The IWGSC: Strategies & Activities to Sequence the Bread Wheat Genome Kellye A. Eversole IWGSC Executive Director & The IWGSC Wheat Breeding 2014: Tools, Targets, & Progress Harpenden, United Kingdom 29 January 2014 The International Wheat Genome Sequencing Consortium Launched in 2005 on the initiative of Kansas Growers Executive director K. Eversole Co-chairs R. Appels J. Dvorak C. Feuillet B. Gill B. Keller Y. Ogihara General members Coordinating Committee Sponsors Why Vision • Lay a foundation to accelerate wheat improvement • Increase profitability throughout the industry • High quality annotated genome sequence, comparable to rice genome sequence • Physical map-based, integrated and ordered sequence Wheat Improvement is Complex Yield potential and yield stability Adaptation to climate change Durable resistance to biotic stress Quality of grain and co-products Training, capacity building -> expertise and critical mass Complexity Requires an Integrated Toolbox Gene and QTL mapping Map-based cloning Candidate genes Perfect markers Allele mining Improved wheat varieties Managing the 17 Gb, Hexaploid Genome AA BB Triticum aestivum (2n = 6x = 42) 1C ~ 17,000 Mbp DD Dissection of the genome into single chromosomes (arms) Sheath fluid D Flow chamber Fluorescence emission Laser Excitation light B A Deflection plates Scattered light ; Waste Doležel et al., Chromosome Res. 15: 51, 2007 Chromosomes: 605 - 995 Mbp (3.6 – 5.9% of the genome) Chromosome arms: 225 - 585 Mbp (1.3 – 3.4% of the genome) Chromosome genomics Chromosome specific BAC libraries and sequencing IEB Faster and cheaper methods to tackle the wheat genome http://flxlexblog.wordpress.com/2012/12/03/developments -in-next-generation-sequencing-a-visualisation/ Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI www.genome.gov/sequencingcosts. A sequence for whom & for what purposes Feuillet et al, TIPS, 2010 BAC by BAC vs WGS BAC by BAC (physical map) √ TEs Genes Whole genome shotgun 500 kb IWGSC Strategy for a Reference Wheat Genome Sequence 1. BAC library construction 2. BAC fingerprinting (HICF/WGP) GAATTCTTGGTCAGCAATAAGGACAAAGAA GAATTCCTCCTGTGCGGCCGTTTTA GAATTCATGCTCCAGCCAACTCATCCAAAA GAATTCAACAATATAAATATCACCTAAAGC GAATTCCATCAGTATGGAGTTTCTTCATGC GAATTCAAGCTTGAGTATTCTATAGTGTCA GAATTCAATATGTAGAAATTATAGGATGGC GAATTCACCGGAAGGGGTTCCGGGTGTTTC GAATTCCGGAACGCTTCCGGAGACCAAACA GAATTCTGGAATCACTTGATGATGAATCAG GAATTCTGGAGTCTTCCTTTCCGCAGCGAA GAATTCAACGAAATAGTTATGAAATAGAAG GAATTCTGGGGTAACGATGGAATCCTACAC GAATTCTGTCAACGACACTATCATCAGGAA GAATTCTTCGATGCACTGAGTCGCACGGTT GAATTCTTGTGTGAGGTCCGCGTCCTAGAT 3. Contig assembly by FPC/LTC 4. MTP sequencing /Scaffold assembly 5. Pseudomolecule construction (meiotic/LD/RH mapping) 6. Automated and curated annotation SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 Roadmap to the Wheat Genome Sequence Physical mapping of individual chromosomes Short term MTP sequencing Long term Survey sequencing of individual chromosomes Gene catalog Virtual order Markers A reference sequence anchored to the genetic and phenotypic maps Current status of individual projects Physical maps Illumina Survey sequences Pseudomolecules IWGSC Chromosome Survey Sequencing Initiative Amplified DNA- sorted individual chromosomes ~50X Illumina sequence Chromosome arm sequence assemblies A, S, D, & AB genomes (7) >30X Illumina sequence Read/assembly alignment to chromosome arms Gene modeling, virtual ordering (GZ), annotation, functional, structural analyses Composition and Evolution of the 21 Bread Wheat Chromosomes IWGSC Chromosome Summary Survey Sequencing - Summary • Almost full wheat gene complement identified and allocated to chromosome arms • On average, 53% of genes virtually ordered along chromosomes • High level of inter- and intrachromosomal duplication • Over 3.5 M markers mapped to contigs (1.3M wheat markers + 2.3M SNPs) - SSR, EST, DArT, SNP (90k) markers... • 13.2 million SNPs from POPSeq aligned to contigs IWGSC CSS Resources are Facilitating • New phylogenetic analyses of wheat genome evolution • Definition of core and pan gene sets for Triticeae by comparing di-tetra- and hexaploid genomes • Homoeologue-specific gene expression analyses • Wheat haplotype map – E. Akhunov • TILLING projects in T. durum and bread wheat – UC, Davis, JIC, Rres • Establishment of WheatNet – UC, Davis 3B SEQuencing Project Chr 3B physical map 1,282 BAC-contigs 8,441 BACs Pool of 10 BACs Sorted chr. 3B (Roche 454 GSFLX Titanium, 8 Kb MP) 922 pools (~35X) BAC pool Illumina (82X) 454 scaffolds Sanger Illumina contigs BAC-ends (2*600 bp) Super-scaffolds 3B pseudomolecule assembly and analyses Catherine Feuillet & Fred Choulet (2*108 bp) PE 0.5 kb An integrated and ordered 3B reference sequence MetaQTL analysis 3B consensus map (5000 markers) 3B Physical map 3B pseudomolecule Map-based cloning projects on 3B 40 genes and QTL mapped on 3B 4722 markers on 3B consensus map, 3102 in 964 SC (679 Mb =82 % of the sequence) 13 map-based cloning projects Disease resistance genes (Sr, Lr, Yr, Stb…) Solid stem (saw fly) Yield Drought tolerance Boron transporter Flowering time NUE Chromosome pairing… Curtis Pozniak A Breeder’s Perspective SSt1 3B Physical SSt1 3BL Xgwm114 XBE200774 XPSP3001 SSt1 Xgpw4513 Xgwm340 Xgwm247 Xgwm181 Xgwm114 Xfba217 XBE200774 ctg580 ctg854 Xgwm4703 ctg668 Xwmc274 ctg165 Xgwm247 Xgwm340 Xtam63 Xfba310 Xfba133.2 Xfbb293 Xdarts149 Xgwm181 Xgwm547 Xbarc68.2 Xgpw4513 1 year -1 EST marker, not closer - ascertainment bias 0.0 3.2 6.5 7.2 9.3 10.7 14.1 15.1 16.2 21.5 gwm114 9K_0808_ck PSP3001 EI_02_115946 EI_01_145834 EI_05_46657 EK_02-210770 EK_02-276963 EK_03-83684 EK_03-59414 SSt1 EK_08-5169 EK_02-239361 EK_02-21792 EK_03-83026 BF200774 gwm340 gpw4513 gwm247 Xgwm181 3 weeks -12 cosegregating markers (SNPs) - no phenotyping in the fields - No ascertainment bias Speed Gene Discovery: Towards Cloning SSt1 B Fine map C 3B Pseudomolecule A High-density map EI_05-46657 EI_05-46657 10.6 EK_08-5169 XBF200774 EK_08-5169 XBF200774 EK_02-239361 EK_02-292495 SSt1 EK_02-239361 EK_02-292495 2.8 cM SSt1 12.6 Approx. 2.2 Mb Ctg1109-90254 13.3 15.3 Xgwm247 16.6 Xgwm247 4000 Kbp Power of A High Quality Reference Sequence Number of QTLs Cloned Rice Wheat Feuillet et al, Trends in Plant Sciences, 2010; Rey et al, unpublished update) Wheat Sequences Available Now WCS WGS CS WGS 5x (2012) A and D genome related ancestors (2013) CS chromosome survey sequences (2013) Max 50% using synteny and genetic mapping (GZ): « virtual order » MTP CS 3BSEQ (2013) 94% real order Gold completeness of information standard 5X CS Applications « blind » SNP marker development x Ae. T. tausc urartu hii x x Targeted SNP marker development 45% Map-based cloning time (years) 10 MTP based (3B) x x Conversion rate in genotyping for breeding Fundamental studies CS CSS x 95% 10 10 8 limited to genes 2 complete IWGSC Projects The Annotated Reference Sequence of the Bread Wheat Genome Pseudomolecules (1 of 21 completed) Chromosome Shotgun Sequences and marker alignment (completed) Physical Maps with markers (12 of 21 completed) Curtis Pozniak 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 IWGSC Resource Access • All resources accessible at URGI, Versailles http://wheat-urgi.versailles.inra.fr/Seq-Repository/ • Raw sequence reads in the SRA • IWGSC CSS assemblies available at URGI and EBI • IWGSC CSS assemblies & gene models integrated into EnsemblPlants http://plants.ensembl.org/Triticum_aestivum 272 institutions 40 countries 52,000 BLAST searches 2.500 downloads Thank you for your attention! www.wheatgenome.org @wheatgenome