Single nucleotide polymorphisms (SNPs) are the most abundant variation in plant genomes. As DNA markers, SNPs are rapidly replacing simple sequence repeats (SSRs) and sequence tagged sites (STSs) markers, because SNPs are more abundant, stable, easy to automation, efficient, and increasingly cost-effective. We developed a 96-plex indica/japonica SNP genotyping set for genetic analysis and molecular breeding in rice using Fluidigm platform. Informative SNPs for indica/japonica populations were selected from 1536 Illumina SNPs and 44K Affymetrix SNP chip data of Rice Diversity and our resequencing data sets. Selected SNPs were evenly distributed across 12 chromosomes and average physical distance between adjacent SNP markers was 4.38Mb. We conducted genetic diversity analysis of 49 Bangladesh germplasm and check varieties to test a 96-plex indica/japonica SNP genotyping set we developed. High-throughput Fluidigm SNP genotyping system will serve a more efficient and valuable tool for genetic diversity analysis, DNA fingerprinting, quantitative trait locus (QTL) mapping and background selection for crosses between indica and japonica in rice. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.

The architecture of rice panicle is primarily determined by the arrangement of branches and spikelets, and it directly affects grain yield. We identified a mutant for panicle apical abortion from a japonica cultivar Hwacheongbyeo treated with N-methyl-N-nitrosourea. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as a slight reduction in plant height, narrow and dark green leaf blades, and small erect panicles with clear panicle apical abortion compared to the wild-type plants. Genetic analysis revealed that the panicle apical abortion was controlled by a single recessive gene, which is tentatively designated as paa. The paa gene was fine mapped at an interval of 71 kb flanked by STS markers aptn3 and S6685-1 at the long arm of chromosome 4. Sequence analysis of the candidate genes within the delimited region showed a single base-pair change corresponding to an amino acid substitution from glycine to glutamic acid. We expect that the paa gene will be a clue to uncover the molecular mechanism of panicle apical abortion and to maintain the panicle identity for grain yield in rice breeding programs.