Abstract
BackgroundMeiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig.ResultsOur results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1.ConclusionsOur results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.
Highlights
Meiotic recombination results in the exchange of genetic material between homologous chromo‐ somes
We performed six analyses: (1) an analysis of the average number of recombination events on each chromosome to estimate between-sex and between-line differences in genetic length and compared these estimates to previously published estimates; (2) an analysis of the distribution of recombination events along the chromosomes to estimate between-line and between-sex differences; (3) estimation of the correlation between recombination rate and DNA sequence features that are known to correlate with recombination rate; (4) estimation of pedigree-based and genomic heritabilities of recombination rate; (5) a genome-wide association study to detect chromosomal regions associated with recombination rate; and (6) a simulation to test the accuracy of the inference method
Our results show that: (1) the genetic length of chromosomes differs between sexes and lines; (2) the recombination landscape is similar between lines but differs between sexes; (3) as previously reported, the local recombination rate is correlated with GC content, repeat content, the CCCCACCCC sequence motif, but we do not confirm the previously described correlation with the PRDM9 consensus motif; (4) the heritability of recombination rate was on average 0.07 for females and 0.05 for males; and (5) six regions of the genome were associated with recombination rate, of which five contained known candidate genes, i.e. RNF212, SHOC1, SYCP2, MSH4 and HFM1
Summary
Meiotic recombination results in the exchange of genetic material between homologous chromo‐ somes. We assessed the genetic variation in recombination rate along the genome and between indi‐ viduals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombina‐ tion in the pig. After chromosomes have paired up and duplicated, they can break and exchange segments of chromosomes Such recombination events are not evenly distributed along the chromosomes and result in a variable landscape of recombination rate across the genome, with peaks and troughs.
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