Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Comparison of hom(oe)ologous regions containing clusters of duplicated RGAs within Musa species and with rice

Understanding structure and evolution of genomic regions coding for proteins of agronomical interest is an important objective for crop improvement. We compare hom(oe)ologous regions within monocot genomes through BAC annotation. Here, we present putative orthologous and paralogous relationships of a highly duplicated Resistance Gene Analog (RGA) locus within Musa species and between Musa and rice species. (Résumé d'auteur

Design of source coders and joint source/channel coders for noisy channels

A theory behind a proposed joint source/channel coding approach is developed and a variable rate design approach which provides substantial improvement over current joint source/channel coder designs is obtained. The Rice algorithm as applied to the output of the Gamma Ray Detector of the Mars Orbiter is evaluated. An alternative algorithm is obtained which outperforms the Rice both in terms of data compression and noisy channel performance. A high-fidelity low-rate image compression algorithm is developed which provides almost distortionless compression of high resolution images

Use of EcoTILLING to Find Genes Related to Salt Tolerance in Rice. W622

Salinity is considered one of important physical factors influencing rice (Oryza sativa L.) production. Roots are the first parts of the plant to experience any soil-based salt stress and it is at the roots that the entry of Na+ and Cl? is determined. Rice as other plants, have several strategies to cope with salinity including minimizing the entry of toxic ions through roots, and/or maintaining low Na+/K+ ratios at shoot level, etc...A tremendous variation for salt tolerance within genotypes provides opportunities to improve rice salt-stress tolerance through genetic means. Aiming to find alleles associated with salinity tolerance we used the EcoTILLING technique to explore the natural variability existing in 390 rice germplasm accessions at key genes related to salt stress. This working collection is representative of the large morphological, physiological, and ecological variation available in domesticated rice. All targets genes, namely OsNHX1, OsHKT1;5, SalT, OsRMC and OsCPK17, have been previously described and characterized as related to salt-tolerance enhancement in rice, through different mechanisms such as Na+/K+ equilibrium, signaling cascade and stress protection. Sequence results showed hundreds of SNPs (Single Nucleotides Polymorphisms) and small INDELs, resulting in a total of 40 allelic variants, thus coding 31 different proteins. After phenotypic characterization of the allelic variants at CDS level, we found significant statistical associations between some particular gene haplotypes and phenotypic parameters under salt stress. We will discuss the utility of EcoTILLING and SNP discovery in breeding efforts for salt tolerance, with particular emphasis to the mechanisms related to root genomics. (Texte integral

Early selection of \u3cem\u3ebZIP73\u3c/em\u3e facilitated adaptation of \u3cem\u3ejaponica\u3c/em\u3e rice to cold climates

Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Although the growth range of japonica subspecies has expanded northward compared to modern wild rice (O. rufipogon), the molecular basis of the adaptation remains unclear. Here we report bZIP73, a bZIP transcription factor-coding gene with only one functional polymorphism (+511 G\u3eA) between the two subspecies japonica and indica, may have facilitated japonica adaptation to cold climates. We show the japonica version of bZIP73 (bZIP73Jap) interacts with bZIP71 and modulates ABA levels and ROS homeostasis. Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73Ind was subsequently selected for reasons that remain unclear. Our findings reveal early selection of bZIP73Jap may have facilitated climate adaptation of primitive rice germplasms

A key variant in the cis-regulatory element of flowering gene Ghd8 associated with cold tolerance in rice.

Variations in the gene promoter play critical roles in the evolution of important adaptive traits in crops, but direct links of the regulatory mutation to the adaptive change are not well understood. Here, we examine the nucleotide variations in the promoter region of a transcription factor (Ghd8) that control grain number, plant height and heading date in rice. We find that a dominant promoter type of subspecies japonica displayed a high activity for Ghd8 expression in comparison with the one in indica. Transgenic analyses revealed that higher expression levels of Ghd8 delayed heading date and enhanced cold tolerance in rice. Furthermore, a single-nucleotide polymorphism (T1279G) at the position -1279 bp that locates on the potential GA-responsive motif in the Ghd8 promoter affected the expression of this gene. The 1279 T variant has elevated expression of Ghd8, thus conferring increased cold tolerance of rice seedlings. Nucleotide diversity analysis revealed that the approximately 25-kb genomic region surrounding Ghd8 in the subspecies japonica was under significant selection pressure. Our findings demonstrate that the join effects of the regulatory and coding variants largely contribute to the divergence of japonica and indica and increase the adaptability of japonica to the cold environment