In silico curation of QTL-rich clusters and candidate gene identification for plant height of bread wheat

IF 6 1区农林科学 Q1 AGRONOMY Crop Journal Pub Date : 2023-10-01 DOI:10.1016/j.cj.2023.05.007

Dengan Xu , Chenfei Jia , Xinru Lyu , Tingzhi Yang , Huimin Qin , Yalin Wang , Qianlin Hao , Wenxing Liu , Xuehuan Dai , Jianbin Zeng , Hongsheng Zhang , Xianchun Xia , Zhonghu He , Shuanghe Cao , Wujun Ma

{"title":"In silico curation of QTL-rich clusters and candidate gene identification for plant height of bread wheat","authors":"Dengan Xu , Chenfei Jia , Xinru Lyu , Tingzhi Yang , Huimin Qin , Yalin Wang , Qianlin Hao , Wenxing Liu , Xuehuan Dai , Jianbin Zeng , Hongsheng Zhang , Xianchun Xia , Zhonghu He , Shuanghe Cao , Wujun Ma","doi":"10.1016/j.cj.2023.05.007","DOIUrl":null,"url":null,"abstract":"<div>Many genetic loci for wheat plant height (PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters (QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II (Rht24) as well as GA 20-oxidase 2 (TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for map-based cloning of wheat dwarfing genes and application in breeding.</div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.0000,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Crop Journal","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2214514123000818","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRONOMY","Score":null,"Total":0}

引用次数: 1

Abstract

Many genetic loci for wheat plant height (PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters (QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II (Rht24) as well as GA 20-oxidase 2 (TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for map-based cloning of wheat dwarfing genes and application in breeding.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

面包小麦株高QTL富集簇的计算机调控及候选基因鉴定

目前已报道了许多小麦株高的遗传位点，并对26个矮化基因进行了编目。为了确定PH的主要和稳定遗传位点，我们从2003年至2022年发表的QTL连锁分析和全基因组关联研究中全面总结了这些功能或遗传验证的矮化位点。根据其在IWGSC RefSeq v2.1中的位置，共有332个QTL、270个GWAS位点和83个PH基因整合到染色体上，并定义了65个QTL富集簇（QRC）。基于IWGSC Annotation v2.1和其他物种同源基因功能验证信息预测每个QRC中的候选基因。共预测了38个候选基因用于65个QRC，包括QRC-4B-IV、QRC-5A-VIII和QRC-6A-II中的3个GA2ox基因（Rht24）以及QRC-3A-IV中的GA20氧化酶2（TaSD1-3A）。这些结果为基于图谱的小麦矮化基因克隆及其在育种中的应用奠定了具体基础。

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分钟内获得全文去求助

来源期刊

Crop Journal Agricultural and Biological Sciences-Agronomy and Crop Science

CiteScore

9.90

自引率

3.00%

发文量

638

审稿时长

41 days

期刊介绍： The major aims of The Crop Journal are to report recent progresses in crop sciences including crop genetics, breeding, agronomy, crop physiology, germplasm resources, grain chemistry, grain storage and processing, crop management practices, crop biotechnology, and biomathematics. The regular columns of the journal are Original Research Articles, Reviews, and Research Notes. The strict peer-review procedure will guarantee the academic level and raise the reputation of the journal. The readership of the journal is for crop science researchers, students of agricultural colleges and universities, and persons with similar academic levels.