Growth and development of a plant are controlled by programmed expression of suits of genes at the appropriate time, tissue and abundance. Although genomic resources have been developed rapidly in recent years in rice, a model plant for cereal genome research, data of gene expression profiling are still insufficient to relate the developmental processes to transcriptomes, leaving a large gap between the genome sequence and phenotype. In this study, we generated genome-wide expression data by hybridizing 190 Affymetrix GeneChip Rice Genome Arrays with RNA from 39 tissues collected throughout the life cycle of the rice plant from two varieties, Zhenshan 97 and Minghui 63. Analyses of the global transcriptomes revealed many interesting features of dynamic patterns of gene expression across the tissues and stages. In total, 38 793 probe sets were detected as expressed and 69% of the expressed transcripts showed significantly variable expression levels among tissues/organs. We found that similarity of transcriptomes among organs corresponded well to their developmental relatedness. About 5.2% of the expressed transcripts showed tissue-specific expression in one or both varieties and 22.7% of the transcripts exhibited constitutive expression including 19 genes with high and stable expression in all the tissues. This dataset provided a versatile resource for plant genomic research, which can be used for associating the transcriptomes to the developmental processes, understanding the regulatory network of these processes, tracing the expression profile of individual genes and identifying reference genes for quantitative expression analyses.

Significance: New discoveries have been continuously made in recent years on the roles of noncoding RNAs in regulating biological processes. Phased small-interfering RNAs (phasiRNAs) may be the newest member discovered in recent years. The photoperiod-sensitive male sterility (PSMS) rice is a very valuable germplasm that started the era of two-line hybrid rice. Here we show that phasiRNAs generated by a long-noncoding RNAPMS1Tencoded by thePms1locus regulates PSMS in rice. This work provides a case associating the phasiRNAs with a biological trait, especially an agriculturally highly important trait, thus confirming that the phasiRNAs indeed have biological functions.

Conquering Rice Sterility: The hybrid sterility occurring among rice species has long been a puzzle and hampers progress in breeding crops with improved performance and yield characteristics. Yang et al. (p. 1336 ) have identified three linked genes encoding a killer, a partner, and a protector protein. The killer and partner work together to kill female gametes not carrying the functional protector, resulting in preferential transmission of gametes carrying the functional protector, which also causes segregation distortion in the progeny. This explanation for how reproductive isolation is maintained among species of rice, and perhaps other organisms, also offers approaches for boosting yields by intersubspecific heterosis.

Hybrid sterility is a major form of postzygotic reproductive isolation. Although reproductive isolation has been a key issue in evolutionary biology for many decades in a wide range of organisms, only very recently a few genes for reproductive isolation were identified. The Asian cultivated rice ( Oryza sativa L.) is divided into two subspecies, indica and japonica . Hybrids between indica and japonica varieties are usually highly sterile. A special group of rice germplasm, referred to as wide-compatibility varieties, is able to produce highly fertile hybrids when crossed to both indica and japonica . In this study, we cloned S5 , a major locus for indica–japonica hybrid sterility and wide compatibility, using a map-based cloning approach. We show that S5 encodes an aspartic protease conditioning embryo-sac fertility. The indica ( S5 -i) and japonica ( S5 -j) alleles differ by two nucleotides. The wide compatibility gene ( S5 -n) has a large deletion in the N terminus of the predicted S5 protein, causing subcellular mislocalization of the protein, and thus is presumably nonfunctional. This triallelic system has a profound implication in the evolution and artificial breeding of cultivated rice. Genetic differentiation between indica and japonica would have been enforced because of the reproductive barrier caused by S5 -i and S5 -j, and species coherence would have been maintained by gene flow enabled by the wide compatibility gene.

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.

Rhizomes are root-like underground stems which grow horizontally, and their growth and development are regulated by both genetic and environmental factors (McIntyre 1967, McIntyre 1970, McIntyre 2001). Yoshida et al. (2016) recently reported on rhizome development in Oryza longistaminata in Plant & Cell Physiology. They demonstrated the light dependency of bud development, reporting that axillary buds grown under light and dark conditions developed as new aerial shoots and new rhizomes, respectively (refer to their fig. 5 and corresponding text). However, we obtained independent results suggesting that light is not the decisive factor. We argue that it is mainly the bud position that determines the developmental fate of axillary...