an evolutionary approach towards bean conservation – from wild bean to its genome to the field
Post on 24-Feb-2016
29 Views
Preview:
DESCRIPTION
TRANSCRIPT
An Evolutionary Approach towards Bean Conservation – from Wild Bean to its Genome to
the Field
Paul GeptsPlant Sciences, UC Davis
6o Congreso Brasileiro de Melhoramento de Plantas1 a 4 de agosto, 2011 – Búzios, RJ
Applied Plant Breeding and Cultivar Development
Empiricism in plant breeding and genetic resources conservation
• Boon or bane of the field?– Highly successful
• Progress from selection• Different types of inheritance• Different degrees of environmental effects• Combination and correlation of traits• Adoption of new technologies
– “Cannot get no respect”• “Basic information is lacking” • “Less precise”
• Response?– Examples from germplasm conservation: Adoption of wide
range of approaches: How to penetrate the “Black Box”?
Crop Biodiversity Conservation (I)
• Ex situ: gene banks:– Largest: USA: 500,000
samples; China: 390, 000; Germany: 160,000; Brazil: 150,000 (EMBRAPA 2008 data)
– CGIAR gene banks– Svalbard seed vault– Many other gene banks:
1,750 individual genebanks worldwide, about 130 of which hold more than 10,000 accessions each
Gene Banks around the World:> 10,000 accessions
State of the World’s Plant Genetic Resources for Food and Agriculture (SOTW2), 2009
Crop Biodiversity Conservation (II)
• In situ:– Natural vegetation– Farmers’ fields and backyards
• Complements ex situ– Subject to evolutionary forces– Provides a bio-cultural context
• More urgency– Global environmental change
Outline
How to penetrate the “Black Box”?– A phylogenetic/genealogical approach to understanding
genetic diversity of a crop species:• The diversification of common bean (Phaseolus vulgaris)
– A GIS approach the discovery and use of genetic diversity in gene banks• Example of Brasilian bean landraces
– A genomic approach to discovery and transfer of genetic diversity• Development of PhaseolusGenes: Bean breeder’s toolbox for
marker discovery• Comparative genomics with model experimental systems
7
What are beans and why study them?
Phaseolus beans
Complement cereals as a source of nitrogen during cultivation
Complement cereal and root crops as a source of protein
Among the 10 foods that pack the most anti-oxidants (USDA study, 2004): Small red, red kidney, pinto beans
CompositionPlant proteinsMinerals: iron and zinc (~ meats, poultry, and fish)Dietary fiberVitamins: folate (low in diets of many Americans)
Reduces breast cancer (Thompson et al. 2008)
San Agustín del Pulque, MEX (2004)
A Phylogenetic/Genealogical Approach to Understanding Genetic Diversity of a Crop Species: The Diversification of Common Bean (Phaseolus vulgaris)
How to Penetrate the “Black Box”?
9
Gene flow
Feral or
weedy
Feral or weedy
Phylogeny/Genealogy of Common Bean
Domestication
Wild Mesoamerican
Domesticated outsideCenter of origin
Dissemination
Wild Andean
Domesticated outsideCenter of originDomesticated landraces
in Andes
P NG
C
WildECD &N. PER
Domesticated landracesin Mesoamerica
J
M
D
G
Other Phaseolus species
Multiple Sources, Several Years
• Applications to Bean Breeding
10
Two major geographic gene pools
• Observation: Andean and Mesoamerican gene pools– Geographic differentiation
prior to domesticationGepts & Bliss 1985; Gepts et al. 1986; Singh et al. 1991a,b,c,; Becerra-Velasquez & Gepts 1984; Debouck et al. 1993; Freyre et al. 1996; Papa & Gepts 2003; Kwak & Gepts 2009
• Consequence:– Bean breeding:
• 2 breeding pools, Andean and Mesoamerican
• 7 racesinter-racial crosses within
gene pools• For inter-gene pool crosses:
Adapt breeding method to account for wider genetic distance: e.g., 1 BC
11
