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Exploring Rice DNA Polymorphisms by Whole-Genome Resequencing
- 언어ENG
- URLhttps://db.koreascholar.com/Article/Detail/297811
Progress in next-generation sequencing technologies have enabled discovery of massive amount of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDels), which are an invaluable resource to analyze genetic diversity in a population. We performed whole-genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. A total of 2,448 million raw reads was generated with 58-fold coverage and uniquely mapped to 87.5% of the Nipponbare as a reference genome. We identified 3,240,025 DNA polymorphisms including 2,867,878 SNPs, 151,845 insertions and 220,302 deletions between the Korean rice accessions and Nipponbare. We observed that in ten Korean rice accessions, the frequency of potential SNPs was estimated to be one per 2.1kb on Nipponbare (382Mb). According to annotation of DNA polymorphisms, 634,617 SNPs were found in gene region, and only 169,738 SNPs were occurred in coding region. Altogether, 86,251 non-synonymous SNPs were located on 76,891 genes. We also examined the cultivar-specific SNPs to select candidate SNPs which would have possibility of being associated with unique phenotype or agronomical trait of each cultivar. It was estimated that the portion of cultivar specific SNPs is 1~12% of the total SNPs. These DNA polymorphisms obtained from our result will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.
