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Characterization of genomic variation in Indonesian soybean (Glycine max) varieties using next-generation sequencing

Published online by Cambridge University Press:  16 July 2014

Dani Satyawan ,
Habib Rijzaani  and
I. Made Tasma
Dani Satyawan*
Affiliation:
Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development – IAARD, Jl. Tentara Pelajar No. 3A, Bogor 16111, Indonesia
Habib Rijzaani
Affiliation:
Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development – IAARD, Jl. Tentara Pelajar No. 3A, Bogor 16111, Indonesia
I. Made Tasma
Affiliation:
Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development – IAARD, Jl. Tentara Pelajar No. 3A, Bogor 16111, Indonesia
*
* Corresponding author. E-mail: [email protected]
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Abstract

Soybean is an important crop in Indonesia and its consumption has consistently surpassed local production in recent times. As the average yield is relatively low, a more efficient breeding programme that utilizes the latest technological developments in DNA analysis is required. To provide a genomic data resource for future breeding programmes, in this study, whole-genome sequencing was performed for five Indonesian soybean varieties, with an average sequencing depth of 34 reads. Comparison of these sequences with the Williams 82 reference sequence revealed 3,150,869 DNA variations, which averages to one variation in every 308 bases. Comparison of these variations with known single-nucleotide polymorphisms (SNPs) in the SoyKB database revealed that approximately 29% of them were novel SNPs unique to the Indonesian cultivars. Variations found within exons totalled 95,154. Of these, 57,171 were capable of causing mutations that would modify the amino-acid composition of the encoded proteins (nonsynonymous mutations). Phylogenetic analysis using a subset of these SNP data indicated that the cultivars had genetic similarities to landraces from China and Japan, which could provide clues to the origin of soybeans that were introduced into Indonesia.

Keywords

deep sequencinggenome comparisonphylogenetic analysissequence variations
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S109 - S113
Copyright
Copyright © NIAB 2014 

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