Mesoamerican
Andean
Domestications
Reduction in Levels of Genetic Diversity
• Observation: Reduction in genetic diversity– Single domestication
in each gene pool– Plant breeding
Gepts et al. 1986; Sonnante et al. 1994
• Consequence:– Use landraces and
wild germplasm in breeding
– Use other Phaseolus species
Wild Landraces US Cultivars0
0.05
0.1
0.15
0.2
0.25
MesoAndean
12
M13-related RFLPs
13
Breeding Strategies to Broaden the Genetic Diversity of Common Bean
Kelly et al. 1998
Results of Gene Flow Studies in Mexico
• Gene flow:–Introgression: 20-50% of wild individuals in sympatric populations–Asymmetric: Three- to four-fold higher in D W than in W D
– Paradox: Self-pollinated species; yet, measurable effect of outcrossing
–Displacement of alleles in W by alleles of D, except around genes for domestication in ~ 80 % of the genome
• Implications:--In situ conservation? Complemented with
ex situ conservation--Unwanted escape of genes but also
strategy against escape: genetic footprintPapa & Gepts 2003, 2004; Payró de la Cruz et al. 2004; Zizumbo-Villareal et al. 2005; Papa et al. 2007
Photo: R. Papa
Co-evolution between Common Bean and Pathogens
Colletotrichum lindemuthianumInteractions
MEXICO ECUADOR ARGENTINA
MEXICO
ECUADOR
ARGENTINA
Phaseolus
vulgaris
• Observation: – Parallel geographic
distribution of genetic diversity between beans and pathogens: angular leafspot, anthracnose, rust, BDMVGuzmán et al. 1995, Geffroy et al. 1999, 2000; Seo et al. 2004
• Consequence:– Facilitates breeding:
• Identification of resistance
• Broad representation of pathogen variation
15Geffroy et al. 1999
• The presumed domestication center of Phaseolus vulgaris in Mesoamerica
PhD thesis Myounghai Kwak (Korea) with Jim Kami
16
1
17
Gene flow
Feral or
weedy
Feral or weedy
Phylogeny/Genealogy of Common Bean
Domestication
Wild Mesoamerican
Domesticated outsideCenter of origin
Dissemination
Wild Andean
Domesticated outsideCenter of originDomesticated landraces
in Andes
P NG
C
WildECD &N. PER
Domesticated landracesin Mesoamerica
J
M
D
G
12
Other Phaseolus species
Relationship between Wild & Domesticated types in the Mesoamerican Gene Pool
18
Also, close genetic relationship based on phaseolin protein electrophoresis (Gepts 1988) Kwak et al. 2009
The Suggested Domestication Center of Common Bean in Mexico
M. Kwak, J. Kami & P. Gepts, Crop Sci., March 200919
Why the Lerma-Santiago Basin?
Climate: Cwa Subtropical: t° coldest
month: 5-18 °C Subhumid: 4-6 months
of humidity in summer Semi-warm: average
annual t°: 18-22 °C Vegetation:
Dry deciduous forest to drier thorn forest
Westernmost putative domestication location, Mascota-Ameca Basin
21
Domestication Areas within Mesoamerica
22
A GIS approach the discovery and use of genetic diversity in gene banks:
Example of Brazilian bean landraces PhD thesis of Marilia Lobo Burle (EMBRAPA/CENARGEN) with help of M.J. del Peloso & L.C. Melo (EMBRAPA/CNPAF)
How to Penetrate the “Black Box”?
• Genetic Diversity in a Secondary Center of Origin: Brazil
24
2
25
Gene flow
Feral or
weedy
Feral or weedy
Phylogeny/Genealogy of Common Bean
Domestication
Wild Mesoamerican
Domesticated outsideCenter of origin
Dissemination
Wild Andean
Domesticated outsideCenter of originDomesticated landraces
in Andes
P NG
C
WildECD &N. PER
Domesticated landracesin Mesoamerica
J
M
D
G
12
Other Phaseolus species
2
26
General Approach• Combined analysis of genetic
diversity:– Molecular analysis:
• Genetic relationships• Admixture
– Phenotypic analysis:• Characterization: morphological
and agronomic traits (UC Davis)• Agronomic traits: Yield, field
resistance to CBB, rust (EMBRAPA)– Geographic information systems
(GIS)• Climate• Biomes, etc.
