Abstract
Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.
Highlights
Crossbreeding exploits genetic diversity between breeds with different objectives including the contribution of new genes, the heterosis effect, complementarity between production traits, and increased genetic variability (Bidanel, 1992)
The crossbred PLW are halfway between Pietrain and Large White populations. This result is consistent with the chromosome composition of PLW: half Pietrain and half Large White
We have shown that runs of homozygosity (ROH) detection is an interesting tool to characterize inbreeding in crossbred animals
Summary
Crossbreeding exploits genetic diversity between breeds with different objectives including the contribution of new genes, the heterosis effect, complementarity between production traits, and increased genetic variability (Bidanel, 1992). Increase in genetic variability in crossbred animals is related to their heterozygous status. Crossbred animals become heterozygous for all loci when parental breeds are homozygous for a different allele. When crossbreeding is used to create a new synthetic line, two or more parental breeds can be crossed. Crossbred offspring can be mated among themselves at each generation. The animals will become genetically homogeneous and this population can be considered a new line.
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