Determining crossover count and position in two pig lines with different selection histories

Crossovers are crucial in meiosis and can break up the link between neighboring loci, creating novel allele combinations and genetic variation. However, their potential use in livestock breeding programs remains unexplored. Here, we studied the patterns of crossover count in two pig lines with different selection histories. We analyzed genomic data from over 47,000 individuals in a boar line and 78,000 individuals in a sow line, using over 20,000 autosomal single nucleotide polymorphisms (SNPs). We estimated and compared autosomal crossover counts (ACC), intrachromosomal genetic shuffling, and inter-crossover distances when two crossovers are transmitted on a chromosome. Finally, we compared the recombination landscapes of individuals transmitting a high versus a low number of crossovers.

The mean ACC was 19.9 (SD: 4.7) for the boar line and 20.9 (SD: 5.0) for the sow line. On all chromosomes and in both lines, 0, 1 or 2 crossovers were transmitted in > 93% of the cases. In the sow line, parents transmitted nearly one additional crossover and exhibited slightly higher overall intrachromosomal genetic shuffling than in the boar line in both sexes. Dams generally transmitted more crossovers than sires in both lines. Particularly when transmitting two crossovers, intrachromosomal shuffling was higher in sires than in dams, except for the five shortest chromosomes, suggesting that sires space crossovers more evenly across chromosomes. Sires also showed greater mean inter-crossover distances on all chromosomes, except for Sus scrofa chromosomes 1, 13, and 18, which may reflect less potential to release genetic variance in the shortest chromosomes. Lastly, individuals with the highest crossover count more often localize crossovers near chromosome centers than those with the lowest counts, which might generate more genetic variance towards center regions.

Our results confirm that dams transmitted more crossovers than sires in both lines. Additionally, crossover counts were higher in the sow line, possibly due to different selection histories. Individuals with the most transmitted crossovers localized more often crossovers towards chromosome centers. The different patterns of crossover counts can generate different levels of genetic variance, which might be important to consider before applying selection on crossover count in commercial breeding programs.