The goat pan‑genome reveals patterns of gene loss during domestication  

作　　者：Jiaxin Liu Yilong Shi Dongxin Mo Lingyun Luo Songsong Xu Fenghua Lv 

机构地区：[1]Frontiers Science Center for Molecular Design Breeding(MOE),State Key Laboratory of Animal Biotech Breeding,College of Animal Science and Technology,China Agricultural University,Beijing 100193,China

出　　处：《Journal of Animal Science and Biotechnology》2025年第1期49-58,共10页畜牧与生物技术杂志(英文版)

基　　金：Strategic Priority Research Program of Chinese Academy of Sciences(No.XDA24030205);National Natural Science Foundation of China(Nos.U21A20246,32102511);National Key Research and Development Program-Key Projects(2021YFD1200900 and 2021YFD1300904);Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(No.2019QZKK0501);Biological Breeding-National Science and Technology Major Project(2023ZD0407106);Chinese Universities Scientific Fund(2024TC162).

摘　　要：Background Unveiling genetic diversity features and understanding the genetic mechanisms of diverse goat pheno-types are pivotal in facilitating the preservation and utilization of these genetic resources.However,the total genetic diversity within a species can’t be captured by the reference genome of a single individual.The pan-genome is a col-lection of all the DNA sequences that occur in a species,and it is expected to capture the total genomic diversity of the specific species.Results We constructed a goat pan-genome using map-to-pan assemble based on 813 individuals,including 723 domestic goats and 90 samples from their wild relatives,which presented a broad regional and global represen-tation.In total,146 Mb sequences and 974 genes were identified as absent from the reference genome(ARS1.2;GCF_001704415.2).We identified 3,190 novel single nucleotide polymorphisms(SNPs)using the pan-genome analysis.These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives.Presence/absence variation(PAV)analysis revealed gene loss and intense negative selection during domestication and improvement.Conclusions Our research highlights the importance of the goat pan-genome in capturing the missing genetic variations.It reveals the changes in genomic architecture during goat domestication and improvement,such as gene loss.This improves our understanding of the evolutionary and breeding history of goats.

关 键 词：DOMESTICATION GOAT Improvement PAN-GENOME Presence/absence variation 

分 类 号：S827.2[农业科学—畜牧学]