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Cadmium (Cd)-contaminated rice is a serious issue affecting food safety. Understanding the molecular regulatory mechanisms of Cd accumulation in rice grains is crucial to minimizing Cd concentrations in grains. We identified a member of the low-affinity cation transporter family, OsLCT2 in rice. It was a membrane protein. OsLCT2 was expressed in all tissues of the elongation and maturation zones in roots, with the strongest expression in pericycle and stele cells adjacent to the xylem. When grown in Cd-contaminated paddy soils, rice plants overexpressing OsLCT2 significantly reduced Cd concentrations in the straw and grains. Hydroponic experiment demonstrated its overexpression decreased the rate of Cd translocation from roots to shoots, and reduced Cd concentrations in xylem sap and in shoots of rice. Moreover, its overexpression increased Zn concentrations in roots by up-regulating the expression of OsZIP9, a gene responsible for Zn uptake. Overexpression of OsLCT2 reduces Cd accumulation in rice shoots and grains by limiting the amounts of Cd loaded into the xylem and restricting Cd translocation from roots to shoots of rice. Thus, OsLCT2 is a promising genetic resource to be engineered to reduce Cd accumulation in rice grains. [ABSTRACT FROM AUTHOR]

Background: Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas. Results: By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice. Conclusions: Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice. [ABSTRACT FROM AUTHOR]

Main conclusion : The comprehensive transcriptome analysis of rice female-sterile line and wild-type line ovule provides an important clue for exploring the regulatory network of the formation of rice fertile female gametophyte. Ovules are the female reproductive tissues of rice ( Oryza sativa L.) and play a major role in sexual reproduction. To investigate the potential mechanism of rice female gametophyte fertility, we used RNA sequencing, combined with genetic subtraction, to compare the transcriptome of the ovules of a high-frequency female-sterile line ( fsv1) and a rice wild-type line (Gui 99) during ovule development. Ovules were harvested at three developmental stages: ovule containing megaspore mother cell in meiosis process (stage 1), ovule containing functional megaspore in mitosis process (stage 2), and ovule containing mature female gametophyte (stage 3). Six cDNA libraries generated a total of 42.2 million high-quality clean reads that aligned with 30,204 genes. The comparison between the fsv1 and Gui 99 ovules identified a large number of differentially expressed genes (DEGs), i.e., 45, 495, and 932 DEGs at the three ovule developmental stages, respectively. From the comparison of the two rice lines, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and MapMan analyses indicated that a large number of DEGs associated with starch and sucrose metabolism, plant hormone signal transduction, protein modification and degradation, oxidative phosphorylation, and receptor kinase. These DEGs might play roles in ovule development and fertile female gametophyte formation. Many transcription factor genes and epigenetic-related genes also exhibit different expression patterns and significantly different expression levels in two rice lines during ovule development, which might provide important information regarding the abortive mechanism of the female gametophyte in rice. [ABSTRACT FROM AUTHOR]

The future of rice breeding will likely be built on the basis of the further utilization of heterosis between elite cultivars and genetic resources from distant subspecies of rice. Previous studies have proved that exogenous genomic DNA transformation methods can be used to transfer genetic information from distant relatives (donor) into cultivated rice (recipient). However, the mechanism underlying this form of genetic transfer is poorly characterized, and the genes that cause the phenotypic changes in these variants are typically difficult to identify. This study examined YVB, a stable variant line with greatly improved grain quality traits that was derived from an indica variety (V20B) by transferring genomic DNA of O.minuta through the 'spike-stalk injection method (SIM)'. We used restriction-site associated DNA sequencing technology (RAD-seq) to evaluate a population of BCF backcross lines (YVB × V20B); the RAD-seq data were used to construct a genetic linkage map with high-density SNPs for use in association analysis exploring genotype-phenotype relationships at the whole-genome level. A total of 17 quantitative trait loci (QTLs) for rice quality traits were mapped to chromosomes 3, 5, 6, 8, and 9. 8 major QTLs controlling different phenotypic variations were mapped to the same region of chromosome 5. This region contained the GS5 gene for grain weight and the qSW5/ GW5 gene for grain width. This study provides new resources and insights into the molecular mechanisms of grain trait phenotypic variation and the transmission of genetic information via the introduction of genomic DNA to a distantly related crop relative species. [ABSTRACT FROM AUTHOR]

