Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.qTSN4 | gene validation | pleiotropy | marker-assisted breeding

Summary• A sex-independent transmission ratio distortion (siTRD) system detected in the interspecific cross in rice was analyzed in order to understand its significance in reproductive barriers. The S 1 gene, derived from African rice Oryza glaberrima, induced preferential abortion of both male and female gametes possessing its allelic alternative ( ), from Asian rice O. sativa, only in the heterozygote.• The siTRD was characterized by resolving it into mTRD and fTRD occurring through male and female gametes, respectively, cytological analysis of gametophyte development, and mapping of the S 1 locus using near-isogenic lines. The allelic distribution of the S 1 locus in Asian and African rice species complexes was also analyzed.• The siTRD system involved at least two components affecting male and female gametogeneses, respectively, including a modifier(s) that enhances fTRD. The chromosomal location of the major component causing the mTRD was delimited within an approx. 40 kb region. The S 1 locus induced hybrid sterility in any pairwise combination between Asian and African rice species complexes.• The allelic state of the S 1 locus has diverged between Asian and African rice species complexes, suggesting that the TRD system has a significant role in the reproductive barriers in rice.

Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, and The-derived allele (denoted ) on the locus causes preferential abortion of gametes with its allelic alternative (denoted ) in/ heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, , which does not confer sterility in the/ and / hybrids. We found that the causal mutation of the allele was a deletion in the peptidase-coding gene (denoted "") in the locus of No orthologous genes of were found in the genome. Transformation experiments indicated that the introduction of in carriers of the allele did not induce sterility. In / heterozygotes, the insertion of led to sterility, suggesting that complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a "neutral" allele, which facilitates interspecific hybridization for breeding programs.

Blast is a serious disease caused by a fungal pathogen Pyricularia oryzae Cavara of rice (Oryza sativa L.). The use of resistant varieties is considered one of the most efficient ways of crop protection from the disease. In addition to a large amount of information accumulated during the long history of genetic studies on resistance to rice blast, recent progress in rice genomics has enabled us to use DNA markers for breeding the resistant varieties by marker assisted selection (MAS). In this report, we summarize the reported rice blast resistance genes and their selection markers to encourage further utilization for breeding. First, we assemble the information about the reported genes with regard to their number, chromosomal locations, patterns of resistance, donor strains, and molecular characterization of the cloned genes by reviewing the literature. In addition, we present some remaining issues about the nomenclature system and identification of the resistance genes. Then, we provide the first assembled list of the reported DNA markers for blast resistance genes, including the sequences of the primer pairs, genetic distances from the resistance genes, and cross combinations of the parental strains used to detect the polymorphisms. This information will help rice breeders to improve the resistance to rice blast by MAS.