugh R, Powell W (1992) Genetic fingerprinting of Theobroma clones

using randomly amplified polymorphic DNA markers. Theor Appl Genet 83: 871-

877

Wilkinson AG, Edwards WRN, Gilchrist AN, Hathway RL, Spiers AG (1998)

National report on activities related to poplar and willow cultivation: Period: 1985-

1988. Plant Materials Group. Dept. of Scientific and Industrial Research,

Palmerston North, New Zealand. 28p

Williams JGK, Kubelik AR, Livak KJ, Rafalaski JA, Tingey SV (1990) DNA

polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl

Acids Res 18: 6531-6535

Willing RR, Pryor LD (1976) Interspecific hybridization in Poplar. Theor Appl Genet

47: 141-151

Winfield MO, Arnold GM, Cooper F, Le ray M, White J, Karp A, Edwards KJ (1998)

A study of genetic diversity in Populus nigra subsp. betulifolia in the Upper Severan

area of the UK using AFLP markers. Mol Ecol 7: 3-10

Wittsenboer H, Kesseli RV, Fortin MG, Stanghelljni M, Michelmore RW (1995)

Sources and genetic structure of a cluster of genes resistant to three pathogens in

lettuce. Theor Appl Genet 91:178-188

Witsenboer H, Vogel J, Michelmore RW (1997) Identification, genetic localization

and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce

and wild relatives (Lactuca spp.) Genome 40: 923-936

Woeste K (1996) Randomly amplified polymorphic DNA loci from a walnut backross

[(Juglans hindsii X J. regia) X J. regia) ] J Amer Soc Hort Sci 121: 358-361

Wolff K, Zeitkeiwicz E, Hofstra H (1995) Ientification of Chrysanthemum cultivars

and stability of DNA fingerprint patterns. Theor Appl Genet 91: 439-447

Wolters J, Erdmann VA (1988) Compilation of 5S rRNA and 5S rDNA gene

sequences. Nucl Acid Res 16 (Suppl): r1-r70

Wu KS, Jones R, Dannenberg L, Scolnik PA (1994) Detection of microsatellite

polymorphisms without cloning. Nucl Acids Res 22: 3257-3258

Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of

microsatellites in rice. Mol Gen Genet 241: 225-235

Wu RL, Han YF, Hu JJ, Fang JJ, Li L, Li ML, Zeng ZB (2000) A integrated genetic

map of Populus deltoides based on amplified fragment length polymorphisms.

Theor Appl Genet 100: 1249-1256

Wu R, Ma CX, Zhao W, Casella G (2003) Functional mapping of quantitative trait

loci underlying growth rates: A parametric model. Physiological Genomics. 14: 241-

249

Wullschleger SD, Jansson S, Taylor G (2002) Genomics and forest biology: Populus

emerges as the perennial favorite. Plant Cell Vol 14: 2651-2655

References

Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based upon

their reverse transcriptase sequences. EMBO J. 9: 3353–3362

Xu RQ, Tomooka N, Vaughan DA (2000) AFLP markers for characterizing the Azuki

bean complex. Crop Sci 40: 808-815

Xu M, Huaracha E, Korban SS (2001) Development of sequence-characterized

amplified regions (SCARs) from amplified fragment length polymorphism (AFLP)

markers tightly linked to the Vf gene in apple. Genome 44: 63-70

Yang G, Hall TC (2003) MAK, a computational tool kit for automated MITE

analysis. Nucleic Acids Res. 31: 3659–3665

Yang YW, Lai KN, Tai PY, Ma DP, Li WH (1999) Molecular phylogenetic studies of

Brassica, Rorippa, Arabidopsis, and allied genera based on the internal transcribed

spacer region of18S–25S rDNA. Mol Phyl Evol 13: 455–462.

Yap IV, Nelson RJ (1995) WINBOOT, a program for performing bootstrap analysis

of binary data to determine the confidence limits of UPGMA-based dendrograms.

