Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis  

作　　者：Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang 

机构地区：[1]Chongqing Academy of Animal Science,Rongchang District,Chongqing 402460,China [2]Livestock and Poultry Multi‑Omics Key Laboratory of Ministry of Agriculture and Rural Affairs,College of Animal Science and Technology,Sichuan Agricultural University,Chengdu 611130,China [3]Chongqing Engineering Research Center of Goose Genetic Improvement,Rongchang District,Chongqing 402460,China [4]Department of Cardiovascular Ultrasound and Non‑Invasive Cardiology,Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital,University of Electronic Science and Technology of China,Chengdu,611731,China [5]Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province,University of Electronic Science and Technology of China,Chengdu,611731,China [6]JiguangGene Biotechnology Co.,Ltd.,Nanjing,210032,China [7]Jiangsu Agri-Animal Vocational College,Taizhou,225300,China [8]Poultry Science Institute,Chongqing Academy of Animal Science,No.51 Changzhou Avenue,Rongchang District,Chongqing 402460,P.R.China

出　　处：《Journal of Animal Science and Biotechnology》2024年第1期88-107,共20页畜牧与生物技术杂志（英文版）

基　　金：funding from several sources,including the Chongqing Scientific Research Institution Performance Incentive Project(grant number cstc2022jxjl80007);the Earmarked Fund for China Agriculture Research System(grant number CARS-42-51);the Chongqing Scientific Research Institution Performance Incentive Project(grant number 22527 J);the Key R&D Project in Agriculture and Animal Husbandry of Rongchang(grant number No.22534C-22);Natural Science Foundation of Chongqing Project,grant number CSTB2022NSCQ-MSX0434;Natural Science Foundation of Sichuan Project,grant number 2022NSFSC0605;Natural Science Foundation of Sichuan Project,grant number 2021YFS0379;the Chongqing Technology Innovation and Application Development Project(grant number No.cstc2021ycjh-bgzxm0248)。

摘　　要：Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing po

关 键 词：Gene-CDS haplotype Goose GWAS PAN-GENOME Presence-absence variation Selection signal 

分 类 号：S835.2[农业科学—畜牧学]