Utilization of the IWGSC Resources: Application to Wheat Breeding

Transcription

1 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

2 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

3 Marker Assisted Breeding No Markers No. Data points (x1000) Focus: Stacking of single genes Biotic Stress Agronomic Quality

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5 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

6 Speeding Gene Discovery: Stem Solidness in Wheat Saint Pierre et al. 2010; Functional Plant Biology, 37, 166.

7 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

8 Stem Solidness in Wheat 3BL DH population of durum wheat (155 lines) 0.0 Xgwm SSt Xgwm Xgwm181 Houshmand et al. (2007) Mol Breeding 20:261

9 Physical Map -- High Density Map SSt1 Xgwm114 XBE XPSP3001 SSt1 Xgpw4513 Xgwm340 Xgwm247 Xgwm181 3B Physical Xgwm114 Xfba217 XBE ctg580 ctg854 Xgwm4703 ctg668 Xwmc274 ctg165 Xgwm247 Xgwm340 Xtam63 Xfba310 Xfba133.2 Xfbb293 Xdarts149 Xgwm181 Xgwm547 Xbarc68.2 Xgpw4513

10 Speed Gene Discovery: Towards Cloning SSt1 A High-density map B Fine map C 3B Pseudomolecule EI_ EI_ EK_ XBF EK_ XBF EK_ EK_ SSt EK_ EK_ SSt1 2.8 cm Approx. 2.2 Mb Ctg Xgwm Xgwm Kbp

11 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

12 ap Fine Map Fine Map B Fine map C 3B Pseudomolecule EI_ No. SNPs No. SNPs 735 SNPs a EK_ XBF EK_ EK_ SSt1 Candidate Genes? Three genes association with cell wall biosynthesis 3 Duplicated lignin biosynthesis regulatory genes Xgwm Kbp a Includes INDELS 20 kb sliding window

13 Marker Assisted Selection 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

14 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

15 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

16 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

17 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 Sm contig b Contig gwm210 contig t Contig BS BS contig b contig b contig t contig b Contig BS contig b contig t contig t contig b contig b contig t contig b contig b contig t contig t contig t contig t BS BS contig b contig t contig t contig t contig t contig t contig b contig b contig b contig t contig b contig b contig t contig b contig t contig b contig b contig t contig b contig t contig b contig t Sm1 contig t contig t contig t contig t contig b contig b BS contig t contig t

18 Sm1 Associated SNPs Locus 2BS BS Putative Function (Rice proteome) Protein Unknown function NBS-LRR RGA Ascertainment BIAS Known Sm1 Carriers 2BS DNA replication initiation protein 2BS BS BS BS C3HC4 zinc-finger protein Protein Unknown function SAM dependent carboxyl methyltransferase Protein Unknown function Known Sm1 Carriers

19 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 , , , , , , ,000 50,000 Anchoring of >3.6 Million Markers WGS/GBS 3.3 MILLION A Genome B Genome D Genome

20 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 SNPs High LOX Dominant marker Low LOX

21 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