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Combining Knowledge from Field and from Laboratory for Pre-breeding in Barley
Consortium: Public Private Partnership in Pre-Breeding
Public Private Partnership in Pre-Breeding
partners
Graminor Breeding AS Norway
Sejet Planteforædling
Facu
lty
of S
cien
ce
Den
mar
k
Nordic Seed
Denmark
Nordic Barley Pre-Breeding Consortium
Jens Due Jensen, Ahmed Jahoor: Nordic Seed, Denmark
Therese Christerson, Stine Tuvesson, Bo Gertsson: Lantmännen Lantbruk, Sweden
Lars Reitan, Muath Alsheikh, Stein Bergersen: Graminor, Norway
Reino Aikasalo, Mika Isolahti, Hanna Haikka, Outi Manninen, Merja Veteläinen: Boreal Plant
Breeding, Finland
Marja Jalli: MTT Agrifood Research Finland, Finland
Lene Krusell, Rasmus L. Hjortshøj, Birger Eriksen: Sejet Plant Breeding, Denmark
Jihad Orabi, Gunter Backes: Faculty of Science, University of Copenhagen, Denmark
Magnus Göransson, Áslaug Helgadóttir: Agricultural University of Iceland, Iceland
Coordinator: Ahmed Jahoor [email protected]
Project Goals
Foundation for effective cereal breeding for resistance and
adaptation to changing climatic conditions :
– To develop and use available molecular markers to screen
current breeding material
– To verify already published and available molecular markers in
breeding material
– Identify linked DNA markers by association mapping for
disease resistance and agronomic traits for climate changes
– Assist in breeding of varieties with plasticity for a climate with
more extreme weather conditions in Nordic Regions.
The Project Work Packages
1. Database development and association mapping.
2. Disease resistance.
3. Climatic changes.
4. Preparing for the future.
1- Database development and association mapping
Collect publicly available information on DNA markers and
genetic resources.
To make this informa-tion available to the project
participants in the form of a database
To convert valuable markers into PCR-based markers
Genotyping 30 breeding lines from each of breeder for
association mapping with high throughput SNPs
2- Disease resistance
The project includes the following diseases:
1. Scald (Rhynchosporium secalis)
2. Net blotch (Drechlera teres)
3. Ramularia leaf spot (Ramularia collo-cygni)
4. Spot blotch or Bipolaris (Bipolaris sorokiniana)
5. Fusarium head blight (Fusarium spp.)
Resistance to different races of cereal cyst nematodes was
outsourced
3- Climatic changes and harvest stability
– Under different nitrogen rates in two years at two locations
(Sejet and LHBI):
Lodging
– Earliness
– Plant height at several growth stages
– Straw and ear breaking and
– Alleles of the Denso gene.
– The setup with field trials at two of the most different
locations in the Nordic region will enable evaluation of the
plasticity for the traits under different day and season
length, and with germplasm of different origin
4- Preparing for the future
The initial project period of two years is too short time for long term pre-breeding activities.
