High resolution mapping of cross-over events in cattle using NGS data Keywords: recombination, cattle, NGS Homologous recombination plays an important role in proper segregation of homologues in the first meiotic division. Failure in proper segregation results in aneuploidy, which is a leading cause for pregnancy loss in humans. Recently, global recombination rate has been studied in large cattle populations genotyped with SNP arrays ( 50K). However, the fine-scale resolution of these studies remained limited as a result of the relatively low marker density. Here we report high-resolution mapping of cross-over (CO) events in a cattle pedigree using whole genome sequence data. We carry out an extensive cleaning of our sequence data to remove errors (errors in the genome build, sequencing errors and presence of CNVs) that dramatically inflate CO counts. Using 5 million high quality sequence variants we identify 3,880 CO events in 155 male gametes and 3,088 CO events in 124 female gametes. The median resolution of the identified COs was 34 kb with about 70% of the events mapped to an interval less than 100 kb. The male and female map lengths were estimated at 27.5 M and 23.8 M respectively. Consistent with previous studies in cattle, we find higher recombination rate in males and higher frequency of COs at chromosome ends. Interestingly, compared to the map lengths estimated from SNP chip we find an increase of 3.7 and 2.7 M in male and female maps respectively. Despite the cleaning efforts, we cannot determine at this time whether the increased in map lengths correspond to CO missed with genotyping arrays, to spurious CO identified with NGS data (due to unidentified sources of errors) or both. Keywords: recombination, cattle, NGS
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Biology - Reproduction 2, , 808, 2018
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