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Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese

The domestic goose is an important economic animal in agriculture and its beak, a trait with high heritability, plays an important role in promoting food intake and defending against attacks. In this study, we sequenced 772 420-day-old Xingguo gray geese (XGG) using a low-depth (~1 ×) whole-genome r...

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Autores principales: Huang, Jianhua, Wang, Cong, Ouyang, Jing, Tang, Hongbo, Zheng, Sumei, Xiong, Yanpeng, Gao, Yuren, Wu, Yongfei, Wang, Luping, Yan, Xueming, Chen, Hao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8964941/
https://www.ncbi.nlm.nih.gov/pubmed/35372529
http://dx.doi.org/10.3389/fvets.2022.847481
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author Huang, Jianhua
Wang, Cong
Ouyang, Jing
Tang, Hongbo
Zheng, Sumei
Xiong, Yanpeng
Gao, Yuren
Wu, Yongfei
Wang, Luping
Yan, Xueming
Chen, Hao
author_facet Huang, Jianhua
Wang, Cong
Ouyang, Jing
Tang, Hongbo
Zheng, Sumei
Xiong, Yanpeng
Gao, Yuren
Wu, Yongfei
Wang, Luping
Yan, Xueming
Chen, Hao
author_sort Huang, Jianhua
collection PubMed
description The domestic goose is an important economic animal in agriculture and its beak, a trait with high heritability, plays an important role in promoting food intake and defending against attacks. In this study, we sequenced 772 420-day-old Xingguo gray geese (XGG) using a low-depth (~1 ×) whole-genome resequencing strategy. We detected 12,490,912 single nucleotide polymorphisms (SNPs) using the standard GATK and imputed with STITCH. We then performed a genome-wide association study on the beak length trait in XGG. The results indicated that 57 SNPs reached genome-wide significance levels for the beak length trait and were assigned to seven genes, including TAPT1, DHX15, CCDC149, LGI2, SEPSECS, ANAPC4, and Slc34a2. The different genotypes of the most significant SNP (top SNP), which was located upstream of LGI2 and explained 7.24% of the phenotypic variation in beak length, showed significant differences in beak length. Priority-based significance analysis concluded that CCDC149, LGI2, and SEPSECS genes in the most significant quantitative trait locus interval were the most plausible positional and functional candidate genes for beak length development in the XGG population. These findings not only enhance our understanding of the genetic mechanism of the beak length phenotype in geese, but also lay the foundation for further studies to facilitate the genetic selection of traits in geese.
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spelling pubmed-89649412022-03-31 Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese Huang, Jianhua Wang, Cong Ouyang, Jing Tang, Hongbo Zheng, Sumei Xiong, Yanpeng Gao, Yuren Wu, Yongfei Wang, Luping Yan, Xueming Chen, Hao Front Vet Sci Veterinary Science The domestic goose is an important economic animal in agriculture and its beak, a trait with high heritability, plays an important role in promoting food intake and defending against attacks. In this study, we sequenced 772 420-day-old Xingguo gray geese (XGG) using a low-depth (~1 ×) whole-genome resequencing strategy. We detected 12,490,912 single nucleotide polymorphisms (SNPs) using the standard GATK and imputed with STITCH. We then performed a genome-wide association study on the beak length trait in XGG. The results indicated that 57 SNPs reached genome-wide significance levels for the beak length trait and were assigned to seven genes, including TAPT1, DHX15, CCDC149, LGI2, SEPSECS, ANAPC4, and Slc34a2. The different genotypes of the most significant SNP (top SNP), which was located upstream of LGI2 and explained 7.24% of the phenotypic variation in beak length, showed significant differences in beak length. Priority-based significance analysis concluded that CCDC149, LGI2, and SEPSECS genes in the most significant quantitative trait locus interval were the most plausible positional and functional candidate genes for beak length development in the XGG population. These findings not only enhance our understanding of the genetic mechanism of the beak length phenotype in geese, but also lay the foundation for further studies to facilitate the genetic selection of traits in geese. Frontiers Media S.A. 2022-03-15 /pmc/articles/PMC8964941/ /pubmed/35372529 http://dx.doi.org/10.3389/fvets.2022.847481 Text en Copyright © 2022 Huang, Wang, Ouyang, Tang, Zheng, Xiong, Gao, Wu, Wang, Yan and Chen. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Huang, Jianhua
Wang, Cong
Ouyang, Jing
Tang, Hongbo
Zheng, Sumei
Xiong, Yanpeng
Gao, Yuren
Wu, Yongfei
Wang, Luping
Yan, Xueming
Chen, Hao
Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese
title Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese
title_full Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese
title_fullStr Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese
title_full_unstemmed Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese
title_short Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese
title_sort identification of key candidate genes for beak length phenotype by whole-genome resequencing in geese
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8964941/
https://www.ncbi.nlm.nih.gov/pubmed/35372529
http://dx.doi.org/10.3389/fvets.2022.847481
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