利用来自不同基因分型系统的组合基因型数据进行基因组预测和全基因组关联研究:应用于苹果果实品质性状。

IF 7.6 Q1 GENETICS & HEREDITY
园艺研究(英文) Pub Date : 2024-07-08 eCollection Date: 2024-07-01 DOI:10.1093/hr/uhae131
Mai F Minamikawa, Miyuki Kunihisa, Shigeki Moriya, Tokurou Shimizu, Minoru Inamori, Hiroyoshi Iwata
{"title":"利用来自不同基因分型系统的组合基因型数据进行基因组预测和全基因组关联研究:应用于苹果果实品质性状。","authors":"Mai F Minamikawa, Miyuki Kunihisa, Shigeki Moriya, Tokurou Shimizu, Minoru Inamori, Hiroyoshi Iwata","doi":"10.1093/hr/uhae131","DOIUrl":null,"url":null,"abstract":"<p><p>With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":7.6000,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228094/pdf/","citationCount":"0","resultStr":"{\"title\":\"Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits.\",\"authors\":\"Mai F Minamikawa, Miyuki Kunihisa, Shigeki Moriya, Tokurou Shimizu, Minoru Inamori, Hiroyoshi Iwata\",\"doi\":\"10.1093/hr/uhae131\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).</p>\",\"PeriodicalId\":57479,\"journal\":{\"name\":\"园艺研究(英文)\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":7.6000,\"publicationDate\":\"2024-07-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228094/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"园艺研究(英文)\",\"FirstCategoryId\":\"1091\",\"ListUrlMain\":\"https://doi.org/10.1093/hr/uhae131\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/7/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"园艺研究(英文)","FirstCategoryId":"1091","ListUrlMain":"https://doi.org/10.1093/hr/uhae131","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/7/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

随着新一代测序技术的发展,各种标记基因分型系统已经开发出来,用于基因组学方法,如基因组选择(GS)和全基因组关联研究(GWAS)。随着新基因分型平台的开发,来自不同基因分型平台的数据必须结合起来。然而,合并数据在 GS 和 GWAS 中的潜在用途尚未明确。在这项研究中,当使用来自不同基因分型系统(Illumina Infinium 单核苷酸多态性阵列和随机扩增片段测序-直接基因分型(GRAS-Di)系统)的组合数据时,对于苹果的大多数果实品质性状,基因组预测(GP)的准确性和 GWAS 的检测能力都有所提高。此外,考虑了近交效应的 GP 模型进一步提高了七个果实性状的准确性。在几个水果性状中,同源染色体(ROH)岛与全球基因组分析系统检测到的显著相关区域重叠。育种者可能利用了这些区域,通过育种筛选出有潜力的苹果,从而提高了同源性。这些结果表明,将来自不同基因分型平台的基因分型数据结合起来,有利于苹果果实品质性状的GS和GWAS。近亲繁殖的信息有利于提高苹果果实性状基因组学分析的准确性;然而,要阐明果实性状与近亲繁殖抑制(如活力下降)之间的关系,还需要进一步的分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits.

With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
12.90
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