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Identification of genetic polymorphisms in Korean rice accessions by Whole-genome sequencing
- 언어ENG
- URLhttps://db.koreascholar.com/Article/Detail/298028
Advances in genome sequencing technologies have aided discovery of millions 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 2,447 million raw reads were generated with over 58x coverage and detected 3,240,025 DNA polymorphisms between the Korean rice accessions and Nipponbare as reference genome. We observed that in ten Korean rice accessions, the frequency of potential SNPs was estimated to be one per 2.1kb on Nipponbare (382Mb). Potential SNPs were classified into two types, homozygous SNP and heterozygous SNP, which approximately 87% of the total was homozygous SNPs from ten accessions and heterozygous SNPs accounted for 13%. According to annotation of DNA polymorphisms, 634,620 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 genes which had at least one SNP in all ten accessions. It was estimated that the total of 290 genes had one or more non-synonymous SNPs and 25 genes had only synonymous SNPs. These genes were functionally classified based on gene ontology (GO). 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.