Initiation of crosses with new sources of resistance
A second phase with stronger emphasis on long term goals such as: – New and emerging diseases:
Spot blotch, ramularia
– Climatic change:
spring drought, water logging
– Increased nutrient use efficiency in barley:
reduce use of fertilizers
42 SSRs
2 DArT drived
1 YAC derived (FPM6)
1 ISSR derived (Ha2S18)
1 CAPS (Acri)
1 SCAR (HVS3)
Genotyping with linke and Validated markers to barley diseases from PPP website
Marker type Marker name Gene/QTL Chromosome Bmac0090 Fusarium graminearum QFhs.umn-‐1H 1H Bmag382 Fusarium graminearum QFhs.dah-‐1H.2 1H HVM20 Fusarium graminearum QFhs.umn-‐1H 1H Bmac0140 Fusarium graminearum QFhs.umn-‐2H.2 2H HVM36 Fusarium graminearum QFhs.umn-‐2H.1 2H HVBKASI Fusarium graminearum QFhs.umn-‐2H.2 2H HVM54 Fusarium graminearum QFhs.umn-‐2H.6 2H Bmac0093 Fusarium graminearum QFhs.umn-‐2H.2 2H Bmag0125 Fusarium graminearum QFhs.umn-‐2H.3 2H EBmac0415 Fusarium graminearum QFhs.umn-‐2H.6 2H ISSR-‐derived (Ha2S18) CC nematode Ha2 2H EBmac850 Fusarium graminearum QFhs.dah-‐2H.1 2H EBmac0623 spot blotch QSb.CaBo-‐2H 2H Bmag0518 spot blotch QSb.CaBo-‐2H 2H Bmac0067 Fusarium graminearum QFhs.umn-‐3H.1 3H Bmac0209 Scald Rh3 3H Bmag0013 Fusarium graminearum QFhs.umn-‐3H.2 3H Bmag0606 Fusarium graminearum QFhs.umn-‐3H.2 3H EBmac0705 spot blotch QSb.CaBo-‐3H 3H SCAR (HVS3) Scald Rrs1 3H DArT-‐bpb-‐3865 Spot blotch APR-‐QTL3 3Hs Bmag0919 Spot blotch APR-‐QTL3 3Hs Bmac181 Net Blotch Spot form QRpt5 4H HVM03 Net Blotch Spot form QRpt4 4H HVM67 Fusarium graminearum QFhs.HaTu-‐4H 4H Bmag490 Net Blotch Spot form QRpt6 4H HVML03 Net blotch (adult) QNba-‐VBDa-‐4H 4H HVML03 spot blotch QSb.CaBo-‐4H 4H HVLEU Net Blotch Rpt6 5H Bmac0018 Fusarium graminearum QFhs.umn-‐6H .2 6H Bmac0018 Net Blotch NBQTL 6H Bmag0173 Fusarium graminearum QFhs.umn-‐6H .2 6H Bmag0173 Net Blotch NBQTL 6H Bmag0173 Net Blotch rpt.r 6H HVM11 Fusarium graminearum QFhs.HaTu-‐6H 6H Bmag0500 Fusarium, DON QTL#10 6H Bmag496 Net Blotch rpt.k 6H Bmag496 Net Blotch Net form QRpt6 6H Bmac251 Fusarium graminearum QFhs.dah-‐6H.2 6H Bmag0870 Fusarium, DON QTL#10 6H HVM74 Net Blotch QRpt6 6H HVM74 Net Blotch Net form QRpt6 6H Bmag09 Net Blotch Net form QRpt6 6H HVM65 Net Blotch Rpt5 6H HVM14 Net Blotch Rpt5 6H Bmac0064 Fusarium graminearum QFhs.umn-‐7H 7H Bmag120 Net blotch (adult) QNba-‐TiTa-‐7H 7H Bmag120 Net blotch (seedling) QNbs-‐KeGa-‐7H 7H Bmag120 Net blotch (seedling) QNbs-‐TiTa-‐7H 7H Bmag135 Net blotch (adult) QNba-‐VBDa-‐7H 7H Bmag135 Net blotch (seedling) QNbs-‐VBDa-‐7H 7H EBmac755 Net blotch (adult) QNba-‐CISt-‐7H 7H EBmac755 Net blotch (adult) QNba-‐KeGa-‐7H 7H EBmac755 Net blotch (seedling) QNbs-‐CISt-‐7H 7H EBmac755 Net blotch (seedling) QNbs-‐KeGa-‐7H 7H YAC-‐derived (FPM6) Scald Rh2 7H CAPS (Acri) Scald Rrs2 7H HVM49 Scald Rrs15 7H EBmac0603 Spot blotch APR-‐QTL7 7Hs DArT-‐bPb-‐8660 Spot blotch APR-‐QTL7 7Hs
All SSR markers were polymorphic (high diversity)
The allele number ranged from 2 alleles to 15 alleles.