Maps (1:5,000,000): Map of climate Mean annual
temperature Mean annual
precipitation Biomes Original vegetation Pedology
CIAT: climatic database Latin America
27
Brazilian Beans
http://www.unifeijao.com.br/feijao_do_brasil/mapa.htm
Macaçar pequeño
Rosinha
Fradinho Boca Preta
Mulatinho
Jalo
Bolinha Amarelo
Bico de Ouro
Carioca
Preto
Roxinho Bolinha Vermelho
28
Plant Materials & Molecular Markers• Plant sample:
– 279 landraces• Collected by Jaime Fonseca• 1 per municipality
– 2 control accessions:• BAT93 (Mesoamerican),
Jalo EEP558 (Andean)• Marker sample:
– 67 SSRs (Yu et al. 2000; Gaitan-Solis et al. 2002; Blair et al. 2003; Grisi et al. 2007)
– 4 SCAR markers– 2 Seed proteins + 1 growth
habit candidate gene
29Jalo EEP558: landrace; BAT93: (Veranic 2 x Tlalnepantla 64) x (Negro Jamapa x GN Tara)
Molecular variation: STRUCTURE analysis
30
Molecular variation: NJ tree analysis
K = 3
31
2. Phenotypic diversity• Field experiments: 281 varieties• UC Davis– Morphological traits:
• seed: pattern, color, brilliance, shape, weight
• leaflet: leaflet shape and length• flower: color, days to flowering, …• determinacy, growth habit
• EMBRAPA-CNPAF, Goiânia– Agronomic traits:
• Yield• Disease resistance: CBB, Rust
32
PCA of Morphological & Agronomic Traits• First component:
39%– Flower color,
seed weight, flower standard striping, and pod beak position
• Second component: 13%– Growth habit,
determinacy and number of days to flowering
Andean Mesoamerican Hybrid
33
3. Eco-geographic variation• Biome: mainly semi-
deciduous forest, pine forest
• Only difference between A and M?– Altitude: ~ 100m– Yearly average T°: 23C– Average rainfall
growing season: 549 mm
34
SUMMARY• Three-pronged approach to assessing genetic diversity: genetic,
phenotypic, and environmental:– Reciprocal confirmation of findings– Generates hypotheses– Provides a model for large-scale characterization of germplasm collections
• Availability of geo-referenced germplasm is a must• Most landraces of Mesoamerican origin; strong separation with
Andean gene pool• Large “hybrid” group in Mesoamerican gene pool; may have
superior adaptation to poor soil conditions?• Identification of markers potentially associated with tolerance to
environmental conditions• Needs further corroboration before being adopted as a strategy for
genetic diversity discovery
A Genomic Approach to Marker & Gene Discovery and Transfer:Development of PhaseolusGenes, a breeder’s marker toolbox
How to Penetrate the “Black Box”?
http://phaseolusgenes.bioinformatics.ucdavis.edu
UCD Bioinformatics: Dawei Lin, Jose Boveda, Monica Britton, Joe Fass, Nikhil Joshi, Zhi-Wei LuUCD Gepts group: James Kami, José Vicente Gomes dos Santos, Shelby RepinskiAdriana Navarro Gómez, Paul Gepts
Overall design of PhaseolusGenes
URL: http://phaseolusgenes.bioinformatics.ucdavis.edu
Genome Browser
Early Applications of PhaseolusGenes: EXAMPLE
Theor Appl Genet 122: 893–903 (2011)
Identifying additional markers linked to Co-14 and Phg-1 on PV01
• Previous information:– Phg-1 maps on PV01 & linked to
SH13– Co-14 linked to Phg-1– Location of SH13 is ambiguous:
Pv01 or Pv11• Alternative markers on PV01?– Check Cmap– Run markers against Bulked DNA
for R and S progenies
Two New Markers
• Linkage distances:– CV542014:
0.7 cM– TGA1.1: 1.3
cM
CV542014
TGA1.1
Summary
• PhaseolusGenes:– Includes all known markers established so far– Used soybean whole-genome sequence as anchor
because of macro- and micro-synteny– Facilitates marker discovery after initial mapping– Can also use synteny for candidate gene discovery
• Further work:– Addition of three whole-genome sequences of bean– QTLs from beans
Conclusion• Adoption of different approaches:– Molecular Markers– GIS– Genomics
• Facilitate use of germplasm and reduce the size of the “Black Box”: Black Box Grey Box
Crop Science 46:2278–2292 (2006)
top related