Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population.
Liangyu Shi,Ligang Wang,Jiaxin Liu,Tianyu Deng,Hua Yan,Longchao Zhang,Xin Liu,Hongmei Gao,Xinhua Hou,Lixian Wang,Fuping Zhao +10 more
TLDR
F ROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators and can provide an alternative to inbreeding estimates in the absence of pedigree records.Abstract:
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 (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and pedigree (FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. 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 FROH_total and FHOM, while the lowest was − 0.083 between FGRM and FPED. The correlations between FPED and FROH 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. FROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROH 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.read more
Citations
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Whole-genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs
Wang Xiaopeng,Hui Zhang,Huang Min,Jianhong Tang,Lijuan Yang,Yu Zhiqiang,Desen Li,Guixin Li,Jiang Yongchuang,Yanxiao Sun,Shudong Wei,Pan Xu,Jun Ren +12 more
TL;DR: The current Laiwu population has more abundant genetic diversity than the population of 18 years ago likely due to gene flow from European commercial breeds and a strong signature of introgression from European pigs into Lai Wu pigs at the GPC6 locus that regulates the growth of developing long bones is detected.
Journal ArticleDOI
Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds.
TL;DR: Zhang et al. as mentioned in this paper carried out ROH analyses in five Chinese indigenous sheep breeds; Altay sheep, Large-tailed Han sheep, Hulun Buir sheep, Short-tailed grassland sheep and Tibetan sheep, using genotypes from an Ovine Infinium HD SNP BeadChip.
Journal ArticleDOI
Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza.
TL;DR: It is demonstrated how strong artificial selection has shaped the genome in Mangalitza pigs and left traces in the form of selection signatures as well as in imputed SNP data.
Journal ArticleDOI
Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed
Zhong Xu,Shuqi Mei,Zhou Jiawei,Yu Zhang,Qiao Mu,Sun Hua,Li Zipeng,Li Lianghua,Dong Binke,Favour Oluwapelumi Oyelami,Wu Junjing,Peng Xianwen +11 more
TL;DR: In this paper, the authors used the Porcine SNP50 BeadChip to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection.
Journal ArticleDOI
Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs.
Xudong Wu,Ren Zhou,Wei Zhang,Bangji Cao,Jing Xia,Caiyun Wang,Zhang Xiaodong,Mingxing Chu,Zongjun Yin,Yueyun Ding +9 more
TL;DR: Zhang et al. as mentioned in this paper investigated the number, length, and frequency of runs of homozygosity (ROHs) across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province.
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