Characterization of genomic variation in Indonesian soybean (Glycine max) varieties using next-generation sequencing. (16th July 2014)

• Record Type: Journal Article
• Authors: Satyawan, Dani; Rijzaani, Habib; Tasma, I. Made
• Is Part Of: Plant genetic resources. Volume 12(2014)Supplement 1
• Page Start: S109
• Page End: S113
• Publication Date: 2014-07-16
• Subjects: deep sequencing, -- genome comparison, -- phylogenetic analysis, -- sequence variations; Plant genetics -- Periodicals; Plant breeding -- Periodicals; 632.523
• DOI: 10.1017/S1479262114000380
• Languages: English
• ISSNs: 1479-2621

Abstract

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.