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The IWGSC: Building the sequence-based foundation for accelerated wheat breeding

The IWGSC: Building the sequence-based foundation for accelerated wheat breeding. Kellye A. Eversole IWGSC Executive Director & The IWGSC. Cereals for Food, Feed and Fuel – Challenge for Global Improvement 4 July 2014. A sequence for whom & for what purposes. Feuillet et al, TIPS, 2010.

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The IWGSC: Building the sequence-based foundation for accelerated wheat breeding

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  1. The IWGSC: Building the sequence-based foundation for accelerated wheat breeding Kellye A. EversoleIWGSC Executive Director & The IWGSC Cereals for Food, Feed and Fuel – Challenge for Global Improvement 4 July 2014

  2. A sequence for whom & for what purposes Feuillet et al, TIPS, 2010

  3. Managing the 17 Gb, Hexaploid Genome B A ; Dissection of the genome into single chromosomes (arms) D AA BB Sheath fluid Triticumaestivum (2n = 6x = 42) 1C ~ 17,000 Mbp Flow chamber Laser Fluorescence emission Excitation light DD Deflection plates Scattered light Doležel et al., Chromosome Res. 15: 51, 2007 • Chromosomes: 605 - 995 Mbp(3.6 – 5.9% of the genome) Waste • Chromosome arms: 225 - 585 Mbp(1.3 – 3.4% of the genome) • Chromosome genomics • Chromosome specific BAC libraries and sequencing IEB

  4. Roadmap to the Wheat Genome Sequence Physicalmapping of individual chromosomes Survey sequencing of individual chromosomes Long term MTPsequencing Short term Gene catalog Virtual order Markers A referencesequenceanchored to the genetic and phenotypicmaps

  5. Current status of individual projects Physical maps Pseudo-molecules

  6. IWGSC Chromosome Shotgun Sequencing Initiative ~50X Illumina sequence Amplified DNA- sorted individual chromosomes Gene modeling, virtual ordering (GZ), annotation, functional, structural analyses Chromosome arm sequence assemblies Composition and Evolution of the 21 Bread Wheat Chromosomes >30X Illumina sequence A, S, D, & AB genomes (7) Read/assembly alignment to chromosome arms

  7. IWGSC Chromosome Survey Sequence Data • Sequence assemblies for 40 chromosome arms + chromosome 3B • Total length 10.2 Gb • 128Mb (1DS) – 639Mb (3B) assembled sequence per chromosome • N50 contig length after repeat masking = 6.1kb (1.7kb-8.9kb) • Annotation (RNASeq, FLcDNA, grass genomes): 124,201 allocated to chromosomes

  8. IWGSC Chromosome Survey Sequencing - Summary 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

  9. IWGSC CSS Resources are Facilitating • High density SNP chips • New phylogenetic analyses of wheat genome evolution • Homoeologue-specific gene expression analyses • Wheat haplotype map • TILLING projects in T. durum and bread wheat

  10. 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)

  11. 3B Reference is facilitating map-based cloning • 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…

  12. Wheat Sequences Available Now Whole Chromosome Shotgun Chromosome MTP Whole Genome Shotgun CS 3BSEQ (2013) CS chromosome surveysequences (2013) CS WGS 5x (2012) A and D genomerelatedancestors (2013) 94% real order Max 53% using synteny and geneticmapping (GZ): « virtualorder » completeness of information Gold standard

  13. IWGSC Projects

  14. IWGSC Resources Summary http://wheat-urgi.versailles.inra.fr/Seq-Repository/ • All resources accessible at URGI, Versailles • IWGSC CSS 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

  15. Acknowledgements

  16. Thank you for your attention!www.wheatgenome.org@wheatgenome

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