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The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pib-mediated resistance in rice.

In plants, large numbers of R genes, which segregate as loci with alternative alleles conferring different resistance to pathogens, have been maintained over a long evolutionary time. In theory, there seem to be no reason for hosts to harbor these susceptible alleles in view of their null contribution to resistance. As such, why should populations support disease-susceptible individuals along with disease-resistant individuals? In rice, a single copy R gene Pi-ta segregates for two expressed clades of alleles, one resistant and the other susceptible. We discovered that knockout of the Pi-ta susceptible alleles induced drastic fitness decline in the absence of pathogens. Gene expression profiling and endogenous hormones quantification showed that the susceptible alleles might serve as an off-switch to the downstream immune signaling, thus contributing to fine-tuning of plant defense response. The fitness benefit of carrying a susceptible Pi-ta allele provides a plausible explanation for their retention in the genome.

Controlling the height of crops plays a crucial role for their yields. The large scale utilization of semi-dwarf varieties has greatly improved crop yield, providing an effective support for world food security. In rice, a main food for over half of the world's population, a number of dwarf loci have been identified. However, most of them are recessive, such as the ‘green revolution’ gene sd1. To gain more beneficial loci for rice breeding programs, exploring new mutations is needed, especially the dominant loci which can be used broadly for hybrid breeding. Here, we isolated a novel dominant dwarf rice mutant, slr1-d5. All of the internodes of slr1-d5 are reduced. We find that the responsiveness of slr1-d5 to gibberellin (GA), GA3, was significantly reduced. Map-based cloning revealed that the dominant dwarfism of slr1-d5 was caused by an amino acid substitution in the N-terminal TVHYNP domain of rice DELLA protein, SLR1, where the conserved amino acid Pro (P) was substituted to His (H). Our findings not only further prove the pivotal role of TVHYNP motif in regulating SLR1 stability, but also provide a new dwarf source for improvement of rice germplasms.

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.

Green-revertible albino is a novel type of chlorophyll deficiency in rice (Oryza sativa L.), which is helpful for further research in chlorophyll synthesis and chloroplast development to illuminate their molecular mechanism. In the previous study, we had reported a single recessive gene, gra(t), controlling this trait on the long arm of chromosome 2. In this paper, we mapped the gra(t) gene using 1,936 recessive individuals with albino phenotype in the F(2) population derived from the cross between themo-photoperiod-sensitive genic male-sterile (T/PGMS) line Pei'ai 64S and the spontaneous mutant Qiufeng M. Eventually, it was located to a confined region of 42.4 kb flanked by two microsatellite markers RM2-97 and RM13553. Based on the annotation results of RiceGAAS system, 11 open reading frames (ORFs) were predicted in this region. Among them, ORF6 was the most possible gene related to chloroplast development, which encoded the chloroplast protein synthesis elongation factor Tu in rice. Therefore, we designated it as the candidate gene of gra(t). Sequence analysis indicated that only one base substitution C to T occurred in the coding region, which caused a missense mutation (Thr to Ile) in gra(t) mutant. These results are very valuable for further study on gra(t) gene.

Line 02428h derived from the somatic cell culture of the semi-dwarf line 02428 was a recessive tall mutant in rice(Oryza sativa L.) .Plant height of the mutant 02428h was controlled by eui gene and sd-1 gene.An F2 population devel-oped from a cross between 02428h and Nanjing11 was used to map eui gene.The SSR marker RM3673,which was pub-lished in Gramene and RM0012 which was designed based on the bacterial artificial chromosome(BAC) in NCBI,was linked to eui gene in the order of RM3673-eui-RM0012 with genetic distance of 0.3 cM and 1.0 cM,respectively.These markers can be used in the molecular marker assisted selection(MAS) of eui gene.