Genome-Wide Indel Markers in Diverse Asian Rice Cultivars: Comparison Among Japanese Rice Cultivars, and Potential Application of the Promising Indel Markers

Introgression lines in which chromosomal segments derived from diverse Asian rice cultivars are included in a Japanese rice cultivar genetic background have high potential as materials for genetic analysis and breeding. To detect segments of donors from genetic background of the recurrent parent, it is available to use DNA marker developed by using nucleotide polymorphisms in the rice genome. Because large insertion-deletion (indel) can be particularly easily detected in gel electrophoresis, we discovered all potential indel mutations from re-sequencing data of diverse 10 cultivars with next-generation sequencing technology and extracted only indel regions with both a large size (≥10 bp) and a high depth (≥ 5 folds). Primer pairs for the selected indel regions were designed to develop high accuracy polymerase chain reaction (PCR)-based indel markers showing amplicon size differ from elite Japanese cultivar, `Koshihikari`. Two sets of indel markers, KNJ8-indel (detected in eight or more cultivars, including ‘Khao Nam Jen’) and C5-indel (detected in five to eight cultivars) were established, with 915 and 9899 indel regions, respectively. Validation of the two marker sets by using 23 cultivars showed a high PCR success rate (≥95%) for 67.5% of the KNJ8-indel markers and 73.9% of the C5-indel markers. Universality, an index of the availability of markers for detection of allelic polymorphisms between the Japanese rice cultivars and other diverse Asian cultivars, showed that the KNJ8-indel group had high availability (35.0%). High rates for both PCR-success and universality showed that our marker sets will therefore be useful for developing introgression lines.