Genetic diversity within parental lines of hybrid rice is the foundation of heterosis utilization and yield improvement. Previous studies have suggested that genetic diversity was narrow in cytoplasmic male sterile (CMS/A line) and restorer lines (R line) for Three-line hybrid rice. However, the genetic diversity within maintainer lines (B line), especially at a genome-wide scale, remains largely unknown. In the present study, we performed deep re-sequencing of the elite maintainer line V20B ( Oryza sativa L. ssp. indica). We then compared the V20B sequence with the 93- 11 ( Oryza sativa L. ssp. indica) genome sequence. 112.1 × 106 paired-end reads (PE reads) were generated with approximately 30-fold sequencing depth. The V20B PE reads uniquely covered 87.6 % of the 93- 11 genome sequence. Overall, a total of 660,778 single-nucleotide polymorphism (SNPs) and 266,301 insertions and deletions (InDels) were identified, yielding an average of 2.1 SNPs/kb and 0.8 InDels/kb. Genome-wide distribution of the SNPs and InDels was non-random, and variation-rich and variation-poor regions were identified in all chromosomes. A total of 20,562 non-synonymous SNPs spanning 8,854 genes were annotated. Our results identified DNA polymorphisms at the genome-wide scale and uncovered the high level of genetic diversity between V20B and 93- 11. Our results proved that next-generation sequencing technologies can be powerful tools to study genome-wide DNA polymorphisms, to query genetic diversity, and to enable molecular improvement efforts with Three-line hybrid rice. Further, our results also indicated that 93- 11 could be used as core germplasm for the improvement of wild-abortive CMS lines and the maintainer lines. [ABSTRACT FROM AUTHOR]

The bZIP transcription factor (TF) family plays an important role in the abscisic acid (ABA) signaling pathway of abiotic stress in plants. We here report the cloning and characterization of OsbZIP71, which encodes a rice bZIP TF. Functional analysis showed that OsbZIP71 is a nuclear-localized protein that specifically binds to the G-box motif, but has no transcriptional activity both in yeast and rice protoplasts. In yeast two-hybrid assays, OsbZIP71 can form both homodimers and heterodimers with Group C members of the bZIP gene family. Expression of OsbZIP71 was strongly induced by drought, polyethylene glycol (PEG), and ABA treatments, but repressed by salt treatment. OsbZIP71 overexpressing (p35S::OsbZIP71) rice significantly improved tolerance to drought, salt and PEG osmotic stresses. In contrast, RNAi knockdown transgenic lines were much more sensitive to salt, PEG osmotic stresses, and also ABA treatment. Inducible expression (RD29A::OsbZIP71) lines were significantly improved their tolerance to PEG osmotic stresses, but hypersensitivity to salt, and insensitivity to ABA. Real-time PCR analysis revealed that the abiotic stress-related genes, OsVHA- B, OsNHX1, COR413- TM1, and OsMyb4, were up-regulated in overexpressing lines, while these same genes were down-regulated in RNAi lines. Chromatin immunoprecipitation analysis confirmed that OsbZIP71 directly binds the promoters of OsNHX1 and COR413- TM1 in vivo. These results suggest that OsbZIP71 may play an important role in ABA-mediated drought and salt tolerance in rice. [ABSTRACT FROM AUTHOR]

Epicuticular wax in plants limits non-stomatal water loss, inhibits postgenital organ fusion, protects plants against damage from UV radiation and imposes a physical barrier against pathogen infection. Here, we give a detailed description of the genetic, physiological and morphological consequences of a mutation in the rice gene WSL2, based on a comparison between the wild-type and an EMS mutant. The mutant's leaf cuticle membrane is thicker and less organized than that of the wild type, and its total wax content is diminished by ~80%. The mutant is also more sensitive to drought stress. WSL2 was isolated by positional cloning, and was shown to encode a homologue of the Arabidopsis thaliana genes CER3/WAX2/YRE/FLP1 and the maize gene GL1. It is expressed throughout the plant, except in the root. A transient assay carried out in both A. thaliana and rice protoplasts showed that the gene product is deposited in the endoplasmic reticulum. An analysis of the overall composition of the wax revealed that the mutant produces a substantially reduced quantity of C22-C32 fatty acids, which suggests that the function of WSL2 is associated with the elongation of very long-chain fatty acids. [ABSTRACT FROM AUTHOR]

Due to an error in combining the figure, an incorrect version of Fig. 9e was presented in the original publication. [ABSTRACT FROM AUTHOR]