Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis
Abstract 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 t...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | Journal of Animal Science and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40104-023-00944-y |
| _version_ | 1797451908609212416 |
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| author | Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang |
| author_facet | Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang |
| author_sort | Guangliang Gao |
| collection | DOAJ |
| description | Abstract 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 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 underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive 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. |
| first_indexed | 2024-03-09T15:01:14Z |
| format | Article |
| id | doaj.art-ad42cfbab24a4f409cb44b474ca3c61f |
| institution | Directory Open Access Journal |
| issn | 2049-1891 |
| language | English |
| last_indexed | 2024-03-09T15:01:14Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Animal Science and Biotechnology |
| spelling | doaj.art-ad42cfbab24a4f409cb44b474ca3c61f2023-11-26T13:55:45ZengBMCJournal of Animal Science and Biotechnology2049-18912023-11-0114112010.1186/s40104-023-00944-yInsights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysisGuangliang Gao0Hongmei Zhang1Jiangping Ni2Xianzhi Zhao3Keshan Zhang4Jian Wang5Xiangdong Kong6Qigui Wang7Chongqing Academy of Animal ScienceDepartment 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 ChinaJiguangGene Biotechnology Co., Ltd.Chongqing Academy of Animal ScienceChongqing Academy of Animal ScienceJiangsu Agri-Animal Vocational CollegeJiguangGene Biotechnology Co., Ltd.Chongqing Academy of Animal ScienceAbstract 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 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 underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive 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.https://doi.org/10.1186/s40104-023-00944-yGene-CDS haplotypeGooseGWASPan-genomePresence-absence variationSelection signal |
| spellingShingle | Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis Journal of Animal Science and Biotechnology Gene-CDS haplotype Goose GWAS Pan-genome Presence-absence variation Selection signal |
| title | Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis |
| title_full | Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis |
| title_fullStr | Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis |
| title_full_unstemmed | Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis |
| title_short | Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis |
| title_sort | insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan genome analysis |
| topic | Gene-CDS haplotype Goose GWAS Pan-genome Presence-absence variation Selection signal |
| url | https://doi.org/10.1186/s40104-023-00944-y |
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