Detection and validation of structural variation in cattle whole-genome sequence data — ASN Events
  1. Schedule
  2. Concurrent 14 - Statistical methods & computation II
  3. Detection and validation of structural variation in cattle whole-genome sequence data

Detection and validation of structural variation in cattle whole-genome sequence data (#84)

Long Chen 1 2 3 , Amanda Chamberlain 1 3 , Coralie Reich 1 3 , Hans Daetwyler 1 2 3 , Ben Hayes 1 2 3
  1. AgriBio, Centre for AgriBioscience, Biosciences Research, DEDJTR, Melbourne, Victoria, Australia
  2. La Trobe University, Melbourne, Victoria, Australia
  3. Dairy Futures Cooperative Research Centre, Melbourne, Victoria, Australia

Several examples of structural variation (SV), or copy number variation (CNV) affecting traits exist in cattle. However the effect of SV on complex traits is largely unknown. SV suffers from high false positive and low overlapping rate from different programs. We detected SV in dairy cattle whole-genome sequence from 308 Holsteins and 64 Jerseys, and two programs. We constructed a set of validated SVs based on 28 individuals that were sequenced twice, and were transmitted sire to son. A total of 165,993 candidate SVs covering a total of 8.37 Mb were validated in the 28 twice-sequenced individuals, while 4.4Mb and 0.5 Mb of SV were validated from Holstein and Jersey sire-son transmission.    

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