Development of a set of InDel markers for characterizing three japonica rice (Oryza sativa L.) varieties

IF 1.2 4区生物学 Q3 PLANT SCIENCES Plant Genetic Resources: Characterization and Utilization Pub Date : 2023-03-06 DOI:10.1017/s1479262123000096

Hongmei Wang, Yue Zhu, Chujian Xiao, Jian-Guo Yuan, Yaoguang Liu, Qunyu Zhang

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引用次数: 1

Abstract

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.

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3个粳稻品种InDel标记的建立

分子标记技术是种子遗传纯度鉴定中最灵敏、最有效的技术之一。本研究旨在通过生物信息学方法，建立一套插入和删除(InDel)标记，以有效区分三个具有代表性的粳稻品种:日本、台中65和中华11。利用BWA-MEM对已发表的这些品种的全基因组序列进行比对，然后利用SAMtools的tview功能人工检查大小超过10个碱基对的indel。用PCR方法鉴定了10个InDel标记，并对3个粳稻品种及其杂交杂种进行了验证。结果表明，本研究开发的InDel标记能够可靠地区分这三个粳稻品种。这些分子标记及其检测方法可用于水稻育种中基于dna的遗传纯度评价。

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来源期刊

Plant Genetic Resources: Characterization and Utilization Agricultural and Biological Sciences-Agronomy and Crop Science

CiteScore

2.80

自引率

0.00%

发文量

审稿时长

>12 weeks

期刊介绍： Plant Genetic Resources is an international journal which provides a forum for describing the application of novel genomic technologies, as well as their integration with established techniques, towards the understanding of the genetic variation captured in both in situ and ex situ collections of crop and non-crop plants; and for the airing of wider issues relevant to plant germplasm conservation and utilisation. We particularly welcome multi-disciplinary approaches that incorporate both a technical and a socio-economic focus. Technical aspects can cover developments in technologies of potential or demonstrated relevance to the analysis of variation and diversity at the phenotypic and genotypic levels.