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Background Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown. Results Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others. Conclusions Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.

To better understand the molecular mechanisms that regulate inflorescence and flower architecture, we characterized the rice panicle and spikelet degeneration (psd) mutant, which exhibited small panicles with a reduced number of primary and secondary branches. The psd mutant had few spikelets per panicle, and they were deformed and could not form seeds. The psd mutant had a unique panicle organization phenotype that was not present in other aberrant panicle organization mutants. Genetic analysis revealed that the mutation was controlled by a single recessive gene. A map-based cloning strategy was employed to isolate the PSD locus. The PSD locus was initially located between RM13046 and RM5356 on chromosome 2. Recessive individuals (n = 7307) in F2 mapping populations from two crosses between heterozygous Psdpsd plants and two indica rice varieties, IR28 and 93-11, were used to finely map the PSD locus. The PSD locus was mapped to a 14.6 kb region between two newly developed dCAPS markers, dC7 and dC8, within BAC OJ1115_D03. The candidate regions harbored two ORFs, Os02g0284500 and Os02g0284600. Sequence analysis revealed that only one single amino acid substitution mutation in the Os02g0284500 gene in the candidate region, which altered the predicted three-dimensional Os02g0284500 protein structure. A tetra-primer amplification refractory mutation system-PCR marker, TP-psd, was developed from the psd mutant mutation site. All 7307 homozygote recessive plants in the two F2 populations showed the same band pattern as that of psdpsd. This suggested that Os02g0284500 is most likely the PSD gene. Our results provide a basis for future functional PSD studies.

The rice (Oryza sativa L.) elongated uppermost internode (eui) gene effectively results in a recessive tall plant type. In eui background, we found a mutant 02428ha that exhibited a semidwarf phenotype. Because semidwarf varieties possess high yield potential, this mutant may be useful for hybrid rice breeding. The present study aimed to characterize the dwarfing mechanism in the mutant. Microscopic observation revealed that the cell length in the uppermost internode was reduced compared to the wild type. The mutant showed a decreased sensitivity to exogenous gibberellin A3 (GA3) and gibberellin (GA) biosynthesis inhibitor, uniconazole. Meanwhile, it contained a high level of endogenous gibberellin A1 (GA1). These results indicated that the semidwarf phenotype of 02428ha was caused by impairment of GA signal transduction rather than by block in GA biosynthesis. Furthermore, expression analysis of genes involved in the GA signaling pathway showed that transcript of GIBBERELLIN INSENSITIVE DWARF2 (GID2) was down-regulated in the mutant. Sequence analysis also revealed a 15-base pair (bp) insertion between base 594 and 595 in the coding region of GID2. Consequently, the reason for down-regulation expression of GID2 or sequence variation of GID2 might play roles in the phenotype of 02428ha.