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

作　　者：Daoliang Lan Wei Fu Wenhui Ji Tserang‑Donko Mipam Xianrong Xiong Shi Ying Yan Xiong Peng Sheng Jiangping Ni Lijun Bai Tongling Shan Xiangdong Kong Jian Li 

机构地区：[1]Ministry of Education of Key Laboratory of Qinghai‑Tibetan Plateau Animal Genetic Resource and Utilization,Southwest Minzu University,Chengdu,China [2]College of Animal&Veterinary Sciences,Southwest Minzu University,Chengdu,China [3]Institute of Qinghai‑Tibetan Plateau,Southwest Minzu University,Chengdu,China [4]Jiguang Gene Biotechnology Co.,Ltd.,Nanjing,China [5]Chengdu Genepre Technology Co.,Ltd.,Chengdu,China [6]Shanghai Veterinary Research Institute,Chinese Academy of Agricultural Sciences,Shanghai,China

出　　处：《Journal of Animal Science and Biotechnology》2024年第5期1832-1850,共19页畜牧与生物技术杂志（英文版）

基　　金：This study was supported by the National Key R&D Program of China(2021YFD1600200);Program of National Beef Cattle and Yak Industrial Technol-ogy System(NO.CARS-37);Natural Science Foundation of Sichuan Province(General Program)(24NSFSC0581);the Scientific and Technological Innovation Team for Qinghai-Tibetan Plateau Research in Southwest Minzu University(Grant No.2024CXTD02)。

摘　　要：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 pro-posed 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(Bos-Gru3G009179)that may be associated with the multirib trait in Jinchuan yaks.Furthermore,an integrated transcrip-tome and pangenome analysis highlighted the significant differences in the expression of core genes and the muta-tional 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 m RNAs and lnc RNAs(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.

关 键 词：High-and low-altitude Novel genes Pangenome PAV-GWAS YAK 

分 类 号：S823.85[农业科学—畜牧学]