Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 24, 2024

Abstract Background Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level yak populations using pedigree-based approaches. With aims accurately evaluate two Chinese (Maiwa Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing calculated five SNP-by-SNP estimators ( $$\:{F}_{HOM}$$ , $$\:{F}_{L\&H}$$ $$\:{F}_{VR1}$$ $$\:{F}_{VR2}$$ $$\:{F}_{YAN}$$ ), as well segment-based runs homozygosity (ROH, $$\:{F}_{ROH}$$ ) homozygous-by-descent (HBD, $$\:{F}_{HBD}$$ ). Functional implications were analyzed positional candidate genes located within related genomic regions. Results A total 151,675 190,955 high-quality SNPs from 71 Maiwa 30 Jiulong yaks, respectively. had greater genetic diversity than terms allele frequency diversity. The could be genetically distinguished principal component analysis, with mean differentiation index (Fst) 0.0054. levels yaks consistently supported all estimators. Based on simple proportion homozygous lower was indicated three successfully sequenced old leather samples that may represent historical about generations ago. There 3304 ROH detected among samples, median length 1.97 Mb 1.0 Mb, 94 HBD segments found whereas 92 them belonged shortest class 10.9 Kb. estimates however, there no difference between yaks. Within regions significant Fst or enriched ROH, several pathways have been reported diverse production traits farm animals. Conclusions We evaluated populations. Although different resulted inconsistent conclusions their levels, our results helpful implement conservation utilization programs

Language: Английский

Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs

Genes, Journal Year: 2023, Volume and Issue: 14(3), P. 655 - 655

Published: March 5, 2023

Henan Province is located in central China and rich domestic pig populations; Huainan (HN) pigs are one of three indigenous breeds with great performance, including early maturation, strong disease resistance high meat quality. Yunan (YN) black a typical, newly cultivated breed, synthesized between HN American Duroc, subjected to selection for important traits, such as fast growth excellent However, the genomic differences, signatures loci associated economic traits YN still not well understood. In this study, based on high-density SNP chip analysis 159 samples covering commercial DLY (Duroc × Landrace Large White) pigs, we performed comprehensive phylogenetic relationships genetic diversity among breeds. Furthermore, used composite likelihood ratio tests (CLR) F-statistics (Fst) identify specific potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes differentiation YN-DLY group. HN-DLY group, 169 harbored 58 YN-HN 179 77 addition, QTLs database most overlapping was triglyceride level, number mummified hemoglobin loin muscle depth litter size intramuscular fat content humerus length, linolenic acid feed conversion mainly pigs. Of note, 14 tissue-specific promoters’ annotation top Fst 1% selective systematically demonstrated muscle-specific hypothalamus-specific regulatory elements Taken together, these results contribute an accurate knowledge crossbreeding, thus benefitting evaluation production performance improving genome-assisted breeding other future.

Language: Английский