Increasing crop yield is one of the most important goals of plant science research. Grain size is a major determinant of grain yield in cereals and is a target trait for both domestication and artificial breeding(1). We showed that the quantitative trait locus (QTL) GS5 in rice controls grain size by regulating grain width, filling and weight. GS5 encodes a putative serine carboxypeptidase and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51 rice accessions from a wide geographic range identified three haplotypes that seem to be associated with grain width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield in rice and, potentially, other crops(2).

Hybrid rice has greatly contributed to the global increase of rice productivity. A major component that facilitated the development of hybrids was a mutant showing photoperiod-sensitive male sterility (PSMS) with its fertility regulated by day length. Transcriptome studies have shown that large portions of the eukaryotic genomic sequences are transcribed to long noncoding RNAs (lncRNAs). However, the potential roles for only a few lncRNAs have been brought to light at present. Thus, great efforts have to be invested to understand the biological functions of lncRNAs. Here we show that a lncRNA of 1,236 bases in length, referred to as long-dayspecific male-fertility-associated RNA (LDMAR), regulates PSMS in rice. We found that sufficient amount of the LDMAR transcript is required for normal pollen development of plants grown under long-day conditions. A spontaneous mutation causing a single nucleotide polymorphism (SNP) between the wild-type and mutant altered the secondary structure of LDMAR. This change brought about increased methylation in the putative promoter region of LDMAR, which reduced the transcription of LDMAR specifically under long-day conditions, resulting in premature programmed cell death (PCD) in developing anthers, thus causing PSMS. Thus, a lncRNA could directly exert a major effect on a trait like a structure gene, and a SNP could alter the function of a lncRNA similar to amino acid substitution in structural genes. Molecular elucidating of PSMS has important implications for understanding molecular mechanisms of photoperiod regulation of many biological processes and also for developing male sterile germplasms for hybrid crop breeding.epigenetics | Oryza sativa

Summary 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.

Grain chalkiness is a highly undesirable quality trait in the marketing and consumption of rice grain. However, the molecular basis of this trait is poorly understood. Here we show that a major quantitative trait locus (QTL), Chalk5, influences grain chalkiness, which also affects head rice yield and many other quality traits. Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase (V-PPase) with inorganic pyrophosphate (PPi) hydrolysis and H(+)-translocation activity. Elevated expression of Chalk5 increases the chalkiness of the endosperm, putatively by disturbing the pH homeostasis of the endomembrane trafficking system in developing seeds, which affects the biogenesis of protein bodies and is coupled with a great increase in small vesicle-like structures, thus forming air spaces among endosperm storage substances and resulting in chalky grain. Our results indicate that two consensus nucleotide polymorphisms in the Chalk5 promoter in rice varieties might partly account for the differences in Chalk5 mRNA levels that contribute to natural variation in grain chalkiness.

Manipulating grain size is an effective strategy for increasing cereal yields. Here we identify a pathway composed of five subunits of the heterotrimeric G proteins that regulate grain length in rice. The Gβ protein is essential for plant survival and growth. Gα provides a foundation for grain size expansion. Three Gγ proteins, DEP1, GGC2 and GS3, antagonistically regulate grain size. DEP1 and GGC2, individually or in combination, increase grain length when in complex with Gβ. GS3, having no effect on grain size by itself, reduces grain length by competitively interacting with Gβ. By combining different G-protein variants, we can decrease grain length by up to 35% or increase it by up to 19%, which leads to over 40% decreasing to 28% increasing of grain weight. The wide existence of such a conserved system among angiosperms suggests a possible general predictable approach to manipulating grain/organ sizes.