Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs

TL;DR

This study explores how recombination rates vary in pigs across different breeds and scales, revealing insights into genetic diversity and breeding.

Contribution

The study provides the first evidence suggesting PRDM9 regulates recombination hotspots in pigs using high-resolution SNP data.

Findings

Recombination patterns differ more between Western and Chinese pigs than within their own groups.

Recombination hotspots are distanced from gene transcription start sites and enriched with PRDM9 motifs.

A high-resolution historical recombination map was constructed using 16 million SNPs.

Abstract

The study constructed and compared the broad-scale meiotic recombination maps using populations from four different breeds of Western and Chinese pigs to investigate similarities and differences. At the broad scale, we found that the recombination patterns among different pig breeds are similar, with variations in recombination intensity and locations. Particularly, the differences in recombination patterns between Western and Chinese pigs are more significant compared to within-group variations. Furthermore, this study utilized 16 million SNP variants from unrelated individuals for the first time to construct a fine-scale historical recombination map. At the fine scale, we identified potential recombination hotspots and coldspots and verified the known features of these recombination hotspots and coldspots. Subsequently, by analyzing the overlap between recombination hotspots and regions of TSSs and H3K4me3 peaks, we found that recombination hotspots in pigs are distanced from gene TSSs and potential active promoters. Therefore, we propose for the first time evidence suggesting that recombination hotspots in pigs are regulated by PRDM9, providing a meaningful contribution to enhancing the efficiency of genomic selection breeding and further understanding the molecular mechanism of recombination in pigs.

Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico–predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination.

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