Whole-genome sequencing of three local rice varieties (Oryza sativa L.) in Vietnam

Authors

DOI:

https://doi.org/10.14719/pst.2021.8.3.1047

Keywords:

InDel, DNA markers, Next-generation sequencing, Vietnam, Local rice varieties

Abstract

Recently, a new technology, Next-generation sequencing (NGS) has been launched and providing whole-genome sequences that helps identify molecular markers across the genome. DNA markers such as single nucleotides and insertion – deletion (InDel) polymorphisms were widely used for plant breeding particularly to distinguish important traits in rice. These PCR-based markers can be used for the precision detection of polymorphisms. Moreover, PCR-based approaches are simple and effective methods for dealing with the issue of fraudulent labeling and adulteration in the global rice industry. In this study, three local varieties of Oryza sativa L. in Vietnam were sequenced with up to ten times genome depth and at least four times coverage (~83%) using the Illumina HiSeq2000™ system, with an average of 6.5 GB clean data per sample, generated after filtering low-quality data. The data was approximately mapped up to 95% to the reference genome IRGSP 1.0. The results obtained from this study will contribute to a wide range of valuable information for further investigation into this germplasm.

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Author Biographies

Ky Huynh, Department of Genetic and Plant Breeding, College of Agriculture, Can Tho University, Can Tho 94000, Vietnam

Since I entered into University, I love biology and science. Therefore, I chosen plant molecular biology as my career. So now I do want to understand plant world in the molecular aspects. 

Giang Van Quoc, Department of Genetic and Plant Breeding, College of Agriculture, Can Tho University, Can Tho 94000, Vietnam

As a young and talent scientist, I love to study bioinformatic. From that aspect, I can be fully discovered plant science based on the network build from molecule A, T, G, C… 

Hien Nguyen Loc, Department of Genetic and Plant Breeding, College of Agriculture, Can Tho University, Can Tho 94000, Vietnam

My main studies is applying molecular markers in rice breeding. In this study, I have been selected NTCD elite line for its improvement of quality

Vo Cong Thanh, Department of Genetic and Plant Breeding, College of Agriculture, Can Tho University, Can Tho 94000, Vietnam

My main studies is applying molecular markers in rice breeding.

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Published

01-07-2021

How to Cite

1.
Huynh K, Quoc GV, Thanh TNC, Loc HN, Thanh VC. Whole-genome sequencing of three local rice varieties (Oryza sativa L.) in Vietnam. Plant Sci. Today [Internet]. 2021 Jul. 1 [cited 2024 Nov. 21];8(3):437–444. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/1047

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Research Articles