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

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

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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 collec-tion 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 selec-tion,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide associa-tion 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 population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes under-lying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a com-prehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

Gene-CDS haplotypeGooseGWASPan-genomePresence-absence variationSelection signal

Guangliang Gao、Hongmei Zhang、Jiangping Ni、Xianzhi Zhao、Keshan Zhang、Jian Wang、Xiangdong Kong、Qigui Wang

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Chongqing Academy of Animal Science,Rongchang District,Chong-qing 402460,China

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

Chongqing Engineering Research Center of Goose Genetic Improvement,Rongchang District,Chongqing 402460,China

Department of Cardiovas-cular 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

Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province,University of Electronic Science and Technology of China,Chengdu,611731,China

JiguangGene Biotechnology Co.,Ltd.,Nanjing,210032,China

Jiangsu Agri-Animal Vocational College,Taizhou,225300,China

Poultry Science Institute,Chongqing Academy of Animal Science,No.51 Changzhou Avenue,Rongchang District,Chongqing 402460,P.R.China

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Chongqing Scientific Research Institution Performance Incentive ProjectEarmarked Fund for China Agriculture Research SystemChongqing Scientific Research Institution Performance Incentive ProjectKey R&D Project in Agriculture and Animal Husbandry of RongchangNatural Science Foundation of Chongqing ProjectNatural Science Foundation of Sichuan ProjectNatural Science Foundation of Sichuan ProjectChongqing Technology Innovation and Application Development Project

cstc2022jxjl80007CARS-42-5122527 J22534C-22CSTB2022NSCQ-MSX04342022NSFSC06052021YFS0379cstc2021ycjhbgzxm0248

2024

10.1186/s40104-023-00944-y

畜牧与生物技术杂志(英文版)
中国科学技术协会

畜牧与生物技术杂志(英文版)

CSTPCD
影响因子：0.765
ISSN：1674-9782
年,卷(期)：2024.15(1)
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