{"title":"3个粳稻品种InDel标记的建立","authors":"Hongmei Wang, Yue Zhu, Chujian Xiao, Jian-Guo Yuan, Yaoguang Liu, Qunyu Zhang","doi":"10.1017/s1479262123000096","DOIUrl":null,"url":null,"abstract":"\n The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"publicationDate":"2023-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":"{\"title\":\"Development of a set of InDel markers for characterizing three japonica rice (Oryza sativa L.) varieties\",\"authors\":\"Hongmei Wang, Yue Zhu, Chujian Xiao, Jian-Guo Yuan, Yaoguang Liu, Qunyu Zhang\",\"doi\":\"10.1017/s1479262123000096\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"\\n The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.\",\"PeriodicalId\":1,\"journal\":{\"name\":\"Accounts of Chemical Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":16.4000,\"publicationDate\":\"2023-03-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Accounts of Chemical Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1017/s1479262123000096\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1017/s1479262123000096","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Development of a set of InDel markers for characterizing three japonica rice (Oryza sativa L.) varieties
The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.
期刊介绍：
Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance.
Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.
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