Abstract
DNA markers are of growing importance in molecular breeding approaches. However, closely related cultivars have unsatisfied DNA markers, because of their genetic relatedness. Recently, whole genome resequencing using a next generation sequencer can generate massive DNA polymorphisms, such as single nucleotide polymorphism (SNP) and insertion-deletion (InDel), among the genome sequences having high homology. By using this technology, we performed whole genome sequencing of an ancestral cultivar of japonica rice. We have identified 132,462 SNPs and 35,766 InDels between the ancestral rice and Nipponbare genomes. Selected 731 SNPs were validated based on a SNP array, resulting in validation rates of 95% and 88% on the ancestral rice and Nipponbare genomes, respectively. We present methodology and massive data of SNPs and InDels that will be available DNA markers for whole-genome genotyping and marker-assisted breeding.
This study was supported by Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (S0801025).
