Non-Random Distribution of Runs of Homozygosity Across the Genome of Landrace X Large White Crossbreds

Runs of homozygosity (ROH) are continuous and uninterrupted stretches of DNA sequences without heterozygosity in the diploid state. ROH can be simply detected by searching for DNA stretches of homozygous loci with genotyped information from SNP arrays. A total of 202 Landrace x Large White barrows were genotyped for the Illumina 80K array. Monomorphic SNPs or SNPs with an average GC call rate less than 0.80 were removed, such that 33,194 SNPs were retained for further analyses. A genome-wide search for ROH was carried out for each animal. A likelihood function using the binomial distribution (animals with or without autozygous SNPs in that position) was developed. A likelihood ratio test was used for each SNP in order to test if its position had the same chance of being autozygous than any other SNP on the same chromosome. Under the null hypothesis, the probability of being autozygous is the ratio of the length of the genome covered by ROH over the total chromosome length. An overall genome-wide test constructed by summing up LRT values for each SNP (with the degrees of freedom equal to the number of SNPs) was highly significant, supporting that the distribution of regions of autozygosity is not random across the genome among these crossbred animals. A Bonferroni test with a significance level of 0.001 was used to identify SNPs and regions of high and low autozygosity. The chromosomal regions with the highest autozygosity were on SSC10 (position 2,388,937 to 2,915,401 bp) and SSC11 (position 34,824,047 to 37,398,762 bp). The chromosomal regions with the lowest autozygosity were on SSC2 and SSC15. Landrace and Large White have been bred separately over a long period of time. The existence of a high autozygosity may correspond to either regions harboring genes selected in both breeds or regions that are highly conserved because of their biological function. Generation of these data was supported by the USDA ARS and NIFA award 2012-38420-19286.