Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data DOI

Shuang Li,

Hong Lei, Zulfiqar Ahmed

et al.

Animal Genetics, Journal Year: 2025, Volume and Issue: 56(3)

Published: May 14, 2025

Abstract The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province southern China and boasts a rich history. goats exhibit exceptional traits, including heat insect resistance, strong reproductive capabilities superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole‐genome resequencing on 21 goats. Additionally, performed joint analysis using published data from 119 goats, Chengdu goat, Matou Wuxue Xiangdong Black Qaidam Cashmere Ujumqin Shanbei goat. results revealed that genetically more pure than other Southern Chinese breeds. Furthermore, genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity inbreeding coefficient) goat's genome at low level among eight breeds, indicating need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide integrated haplotype score, fixation index cross‐population extended homozygosity, systematically scanned selective signals within genomic landscape outcomes underscore selection associated with genes implicated immune response, tolerance, performance quality. These findings make significant contribution our understanding genetics framework adaptive traits study explores which may contribute theoretical conserving its resources, while identified trait‐associated variations could inform future strategies optimize breeding programs.

Language: Английский

Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia DOI Creative Commons

Qinqian Wang,

Ying Lü, Mengfei Li

et al.

Animals, Journal Year: 2025, Volume and Issue: 15(6), P. 831 - 831

Published: March 13, 2025

Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. By aligning data to the genome, WGRS enables precise detection genetic variations in individuals or populations. As core technology genomic research, WGS holds profound significance ruminant studies. It not only reveals intricate structure genomes but also provides essential for deciphering gene function, variation patterns, and evolutionary processes, thereby advancing exploration mechanisms. However, still faces several challenges, such as incomplete inaccurate genome assembly, well annotation numerous unknown genes functions. Although can identify vast number variations, specific relationships between these phenotypes often remain unclear, which limits its potential functional studies breeding applications. performing on multiple samples, assembly challenges be effectively addressed, particularly regions high repeat content complex structural variations. accurately subtle among different populations further elucidate their associations traits, overcoming limitations providing more information research This review systematically summarizes latest applications analysis structures, diversity, economic adaptive while discussing faced by this technology. aims provide scientific foundation improvement conservation resources.

Language: Английский

Citations

0
Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data DOI

Shuang Li,

Hong Lei, Zulfiqar Ahmed

et al.

Animal Genetics, Journal Year: 2025, Volume and Issue: 56(3)

Published: May 14, 2025

Abstract The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province southern China and boasts a rich history. goats exhibit exceptional traits, including heat insect resistance, strong reproductive capabilities superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole‐genome resequencing on 21 goats. Additionally, performed joint analysis using published data from 119 goats, Chengdu goat, Matou Wuxue Xiangdong Black Qaidam Cashmere Ujumqin Shanbei goat. results revealed that genetically more pure than other Southern Chinese breeds. Furthermore, genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity inbreeding coefficient) goat's genome at low level among eight breeds, indicating need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide integrated haplotype score, fixation index cross‐population extended homozygosity, systematically scanned selective signals within genomic landscape outcomes underscore selection associated with genes implicated immune response, tolerance, performance quality. These findings make significant contribution our understanding genetics framework adaptive traits study explores which may contribute theoretical conserving its resources, while identified trait‐associated variations could inform future strategies optimize breeding programs.

Language: Английский

Citations

0