Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks.

Autor: Lan D; Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China. landaoliang@163.com.; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China. landaoliang@163.com.; Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China. landaoliang@163.com., Fu W; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China.; Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China., Ji W; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China., Mipam TD; Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China., Xiong X; Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China., Ying S; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China., Xiong Y; Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China., Sheng P; Jiguang Gene Biotechnology Co., Ltd., Nanjing, China., Ni J; Jiguang Gene Biotechnology Co., Ltd., Nanjing, China., Bai L; Chengdu Genepre Technology Co., Ltd., Chengdu, China., Shan T; Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China., Kong X; Jiguang Gene Biotechnology Co., Ltd., Nanjing, China. xdkong@zju.edu.cn., Li J; Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.; College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China.
Jazyk: angličtina
Zdroj: Journal of animal science and biotechnology [J Anim Sci Biotechnol] 2024 May 06; Vol. 15 (1), pp. 64. Date of Electronic Publication: 2024 May 06.
DOI: 10.1186/s40104-024-01027-2
Abstrakt: Background: The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.
Results: We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations.
Conclusions: The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.
(© 2024. The Author(s).)
Databáze: MEDLINE
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