IRRI Discussion Paper Series No. 14, International Rice Research Institute, Los

Banos, Phillipines

Yee E, Kidwell KK, Sills GR, Lumpkin TA (1999) Diversity among selected Vigna

angularis (Azuki) accessions on the basis of RAPD and AFLP markers. Crop Sci 39:

268-275

Yeh FC, Chong KX, Yang RC (1995) RAPD variation within and among natural

populations of trembling aspen (Populus tremuloides) from Alberta. J Heredity

86:454-460.

Yin T, Minren Huang, Mingxiu Wang, Li-Huang Zhu, Zhao-Bang Zeng, and

Rongling Wu (2001) Preliminary interspecific genetic maps of the Populus genome

constructed from RAPD markers. Genome 44: 602-609

Yin T, Zhang X, Huang M, Wang M, Zhuge Q, Tu S, Zhu LH, Wu R (2002) Molecular

linkage maps of the Populus genome. Genome. 45: 541-55

Yu GX, Wise RP (2000) An anchored AFLP and retrotransposon-based map of

diploid Avena. Genome 43: 736-749

Yu S, Wang Y, Zheng X (2003) A Genetic Linkage Map of Brassica campestris

L.ssp.pekinensis (syn.B.rapa L.ssp.pekinensis). Chinese Agricultural Sciences Vol.2

(2003) 56-61

Zabeau M, Vos P (1993) Selective restriction fragment amplification: a general

method for DNA fingerprinting. European Patent Application of 92402629 (Publ

No. 0534858A1)

Zeid M, Schon C, Link W (2003) Genetic diversity in recent elite faba bean lines

using AFLP markers. Theor Appl Genet 107: 1304 –1314

Zhang D, Ghislain M, Huamán Z, Golmirzaie A, Hijmans R (1998) RAPD variation

in Sweetpotato [Ipomea batatas (L.) Lam] cultivars from South America and Papua

New Guinea. Genet Resour Crop Evol 45: 271-277

Zhang Y, Stommel JR (2000) RAPD and AFLP tagging and mapping of Beta (B) and

Beta modifier (MoB), two genes which influence -carotene accumulation in fruit of

tomato (Lycopersicon esculentum Mill.) Theor Appl Genet 100: 368-375

Zhang Y, Wu R (2003) AFLP-based linkage maps in Populus tomentosa. Forest

Research 13: 100-113Zhang X, Chen Li, Yin J, Tang Z, Li J (2003) Genetic Diversity

References

of Testa Pigments and RAPD Marker of Yellow-Seeded Rapeseed (Brassica napus

L.). Chinese Agricult Sci 2: 489-493

Zhang D, Zhang Z, Yang K, Li B (2004) Genetic mapping in (Populus tomentosa x

Populus bolleana) and P. tomentosa Carr. using AFLP markers. Theor Appl Genet

108: 657-62

Zheng X, Chen X, Zhang X, Lin Z, Shang J, Xu J, Zhai W, Zhu L (2004) Isolation

and identification of a gene in response to rice blast disease in rice. Plant Mol Biol.

54: 99-109

Zhu J, Gale MD, Quarrie S, Jackson MT, Bryan GJ (1998) AFLP markers for study

of rice biodiversity. Theor Appl Genet 96: 602-611

Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple

sequence repeats (SSR)-anchored polymerase chain reaction. Genomics 20: 176-183

Zimmer EA, Martin SL, Beverley SM, Kan YW, Wilson AC (1980) Rapid duplication

and loss of genes coding for the alpha-chains of hemoglobin. Proc Natl Acad Sci USA

77: 2158-2162

Zsuffa L, Giordano E, Pryor LD, Stettler RF (1996) Trends in poplar culture: some

global and regional perspectives. In: Stettler RF, Bradshaw HD, Heilman PE,

Hinckley TM [Eds] Biology of Populus and its implications for management and

conservation. NRC Research Press, Ottawa, pp. 515-539.

Zsuffa L (1975) A summary review of interspecific breeding in the genus Populus L.

Proceedings of the 14th meeting of the Canadian Tree Improvement Association, Part

2. Fredericton, NB 1973. Canadian Forestry Service, Ottawa, Ont. pp. 107-123