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CREATION OF A SNP CHIP IN SHEEP

CREATION OF A SNP CHIP IN SHEEP. Rudiger Brauning and John McEwan on behalf of the International Sheep Genomics Consortium MapNet Workshop 27 August 2009. Skim sequencing. Baylor College HGSC. Otago University. 0.5x. 0.5x. Romney. Merino. ~3x coverage (9.74 Gbp ), Roche 454 FLX.

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CREATION OF A SNP CHIP IN SHEEP

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  1. CREATION OF A SNP CHIP IN SHEEP Rudiger Brauning and John McEwan on behalf of the International Sheep Genomics Consortium MapNet Workshop 27 August 2009

  2. Skim sequencing Baylor College HGSC Otago University 0.5x 0.5x Romney Merino ~3x coverage (9.74 Gbp), Roche 454 FLX 0.5x 0.5x Texel Poll Dorset Scottish Blackface Awassi 0.5x 0.5x

  3. Sequence assembly pipeline 454 sequences repeat mask lower case masked 454 reads map uniquely (normal / sensitivemegablast) Bovine genome Uniquely mapped 454 sequences assemble with Newbler / CAP3 Sheep 454 contigs order, orientate and space Ordered sheep contigs position sheep contigs on vsg2, replace cow sequence with sheep sequence, remove remaining cow sequence vsheep Sheep genome assembly v1.0 / v.2.0

  4. Genome coverage - total

  5. Genome coverage – non-repetitive fraction

  6. Sheep assembly - coverage 91.06% 73.80% 66.29%

  7. Turning a cow into a sheep - low resolution OAR1 OAR2 OAR3 OAR4 OAR5 OAR6 BTA3 BTA8 BTA11 BTA4 BTA7 BTA6 BTA1 BTA2 BTA5 OAR9 OAR10 OAR11 OAR12 OAR7 OAR8 BTA9 BTA12 BTA19 BTA16 BTA10 BTA9 BTA14 OAR13 OAR14 OAR15 OAR16 OAR17 OAR18 BTA13 BTA18 BTA15 BTA20 BTA17 BTA21 OAR19 OAR20 OAR21 OAR22 OAR23 OARX BTA22 BTA23 BTA29 BTA26 BTA24 OAR24 OAR25 OAR26 BTAX • 5 chromosome inversions • 4 chromosome fusions • 1 split chromosome BTA25 BTA22 BTA27

  8. The sheep genome assembly • Is comprised of 454 sequence contigs organised into sheep chromosomes • 2.5 million contigs • average length ~480 bases • ordered and oriented using vsheep framework • cover ~52% of the sheep genome • cover ~100% of the unique fraction of the genome 15 sheep contigs – 1 bovine contig

  9. How close is the assembly to the real sheep? • The local order of sheep contigs is heavily dependant on the bovine genome assembly • Used a light pass of 454 sequencing paired end reads as a quality control check of the assembly • short paired ends ~30 bp • ~89% tail-to-tail • long paired ends ~70-100 bp • ~98% tail-to-tail • BAC-end sequences • ~93% tail-to-tail

  10. CNVs assembly

  11. SNP chip - numbers 600,000 putative SNPs 454 59,454 SNPs

  12. SNP distribution 1 SNP per 50 kbp

  13. Illumina Infinium OvineSNP50 BeadChip - performance Quality control 59,454 SNPs average MAF = 0.30 > 20,000 animals genotyped

  14. Future work – simulation results A B C D

  15. Acknowledgments • AgResearch NZ • John McEwan • Gemma Payne • Nessa O’Sullivan • Tracey Van Stijn • Theresa Wilson • Rudiger Brauning • Alan McCulloch • Russell Smithies • Benoit Auvray • University of Otago • Jo Stanton • Chrissie • Mark • Baylor College of Medicine • Richard Gibbs • Donna Muzny • Michael E. Holder • Lynne Nazareth • Rebecca L. Thornton • Christie Kovar • CSIRO Livestock Industries • Brian Dalrymple • James Kijas • David Townley • Abhirami Ratnakumar • Wes Barris • Sean McWilliam • Genesis Faraday • Chris Warkup • sheepGENOMICS • Rob Forage • Terry Longhurst • TIGR • Ewen Kirkness • Uni Melbourne • Jill Maddox • USDA • Tim Smith • Curt van Tassell • UNE • Hutton Oddy • Uni Sydney • Frank Nicholas • Herman Raadsma • Utah State University • Noelle Cockett isgcdata.agresearch.co.nz www.sheephapmap.org www.sheepgenomics.com www.livestockgenomics.csiro.au

  16. THANKS

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