Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology

Abstract The ecotype population of goats (Capra hircus) was created by long‐term artificial selection and natural adaptation. Mile red‐bone goat is an indigenous breed with visible red bones, and its special bone structure has received extensive attention. This study aimed to identify genetic varian...

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Autores principales: Yong‐Meng He, Qiong‐Hua Hong, Dong‐Ke Zhou, Shi‐Zhi Wang, Bai‐Gao Yang, Ying Yuan, Wei‐Yi Zhang, Yong‐Fu Huang, Guang‐Xin E
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Publicado: Wiley 2021
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SNP
Acceso en línea:https://doaj.org/article/ca14d72792b24764980236d3a219f494
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spelling oai:doaj.org-article:ca14d72792b24764980236d3a219f4942021-11-08T17:10:40ZGenome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology2045-775810.1002/ece3.8165https://doaj.org/article/ca14d72792b24764980236d3a219f4942021-11-01T00:00:00Zhttps://doi.org/10.1002/ece3.8165https://doaj.org/toc/2045-7758Abstract The ecotype population of goats (Capra hircus) was created by long‐term artificial selection and natural adaptation. Mile red‐bone goat is an indigenous breed with visible red bones, and its special bone structure has received extensive attention. This study aimed to identify genetic variants and candidate genes associated with specific bone phenotypes using next‐generation sequencing technology (NGS). The results revealed that 31,828,206 single nucleotide polymorphisms (SNPs) were obtained from 72 goats (20 Mile red‐bone goats and 52 common goats) by NGS. A total of 100 candidate genes were identified on the basis top 1% window interaction from nucleotide diversity (π), π ratio (πA/πB), and pairwise fixation index (FST). Exactly 77 known signaling pathways were enriched. Specifically, three coding genes (NMNAT2, LOC102172983, and PNLIP) were annotated in the vitamin metabolism signaling pathways, and NCF2 was annotated to the osteoclast (OC) differentiation pathway. Furthermore, 5862 reliable copy number variations (CNVs) were obtained, and 14 and 24 genes were annotated with the top 1‰ CNV based on FST (>0.490) and VST (>0.527), respectively. Several pathways related to bone development and metabolism of exogenous substances in vivo, including calcium signaling pathway, OC differentiation, and glycerophospholipid metabolism, were annotated. Specifically, six genes from 19 candidate CNVs, which were obtained by interaction of the top 1‰ CNVs with FST and VST, were annotated to mucin‐type O‐glycan biosynthesis and metabolic pathways. Briefly, the results implied that pseudopurpurin and specific genetic variants work together to contribute to the red‐bone color and specific bone structure of Mile red‐bone goat. This study is helpful to understanding the genetic basis of the unique bone phenotype of Mile red‐bone goats.Yong‐Meng HeQiong‐Hua HongDong‐Ke ZhouShi‐Zhi WangBai‐Gao YangYing YuanWei‐Yi ZhangYong‐Fu HuangGuang‐Xin EWileyarticleCNVgenome‐wide sequencegoatred‐boneSNPEcologyQH540-549.5ENEcology and Evolution, Vol 11, Iss 21, Pp 14805-14812 (2021)
institution DOAJ
collection DOAJ
language EN
topic CNV
genome‐wide sequence
goat
red‐bone
SNP
Ecology
QH540-549.5
spellingShingle CNV
genome‐wide sequence
goat
red‐bone
SNP
Ecology
QH540-549.5
Yong‐Meng He
Qiong‐Hua Hong
Dong‐Ke Zhou
Shi‐Zhi Wang
Bai‐Gao Yang
Ying Yuan
Wei‐Yi Zhang
Yong‐Fu Huang
Guang‐Xin E
Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology
description Abstract The ecotype population of goats (Capra hircus) was created by long‐term artificial selection and natural adaptation. Mile red‐bone goat is an indigenous breed with visible red bones, and its special bone structure has received extensive attention. This study aimed to identify genetic variants and candidate genes associated with specific bone phenotypes using next‐generation sequencing technology (NGS). The results revealed that 31,828,206 single nucleotide polymorphisms (SNPs) were obtained from 72 goats (20 Mile red‐bone goats and 52 common goats) by NGS. A total of 100 candidate genes were identified on the basis top 1% window interaction from nucleotide diversity (π), π ratio (πA/πB), and pairwise fixation index (FST). Exactly 77 known signaling pathways were enriched. Specifically, three coding genes (NMNAT2, LOC102172983, and PNLIP) were annotated in the vitamin metabolism signaling pathways, and NCF2 was annotated to the osteoclast (OC) differentiation pathway. Furthermore, 5862 reliable copy number variations (CNVs) were obtained, and 14 and 24 genes were annotated with the top 1‰ CNV based on FST (>0.490) and VST (>0.527), respectively. Several pathways related to bone development and metabolism of exogenous substances in vivo, including calcium signaling pathway, OC differentiation, and glycerophospholipid metabolism, were annotated. Specifically, six genes from 19 candidate CNVs, which were obtained by interaction of the top 1‰ CNVs with FST and VST, were annotated to mucin‐type O‐glycan biosynthesis and metabolic pathways. Briefly, the results implied that pseudopurpurin and specific genetic variants work together to contribute to the red‐bone color and specific bone structure of Mile red‐bone goat. This study is helpful to understanding the genetic basis of the unique bone phenotype of Mile red‐bone goats.
format article
author Yong‐Meng He
Qiong‐Hua Hong
Dong‐Ke Zhou
Shi‐Zhi Wang
Bai‐Gao Yang
Ying Yuan
Wei‐Yi Zhang
Yong‐Fu Huang
Guang‐Xin E
author_facet Yong‐Meng He
Qiong‐Hua Hong
Dong‐Ke Zhou
Shi‐Zhi Wang
Bai‐Gao Yang
Ying Yuan
Wei‐Yi Zhang
Yong‐Fu Huang
Guang‐Xin E
author_sort Yong‐Meng He
title Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology
title_short Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology
title_full Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology
title_fullStr Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology
title_full_unstemmed Genome‐wide selective detection of Mile red‐bone goat using next‐generation sequencing technology
title_sort genome‐wide selective detection of mile red‐bone goat using next‐generation sequencing technology
publisher Wiley
publishDate 2021
url https://doaj.org/article/ca14d72792b24764980236d3a219f494
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AT shizhiwang genomewideselectivedetectionofmileredbonegoatusingnextgenerationsequencingtechnology
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