Genome-wide InDel marker system for application in rice breeding and mapping studies

In order to widen the genetic basis for local rice breeding programs, a set of 506 PCR-based novel insertion/deletion (InDel) markers were designed. The markers have size differences larger than 30 base-pairs and were generated by published genome sequences of rice (Oryza sativa L.) indica and japonica subspecies. Among the 506 InDel markers, 133 markers are polymorphic between the selected parents Taiken 2 and Taichung Sen 10, which are elite Taiwanese japonica and indica varieties, respectively. The InDel to amplicon size ratios, based on the japonica template, were in the range of 8.8–45.6 %, with an average of 21.6 %. As a result, the PCR product can be efficiently separated and easily scored by running 30 min of non-submerging electrophoresis on 2–3 % agarose gels. Commonly observed non-parental bands originated from heteroduplex are considered beneficial in distinguishing homo- and hetero-zygotes. A linkage map constructed solely on these markers arranged in 12 linkage groups and extended over 1,413.9 cM with an average distance of 9.8 cM between markers, based on a segregating population of 286 F2 individuals derived from a cross between Taiken 2 and Taichung Sen 10. The result indicated that InDel markers with moderate size differences were abundant and uniformly distributed across the whole genome of rice. Due to their simplicity in design and robustness in genotyping, these InDel markers have been routinely used in our quantitative trait loci mapping studies and marker-assisted selection programs for rice. We suggest that InDel markers with moderate size differences could be a valuable alternative in addition to the widely used SSR and SNP markers for rice breeding, and particularly suitable for field laboratories at breeding stations and/or laboratories with limited resources.