Utilization of the IWGSC Resources: Application to Wheat Breeding Wheat Breeding: Securing Tomorrow s Profitability. Dr. Curtis J. Pozniak IWGSC Workshop, PAG, Jan 2014 Use and/or distribution of these slides is prohibited unless approval by the author is granted
Wheat Breeding at the UofS Spring and durum wheat breeding Objectives»Yield, maturity»abiotic stresses (terminal drought, heat)»biotic stresses (Rusts, FHB, Leaf-spotting diseases, Insect pests)»quality, Quality, Quality
Marker Assisted Breeding 50 45 40 35 30 25 20 15 10 5 0 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 No Markers No. Data points (x1000) Focus: Stacking of single genes Biotic Stress Agronomic Quality
IWGSC Resources in Breeding BAC Libraries Physical Maps Wheat Survey Sequence 3B Sequence Unlimited source of DNA markers for MAS/Genomic Selection Candidate genes for traits = perfect markers Reduce the time and improve the success of resolving QTL Discovery and exploitation of new alleles
Speeding Gene Discovery: Stem Solidness in Wheat Saint Pierre et al. 2010; Functional Plant Biology, 37, 166.
Genetics of Stem Solidness Quantitative expression in hexaploid wheat Expression influenced by environment Evidence of suppression in hexaploid wheat Single dominant gene in durum wheat Little environmental influence on expression discrete classification
Stem Solidness in Wheat 3BL DH population of durum wheat (155 lines) 0.0 Xgwm114 14.4 SSt1 21.3 Xgwm247 24.7 Xgwm181 Houshmand et al. (2007) Mol Breeding 20:261
Physical Map -- High Density Map SSt1 Xgwm114 XBE200774 XPSP3001 SSt1 Xgpw4513 Xgwm340 Xgwm247 Xgwm181 3B Physical Xgwm114 Xfba217 XBE200774 ctg580 ctg854 Xgwm4703 ctg668 Xwmc274 ctg165 Xgwm247 Xgwm340 Xtam63 Xfba310 Xfba133.2 Xfbb293 Xdarts149 Xgwm181 Xgwm547 Xbarc68.2 Xgpw4513
Speed Gene Discovery: Towards Cloning SSt1 A High-density map B Fine map C 3B Pseudomolecule EI_05-46657 EI_05-46657 10.6 EK_08-5169 XBF200774 EK_08-5169 XBF200774 EK_02-239361 EK_02-292495 SSt1 12.6 EK_02-239361 EK_02-292495 SSt1 2.8 cm Approx. 2.2 Mb Ctg1109-90254 13.3 15.3 Xgwm247 16.6 Xgwm247 4000 Kbp
Additional Marker Discovery BSA, Exome Sequencing WGS, Exome Sequencing 20 H lines SSt1- Bulk 20 S lines SSt1+ Bulk 10 SSt1- Cultivars 8 SSt1+ Cultivars Wheat 3B Pseudomolecule SNPs between bulks should be closely linked to SSt1 Filtering algorithms to identify SNPs in LD with SSt1
ap Fine Map Fine Map B Fine map C 3B Pseudomolecule EI_05-46657 No. SNPs No. SNPs 735 SNPs a EK_08-5169 XBF200774 EK_02-239361 EK_02-292495 SSt1 Candidate Genes? Three genes association with cell wall biosynthesis 3 Duplicated lignin biosynthesis regulatory genes Xgwm247 4000 Kbp a Includes INDELS 20 kb sliding window
Marker Assisted Selection 500 450 400 350 300 250 200 150 100 HOLLOW AC Avonlea AC Morse AC Navigator AC Pathfinder CDC Verona Commander Strongfield Napoleon SOLID DT570 W9262 DT818 Fortore Colosseo Mongibello Lesina Camacho 9661-AF1D Hollow Solid Glenlea 50 0-60 -10 40 90 140 190 240 290 340 390 440
D-Genome Suppression of SSt1 Strongfield DT570 Hexploid GD A0444-PJ03B DT665 DT743 H S H S H H Crossing of Glenlea derivative (AABBDD) to HOLLOW durum wheat (AABB) = SOLID Identification of SSt1 will allow us to design strategies to unsuppress SSt1 in hexaploid wheat
