Characterization of 337 exon-based single nucleotide polymorphisms (SNPs) unique to the Indonesian soybean varieties

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dc.contributor.other Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian en_US
dc.date.accessioned 2021-03-17T07:14:40Z
dc.date.available 2021-03-17T07:14:40Z
dc.date.issued 2020
dc.identifier.isbn -
dc.identifier.uri http://repository.pertanian.go.id/handle/123456789/12086
dc.description.abstract Genome resequencing of five Indonesian soybean varieties resulted in a total of 2,597,286 single nucleotide polymorphisms (SNPs), 257,598 insertions, and 202,157 deletions. Out of those SNPs, only 95,207 (2.15%) were located in the protein-coding region (exon). The objective of this study was to characterize 337 exon-based SNPs unique to the Indonesian soybean varieties. The study was conducted by taking SNP samples located in the exons using criteria of gene fragments containing the SNPs that were sequenced at least five times within each of the soybean varieties. Out of 95,154 gene-based SNPs detected, only 337 SNPs met the criteria. Each of the soybean varieties was genotyped with the 337 SNP loci, and the genotypic data were scored and analyzed. Results showed that 59 SNPs were common to all five soybean genotypes. A total of 43, 41, 25, 32 and 28 SNPs loci were unique to soybean genotype Davros, Grobogan, Malabar, Tambora and B3293, respectively. These unique SNPs can function as DNA fingerprints for each variety. Out of 59 common SNPs, 24 SNPs were mutations that change the amino acid sequence of the encoded proteins. These genes with amino acid change may have high economic values such as those controlling soybean adaptation in tropical climate, photoperiod insensitivity, disease and insect resistance genes. Expression analyses of the genes with amino acid change showed variation in the expression pattern across different soybean tissues. Functional genomic analysis is necessary to isolate genes useful for breeding purposes. en_US
dc.language.iso en en_US
dc.publisher IAARD Press en_US
dc.subject soybean, SNP, genome variation, gene expression, DNA fingerprinting. en_US
dc.title Characterization of 337 exon-based single nucleotide polymorphisms (SNPs) unique to the Indonesian soybean varieties en_US
dc.type Article en_US


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