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

Published online by Cambridge University Press:  06 March 2023

Hongmei Wang Open the ORCID record for Hongmei Wang [Opens in a new window] ,
Yue Zhu ,
Chujian Xiao ,
Jianming Yuan ,
Yaoguang Liu  and
Qunyu Zhang
Hongmei Wang
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Yue Zhu
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Chujian Xiao
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Jianming Yuan
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Yaoguang Liu
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Qunyu Zhang*
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China Main Campus Teaching & Research Base, South China Agricultural University, Guangzhou, 510642, China
*
Author for correspondence: Qunyu Zhang, E-mail: zqy@scau.edu.cn
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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.

Keywords

Genetic purity testingInDelmolecular markerrice
Type
Short Communication
Information
Plant Genetic Resources , Volume 20 , Issue 4 , August 2022 , pp. 304 - 307
Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of NIAB

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