Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indicajaponica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4-5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F 2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice.

BackgroundBalancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle.ResultsIn total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle.ConclusionsFavorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0591-6) contains supplementary material, which is available to authorized users.