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

• DOI: 10.1186/s40104-020-00447-0
• Publication Date: 2020-04-28T05:01:37Z
• Authors: Liangyu Shi; Ligang Wang; Jiaxin Liu; Tianyu Deng; Hua Yan; Longchao Zhang; Xin Liu; Hongmei Gao; Xinhua Hou; Lixian Wang; Fuping Zhao
• Keywords: Runs of Homozygosity

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