Data from: Cattle sex-specific recombination and genetic control from a large pedigree analysis

Meiotic recombination is an essential biological process that generates
genetic diversity and ensures proper segregation of chromosomes during
meiosis. From a large USDA dairy cattle pedigree with over half million
genotyped animals, we extracted 186,927 three-generation families,
identified over 8.5 million maternal and paternal recombination events,
and constructed sex-specific recombination maps for 59,309 autosomal SNPs.
The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in
females, for a total studied region of 2,516 Mb (986 kb/cM in males and
1,085 kb/cM in females). The male map is 10% longer than the female map
and the sex difference is most pronounced in the subtelomeric regions. We
identified 1,792 male and 1,885 female putative recombination hotspots,
with 720 hotspots shared between sexes. These hotspots encompass 3% of the
genome but account for 25% of the genome-wide recombination events in both
sexes. Both males and females showed a decreasing trend in recombination
rate during the past forty years that coincided with the artificial
selection for milk production, with males exhibiting a more striking
reduction. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have
significant effects on genome-wide recombination rate in both sexes. Two
novel loci, NEK9 and REC114, were associated with recombination rate in
both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected
recombination rate in females only. Among the multiple PRDM9 paralogues on
the bovine genome, our GWAS of recombination hotspot usage together with
linkage analysis clearly identified the one on chromosome 1 to be the only
PRDM9 paralogue affecting cattle recombination. Given the largest sample
size ever reported for such studies, our results reveal new insights into
the understanding of cattle and mammalian recombination.