The polymorphism information content(PIC) values ranged from 0.04 to 0.88
Results: SSR markers
PCO of PPP materials based on SSR markers and grouped by breeder
Pairwise modified-Roger's distances between breeders
mRogers BOREAL Graminor LBHI LSW Nordic Seeds Sejet
BOREAL 0.00
Graminor 0.52 0.00
LBHI 0.39 0.12 0.00
LSW 0.13 0.17 0.15 0.00
Nordic Seeds 0.11 0.20 0.17 0.06 0.00
Sejet 0.12 0.19 0.17 0.07 0.04 0.00
1 2 Graminor 1 29 30 LBHI 3 27 30 BOREAL 29 1 30 LSW 25 5 30 Nordic Seeds 30 30 Sejet 30 30 118 62 180
1 2 3 Graminor 29 1 30 LBHI 26 1 3 30 BOREAL 1 10 19 30 LSW 5 13 12 30 Nordic Seeds 16 14 30 Sejet 23 7 30 61 63 56 180
1 2 3 4 Graminor 4 26 30 LBHI 1 9 20 30 BOREAL 18 10 2 30 LSW 11 13 4 2 30 Nordic Seeds 14 16 30 Sejet 7 23 30 50 73 19 48 180
1 2 3 4 5 Graminor 4 8 18 30 LBHI 9 20 1 30 BOREAL 2 18 10 30 LSW 4 11 13 2 30 Nordic Seeds 14 16 30 Sejet 7 23 30 19 50 28 63 20 180
Distribution of PPP lines over different group number (K)
Genotyping with Single Neclutide Polymorphism markers (SNPs)
DNA was extracted from all 180 lines (from single
seedling) and 2000ng sent to TraitGenetics
http://www.traitgenetics.com for genotyping with 9K-
SNP iSelect Illumina platform (7864 SNP markers)
A total of 6996 SNP markeres were passed (89%)
6208 polymorphic SNP markers (89%)
Only one line (PPP_0033) was failed among 180 PPP
lines
Mantel test showing the corelation between the genetic distances calculated based on SSR and SNPs data
Pearson's r=0.864
PCO of PPP materials based on 6208 polymorphic SNP markers and grouped by country
Disease resistance for association mapping
The aim was two location per disease
Disease Loca�on Country
Net Blotch net form Boreal Finland
Net Blotch spot form Boreal Finland
Bipolaris (Spot Blotch) Boreal Finland
Nematode Outsourced (Tysto�e) Denmark
Nematode Outsourced (Tysto�e) Denmark
Scald Boreal Finland
Scald Lantmännen Sweden
Ramularia Graminor Norway
Ramularia Lantmännen Sweden
Fusarium Graminor Norway
Powdrey mildew Lantmännen Sweden
Powdrey mildew Nordic Seed Denmark
Agronomical traits for association mapping
Trait Loca�on Country
Heading date Sejet Denmark
Heading date LBHI Iceland
Days to maturity Sejet Denmark
Days to maturity LBHI Iceland
Heat sum to maturity LBHI Iceland
Plant height Sejet Denmark
Plant height LBHI Iceland
Straw related traits Sejet Denmark
Straw related traits LBHI Iceland
Yield components LBHI Iceland
PPP project material at Korpa, Iceland
Juni 2012 September 2012 field visit Jónatan, Áslaug, Lars, Jahoor
September 2012 PPP meeting March 2013
Genome wide association scan for Powdery Mildew infection in two locations
Several SNPs with significantly high association to Powdery mildew resistance were found on chromosome 4H
Pm.Lm.12 Pm.Ns.12
Pm.Lm.12 0.8937
Pm.Ns.12 0.00000
upper right: pearson r, lower left: error probability
Correlation between powdery mildew two disease assessments
Validation of nematode resistance markers
PPP name Nem-‐r1 Nem-‐r2 Marker 1 Marker 2PPP_091 1.00 1.00 A APPP_092 1.00 1.00 A APPP_093 1.00 1.00 A APPP_094 1.00 1.00 A APPP_106 6.56 6.73 C APPP_120 5.39 7.47 C APPP_123 6.73 7.68 C APPP_125 7.68 7.26 C APPP_156 5.48 7.26 A GPPP_162 3.00 8.03 A GPPP_164 5.99 6.39 A GPPP_167 4.42 8.03 A GPPP_155 4.78 6.73 C GPPP_157 7.01 8.57 C GPPP_158 5.99 8.57 C GPPP_165 2.53 8.57 C G
Association of Plant Height at Sejet and LBHI 2012 at Stage 31, 32, 34 and Harvest
St. 32
St. 34
Harvest
St. 31
Validation of markers for Scald from literature
Acri (CAPS) marker amplified
The full length fragment and + Eco32I (EcoRV)
Digestion into 145-and 179-bp-long
fragments in cultivars which carry Rrs2 scald
resistance gene in barley
Summary
Coorporation among brreding companies
Coorporation between public private partenrs
Development and mamngement of database
Validation of DNA markers
Association mapping for disease resistance
Association mapping for climate changes
Preparing for future
Acknowledgment
Initiating:
– Roland von Bothmer and Anders Nilsson
Finantial support:
– Food and Agriculture Ministries from Nordic
Countries
Administration:
– NordGen, Morten Rasmussen