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Identification of genetic diversity and DNA polymorphisms in Korean rice accessions through resequencing
- 언어ENG
- URLhttps://db.koreascholar.com/Article/Detail/294523
With the rapid development of sequencing technologies, next-generation sequencing is widely utilized for molecular breeding in several crops including rice. We performed whole genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. In total, 2,448 million raw reads were generated with over 58x coverage of Nipponbare genome. We mapped the reads from each of the ten accessions onto genomic sequence of japonica rice cultivar, Nipponbare. We detected 3,144,016 SNPs, which estimated to be one per 2.2kb on average. We found SNPs in genes that have been reported to be involved in rice flowering time regulation and bacterial blight resistance among ten rice accessions. Unmapped region against Nipponbare genome occupied about 1 ~ 2% in each accession. Over 50% of the unmapped region were found in the repeat region. The minimum length of gap in all accessions were 1bp and the maximum length of gap was 45,967bp in Ilpum. We also identified 3,497 possible gene loss events within these unmapped regions. The frequency of gene loss in each chromosome ranged from 33 on chromosome 5 to 913 on chromosome 11. The genetic variations we detected among ten rice accessions will provide invaluable resources for identification of genes associated with diverse traits of agronomical importance for molecular breeding.
