Designing and evaluating a cost-effective single nucleotide polymorphism liquid array for Chinese native chickens

Yifan Liu, Yanju Shan, Yunjie Tu, Ming Zhang, Gaige Ji, Xiaojun Ju, Shiying Shi, Chenyu Fan, Yunlei Li, Jingting Shu
{"title":"Designing and evaluating a cost-effective single nucleotide polymorphism liquid array for Chinese native chickens","authors":"Yifan Liu,&nbsp;Yanju Shan,&nbsp;Yunjie Tu,&nbsp;Ming Zhang,&nbsp;Gaige Ji,&nbsp;Xiaojun Ju,&nbsp;Shiying Shi,&nbsp;Chenyu Fan,&nbsp;Yunlei Li,&nbsp;Jingting Shu","doi":"10.1002/aro2.31","DOIUrl":null,"url":null,"abstract":"<p>Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid-phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high-quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome-wide association study of broilers, resulting in the identification of several growth- and meat quality-related loci. Therefore, the newly developed chip is efficient, cost-effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.31","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Animal Research and One Health","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/aro2.31","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

Abstract

Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid-phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high-quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome-wide association study of broilers, resulting in the identification of several growth- and meat quality-related loci. Therefore, the newly developed chip is efficient, cost-effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.

Abstract Image

设计和评估具有成本效益的中国本土鸡单核苷酸多态性液体阵列
基因分型在育种和种群研究中起着重要作用。目前可用的基因分型技术,包括固相芯片和测序,在中国本地鸡的应用中往往存在一些限制,包括成本高、多样性不足和普遍性差。在本研究中,我们开发了一种适用于鸡5k单核苷酸多态性(SNP)阵列,并利用靶向测序技术进行基因分型和遗传分析。芯片设计基于33个地方品种的基因组数据,筛选出5847个snp用于最终的芯片设计。在这些snp中,有3427个位点与肉鸡经济性状相关。我们的芯片包含25000个高质量的SNP标记,从5个K区域捕获,具有高效的目标位点捕获。对8个品种的群体分析表明,阵列上SNP标记的检出率高,等位基因频率低,可以明确区分不同的群体和群体内的家庭。利用芯片获得的遗传多样性趋势与微卫星分析结果一致。此外,5k阵列应用于肉鸡全基因组关联研究,鉴定出几个与生长和肉质相关的位点。因此,新开发的芯片效率高,成本低,非常适合在中国本地鸡中应用,将加速家禽育种改进和加强保护工作。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信