WSS and Gene Discovery Resistance to the OWBM Resistance to the OWBM (Sm1) - Localized to 2BS Current DNA markers are problematic Phenotyping is difficult/time consuming
Marker Discovery BSA + Exome Capture Cultivar Sequencing (Exome, WGS) 14 S lines Sm1- Bulk 14 R lines Sm1+ Bulk 15 Sm1- Cultivars 6 Sm1+ Cultivars Wheat 2Bs Wheat Survey SNPs between bulks should be closely linked to Sm1 Filtering algorithms to identify SNPs in LD with Sm1
Sm1 Summary of SNPs 3157 SNP calls in 1857 WSS contigs (0.1% Contigs) 100 SNPs converted to KASPar 67 Mapped to chromosome 2BS 59 Mapped with 1 cm of Sm1 0.0 5.8 6.4 7.5 8.2 8.4 8.9 9.0 9.3 9.8 10.3 10.8 12.1 12.3 13.9 14.4 14.8 19.5 contig1430032-740b Contig-138069-1215 gwm210 contig00789-3063t Contig-325685-812 2BS-4317551-1790 2BS-5226543-13235 contig04906-3501b contig4250349-196b contig388901-479t contig719296-408b Contig-104718-1179 BS00022126 contig48410-282b contig00368-4333t contig09243-3870t contig106599-1805b contig707010-787b contig186873-304t contig244876-1076b contig10483-3901b contig323700-1148t contig33895-1221t contig38705-554t contig116411-215t BS00072058 2BS-5182690-15139 contig42476-506b contig932657-433t contig3862336-112t contig85124-307t contig707010-657t contig00368-2147t contig186873-486b contig244876-1276b contig85124-665b contig244876-450t contig33895-498b contig04685-855b contig315021-1234t contig932657-433b contig04685-1865t contig1549704-462b contig1069284-546b contig707010-940t contig85124-463b contig85124-528t contig85124-165b contig104718-379t Sm1 contig124851-354t contig865518-217t contig154687-364t contig896162-357t contig902987-225b contig130189-359b BS00099469 contig1220058-234t contig85124-716t
Sm1 Associated SNPs Locus 2BS-1176771 2BS-5218038 Putative Function (Rice proteome) Protein Unknown function NBS-LRR RGA Ascertainment BIAS Known Sm1 Carriers 2BS-5230237 DNA replication initiation protein 2BS-5239924 2BS-5242325 2BS-5241927 2BS-5244653 C3HC4 zinc-finger protein Protein Unknown function SAM dependent carboxyl methyltransferase Protein Unknown function Known Sm1 Carriers
The WSS as a Resource: Integration of marker types Anchoring of publically available mar Public Markers DArT Markers -- 4,904 Bristol SNP Markers 5,057 Illumina iselect Assay 87,218 Bin-Mapped ESTs 16,091 SSR Markers 290 Wheat MAS 70 400,000 350,000 300,000 250,000 200,000 150,000 100,000 50,000 Anchoring of >3.6 Million Markers WGS/GBS 3.3 MILLION 0 1 2 3 4 5 6 7 A Genome B Genome D Genome
WSS for Marker Improvement: Conversion to HT Genotyping Platforms Existing Markers Position in the WSS Identification of co-localized SNPs Low LOX High LOX CON-495956 3 SNPs 500 450 400 350 300 High LOX Dominant marker 250 200 150 100 50 Low LOX 0-150 -50 50 150 250
U of Saskatchewan John Clarke Pierre Hucl Ron MacLachlan Ruan Yufeng Krysta Wiebe Amidou N Diaye NRC-PBI Andrew Sharpe Christine Sidebottom Darrin Klassen AAFC Curt McCartney Ron Knox Fran Clarke Danny Singh INRA Catherine Feuillet Pierre Sourdille Frédéric Choulet Etienne Paux Jane Rogers Kellye Eversole Klaus Mayer 21