PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice.

Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding.

Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F2 Population.

Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage.

Coordinated regulation of vegetative and reproductive branching in rice.

Grasses produce tiller and panicle branching at vegetative and reproductive stages; the branching patterns largely define the diversity of grasses and constitute a major determinant for grain yield of many cereals. Here we show that a spatiotemporally coordinated gene network consisting of the MicroRNA 156 (miR156/)miR529/SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) and miR172/APETALA2 (AP2) pathways regulates tiller and panicle branching in rice. SPL genes negatively control tillering, but positively regulate inflorescence meristem and spikelet transition.

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts.

Differential expression of GS5 regulates grain size in rice.

Grain weight is a major determinant of grain yield. GS5 is a positive regulator of grain size such that grain width, filling, and weight are correlated with its expression level. Previous work suggested that polymorphisms of GS5 in the promoter region might be responsible for the variation in grain size.

OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice.

Grains from cereals contribute an important source of protein to human food, and grain protein content (GPC) is an important determinant of nutritional quality in cereals. Here we show that the quantitative trait locus (QTL) qPC1 in rice controls GPC by regulating the synthesis and accumulation of glutelins, prolamins, globulins, albumins and starch. qPC1 encodes a putative amino acid transporter OsAAP6, which functions as a positive regulator of GPC in rice, such that higher expression of OsAAP6 is correlated with higher GPC.

Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice.

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.

An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population.

The ability to reveal the regulatory architecture of genes at the whole-genome level by constructing a regulatory network is critical for understanding the biological processes and developmental programmes of organisms. Here, we conducted an eQTL-guided function-related co-expression analysis to identify the putative regulators and construct gene regulatory network. We performed an eQTL analysis of 210 recombinant inbred lines (RILs) derived from a cross between two indica rice lines, Zhenshan 97 and Minghui 63, the parents of an elite hybrid, using data obtained by hybridizing RNA samples of flag leaves at the heading stage with Affymetrix whole-genome arrays.

Grain number, plant height, and heading date7 is a central regulator of growth, development, and stress response.

Grain number, plant height, and heading date7 (Ghd7) has been regarded as an important regulator of heading date and yield potential in rice (Oryza sativa). In this study, we investigated functions of Ghd7 in rice growth, development, and environmental response. As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of Ghd7 on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds.

Genetic analysis of the metabolome exemplified using a rice population.

Plant metabolites are crucial for both plant life and human nutrition. Despite recent advance in metabolomics, the genetic control of plant metabolome remains largely unknown. Here, we performed a genetic analysis of the rice metabolome that provided over 2,800 highly resolved metabolic quantitative trait loci for 900 metabolites.

Rice WRKY13 regulates cross talk between abiotic and biotic stress signaling pathways by selective binding to different cis-elements.

Plants use a complex signal transduction network to regulate their adaptation to the ever-changing environment. Rice (Oryza sativa) WRKY13 plays a vital role in the cross talk between abiotic and biotic stress signaling pathways by suppressing abiotic stress resistance and activating disease resistance. However, it is not clear how WRKY13 directly regulates this cross talk.

OsAP65, a rice aspartic protease, is essential for male fertility and plays a role in pollen germination and pollen tube growth.

Aspartic proteases (APs) comprise a large proteolytic enzyme family widely distributed in animals, microbes, viruses, and plants. The rice genome encodes 96 APs, of which only a few have been functionally characterized. Here, the identification and characterization of a novel AP gene, OsAP65, which plays an indispensable role in pollen tube growth in rice, is reported.

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice.

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).

XIAO is involved in the control of organ size by contributing to the regulation of signaling and homeostasis of brassinosteroids and cell cycling in rice.

Organ size is determined by cell number and size, and involves two fundamental processes: cell proliferation and cell expansion. Although several plant hormones are known to play critical roles in shaping organ size by regulating the cell cycle, it is not known whether brassinosteroids (BRs) are also involved in regulating cell division. Here we identified a rice T-DNA insertion mutant for organ size, referred to as xiao, that displays dwarfism and erect leaves, typical BR-related phenotypes, together with reduced seed setting.

Altered levels of histone deacetylase OsHDT1 affect differential gene expression patterns in hybrid rice.

Hybrids between different inbred varieties display novel patterns of gene expression resulted from parental variation in allelic nucleotide sequences. To study the function of chromatin regulators in hybrid gene expression, the histone deacetylase gene OsHDT1 whose expression displayed a circadian rhythm was over-expressed or inactivated by RNAi in an elite rice parent. Increased OsHDT1 expression did not affect plant growth in the parent but led to early flowering in the hybrid.

Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL) analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g.

Additive and additive × additive interaction make important contributions to spikelets per panicle in rice near isogenic (Oryza sativa L.) lines.

Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F(2) population in which the three QTLs segregated simultaneously.

Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.

Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size.

The bacterial pathogen Xanthomonas oryzae overcomes rice defenses by regulating host copper redistribution.

Pathogen effectors are virulence factors causing plant diseases. How the host targets of these effectors facilitate pathogen infection is largely unknown. An effector of Xanthomonas oryzae pv oryzae (Xoo) transcriptionally activates rice (Oryza sativa) susceptibility gene Xa13 to cause bacterial blight disease.

OsEDR1 negatively regulates rice bacterial resistance via activation of ethylene biosynthesis.

Rice OsEDR1 is a sequence ortholog of Arabidopsis EDR1. However, its molecular function is unknown. We show here that OsEDR1-suppressing/knockout (KO) plants, which developed spontaneous lesions on the leaves, have enhanced resistance to Xanthomonas oryzae pv.

Opposite functions of a rice mitogen-activated protein kinase during the process of resistance against Xanthomonas oryzae.

The pathogen-induced plant defense signaling network consists of multiple components, although only some of them are characterized. Most of the known components function either as activators or repressors in host-pathogen interactions. Here we report that a mitogen-activated protein kinase, OsMPK6, functions both as an activator and a repressor in rice resistance against Xanthomonas oryzae pv.

A global analysis of QTLs for expression variations in rice shoots at the early seedling stage.

Analyses of quantitative trait loci (QTLs) for expression levels (eQTLs) of genes reveal a genetic relationship between expression variation and the regulator, thus unlocking information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and transcript abundance. In this study, we used an Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice shoots at 72 h after germination from 110 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63.

A dynamic gene expression atlas covering the entire life cycle of rice.

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.