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Identification of candidate genomic region associated with seed longevity by re-sequencing in rice
- 언어ENG
- URLhttps://db.koreascholar.com/Article/Detail/298108
It is well known that Dharial (Bangladesh origin and weedy rice line) has longer seed longevity than indica and japonica rice varieties. To study the genetic basis of seed longevity of Dharial, we developed 240 BC3F7 backcross recombinant inbred lines derived from the crosses between Dharial (a donor parent) and two korea rice accessions (recurrent parents) including Ilmi and Gopum, respectively. Among these lines, we selected two introgression lines with longer seed longevity and named them Ilmi-NIL and Gopum-NIL. Also, we developed an EMS-induced mutant line from Dharial which has shortened seed longevity, and named it Dharial-EMS. We performed re-sequencing of four rice accessions that are Dharial, Dharial-EMS, Ilmi-NIL, and Gopum-NIL. A total of 706×106 raw reads were generated which provided sequence data over 46x rice genome coverage per each accession. We did genome-wide variation analysis comparing produced re-sequencing data and the re-sequencing data of Ilmi from NABIC database with the Nipponbare reference sequence. By graphical analysis of SNP distribution in rice genome of the five accessions, we could select candidate chromosomal segments introgressed from Dharial in Ilmi-NIL and Gopum-NIL. The introgressed chromosomal segments were in seven regions in Ilmi-NIL and eight regions in Gopum-NIL, and four common introgressed regions between Ilmi-NIL and Gopum-NIL were identified. 2,758 SNPs between Dharial and Dharial-EMS were found in the introgressed regions. Also, we detected 450 genes including at least one SNP among these SNPs. This result will facilitate identification of genes and development of molecular markers for improvement of seed longevity.
