Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population

Abstract

Background: Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (F ROH), homozygosity (F HOM), genomic relationship matrix (F GRM) and pedigree (F PED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between F ROH_total and F HOM , while the lowest was − 0.083 between F GRM and F PED. The correlations between F PED and F ROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. Conclusion: F ROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, F ROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.

Characterization of Autozygosity in Pigs in Three-Way Crossbreeding

“…LIF has two previously studied polymorphisms, one of which had a significant additive effect on number of piglets born alive in German Large White (Spötter et al, 2009 ). GAL3ST1 was detected in an ROH hotspot in Large White (Shi et al, 2020 ) and is hypothesized to be involved in spermatogenesis (Suzuki et al, 2010 ). In the same genomic region, we also found INPP5J (inositol polyphosphate-5-phosphatase J) and PLA2G3 (phospholipase A2 group III), which are associated with two type of fatty acids (docosahexaenoic acid and n-3 polyunsaturated fatty acid) in Large White (Zappaterra et al, 2018 ).…”

Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs

“…(2) Runs of homozygosity (ROH)-based inbreeding coefficient (F ROH ) that was measured by the ratio of the total length of ROH to the length of autosomes (2.45 Gb in this study; Mcquillan et al, 2008). ROHs were identified for each individual using PLINK v 1.9 (Purcell et al, 2007) with the following parameters (Shi et al, 2020;Xie et al, 2019): (a) The minimum number of SNPs in a sliding window was 50; (b) the minimum ROH length was set to 1 Mb to eliminate the impact of strong linkage disequilibrium; (c) each ROH need contain a minimum of 80 consecutive SNPs, which was calculated by following equation (Lencz et al, 2007), an indicative of ancestral (more than 10 generations), middle (5 to 10 generations), and recent (within 5 generations) inbreeding, respectively (Mastrangelo et al, 2016).…”

Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza

“…In that respect, the need for specific phenotypes has led to similar selective pressures on different domesticated breeds, whereas the genes under selection varied significantly among them 2 . Thus, various studies on SNP data have been performed within or across pig breeds in order to determine regions harboring these genes under potential selection for favored traits [3][4][5][6][7][8][9][10] . It was demonstrated that particularly the detection of homozygous stretches along the genome, designated as runs of homozygosity (ROHs), displayed an effective approach to target functionally important regions as well as to elucidate demography of populations and genetic diversity 4,5 .…”

“…It was demonstrated that particularly the detection of homozygous stretches along the genome, designated as runs of homozygosity (ROHs), displayed an effective approach to target functionally important regions as well as to elucidate demography of populations and genetic diversity 4,5 . ROH regions (ROHR) were found to give evidence for regions of strong directional selection for biological pathways related to desirable phenotypes like coat color and type, fertility, muscle and fat development, growth and metabolism 8,9,[11][12][13][14] significantly characterizing pig breeds.…”