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Rice stripe virus (RSV) causes one of the most serious viral diseases of rice (Oryza sativa L.), but the molecular basis of RSV resistance has remained elusive. Here we show that the resistant allele of rice STV11 (STV11-R) encodes a sulfotransferase (OsSOT1) catalysing the conversion of salicylic acid (SA) into sulphonated SA (SSA), whereas the gene product encoded by the susceptible allele STV11-S loses this activity. Sequence analyses suggest that the STV11-R and STV11-S alleles were predifferentiated in different geographic populations of wild rice, Oryza rufipogon, and remained prevalent in cultivated indica and japonica rice varieties, respectively. Introgression of the STV11-R allele into susceptible cultivars or heterologous transfer of STV11-R into tobacco plants confers effective resistance against RSV. Our results shed new insights into plant viral defense mechanisms and suggest effective means of breeding RSV-resistant crops using molecular marker-assisted selection or genetic engineering., Rice stripe virus (RSV) causes a disease in rice with significant economic consequences. Here, the authors clone an RSV-resistant gene in rice and suggest that this gene encodes a sulphotransferase that catalyses the conversion of salicylic acid (SA) into sulphonated salicylic acid, leading to increased SA accumulation in RSV-infected plants and inhibition of viral replication.

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have produced a draft rice genome sequence of Oryza sativa ssp. indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from both indica and japanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

The phytohormone cytokinin (CK) positively regulates the activity and function of the shoot apical meristem (SAM), which is a major parameter determining seed production. The rice ( Oryza sativa L.) Gn1a / OsCKX2 ( Grain number 1a / Cytokinin oxidase 2 ) gene, which encodes a cytokinin oxidase, has been identified as a major quantitative trait locus contributing to grain number improvement in rice breeding practice. However, the molecular mechanism of how the expression of OsCKX2 is regulated in planta remains elusive. Here, we report that the zinc finger transcription factor DROUGHT AND SALT TOLERANCE (DST) directly regulates OsCKX2 expression in the reproductive meristem. DST-directed expression of OsCKX2 regulates CK accumulation in the SAM and, therefore, controls the number of the reproductive organs. We identify that DST reg1 , a semidominant allele of the DST gene, perturbs DST-directed regulation of OsCKX2 expression and elevates CK levels in the reproductive SAM, leading to increased meristem activity, enhanced panicle branching, and a consequent increase of grain number. Importantly, the DST reg1 allele provides an approach to pyramid the Gn1a -dependent and Gn1a -independent effects on grain production. Our study reveals that, as a unique regulator of reproductive meristem activity, DST may be explored to facilitate the genetic enhancement of grain production in rice and other small grain cereals.

Chloroplast is a new hotspot in the field of plant transformation system of plant genetic engineering. Plastid transformation has several advantages: high expression, multiple expressed genes in a single transformation event, absence of gene silencing, et al. A series of elements for construction of dicistronic site-specific integration expression vector of rice chloroplast have been cloned, including trnl-trnA (rice chloroplast homologous recombination fragments), Prrn (16S rRNA operon promotor), PpsbA (the 3' untranslated region of the chloroplastpsbA gene), hptll gene (encoding hygromycin phosphotransferase) and EGFP (encoding enhanced green fluorescence protein). All the elements were constructed into a rice chloroplast dicistronic expression vector pCTE04 (-trnl-Prrn-RBS-hptlI-RBS-EGFP-PpsbA- trnA-). Then pCTE04 was introduced into chloroplasts of Dunaliella salina through particle bombardment. Strong green fluorescence was observed in chloroplasts of some bombarded Dunaliella salina cells under a stereo fluorescence microscope, indicating that pCTE04 could be expressed in Dunaliella salina chloroplasts transiently. It provides a solid foundation for further genetic engineering in rice chloroplast transformation.

By using a whole-genome oligonucleotide microarray, designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid rice LYP9 and its parental cultivars 93-11 and PA64s . We detected 22,266 expressed genes out of 36,926 total genes set collectively from 7 tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicles at filling stage. Clustering results showed that the F1 hybrid's expression profiles resembled those of its parental lines more than that which lies between the 2 parental lines. Out of the total gene set, 7,078 genes are shared by all sampled tissues and 3,926 genes (10.6% of the total gene set) are differentially expressed genes (DG). As we divided DG into those between the parents (DG PP ) and between the hybrid and its parents (DG HP ), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DG HP rather than in DG PP . In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes.

An interspecific advanced backcross population derived from a cross between Oryza sativa 'V20A' (a popular male-sterile line used in Chinese rice hybrids) and Oryza glaberrima (accession IRGC No. 103544 from Mali) was used to identify quantitative trait loci (QTL) associated with grain quality and grain morphology. A total of 308 BC3F1hybrid families were evaluated for 16 grain-related traits under field conditions in Changsha, China, and the same families were evaluated for RFLP and SSR marker segregation at Cornell University (Ithaca, N.Y.). Eleven QTL associated with seven traits were detected in six chromosomal regions, with the favorable allele coming from O. glaberrima at eight loci. Favorable O. glaberrima alleles were associated with improvements in grain shape and appearance, resulting in an increase in kernel length, transgressive variation for thinner grains, and increased length to width ratio. Oryza glaberrima alleles at other loci were associated with potential improvements in crude protein content and brown rice yield. These results suggested that genes from O. glaberrima may be useful in improving specific grain quality characteristics in high-yielding O. sativa hybrid cultivars.Key words: quantitative trait loci (QTL), grain quality, molecular markers, O. sativa, O. glaberrima.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family., Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes

Publisher Summary This chapter focuses on the recent developments in the field of super hybrid rice breeding in China. Facing the grim situation of population growth pressure and reduction of arable land, a super rice breeding program was set up by China Ministry of Agriculture in 1996 to ensure the food security of China in the new century. By way of morphological improvement plus utilization of intersubspecific (indica/japonica) heterosis, several pioneer super hybrid rice varieties were developed, which attained the Phase I yield standard of the single season super rice (10.5 t/ha on a large scale) by 2000. A combination, P64S/E32, created a record yield of 17.1 t/ha in an experimental plot of 720 m2 in 1999. Now, efforts are focused on breeding of the Phase II super hybrid rice where good progresses have been made. In experimental fields, some newly developed hybrid rice varieties showed a yield level of 13 t/ha and had a yield advantage of 6–18% over the existing pioneer super hybrid rice varieties. Among them, the best one yielded as high as 12.3 t/ha averagely on a large area of about 7 ha at Longshan, Hunan in 2002. According to the above progresses, the yield standard of the Phase II super rice (12 t/ha on a large scale) can be achieved by 2005. With the application of molecular technology in rice breeding, the yield potential of rice can be further increased. Based on the latest research results such as the discovery and utilization of yield enhancing QTLs from wild rice, successful introduction of barnyard grass DNA and C4 genes with a higher photosynthetic efficiency into rice, the Phase III super hybrid rice breeding program is proposed, in which the yield target is 13.5 t/ha on a large scale by 2010.

Wild species are valued as a unique source of genetic variation, but they have rarely been used for the genetic improvement of quantitative traits. To identify trait-improving quantitative trait loci (QTL) alleles from exotic species, an accession of Oryza rufipogon, a relative of cultivated rice, was chosen on the basis of a genetic diversity study. An interspecific BC2 testcross population (V20A/O. rufipogon//V20B///V20B////Ce64) consisting of 300 families was evaluated for 12 agronomically important quantitative traits. The O. rufipogon accession was phenotypically inferior for all 12 traits. However, transgressive segregants that outperformed the original elite hybrid variety, V20A/Ce64, were observed for all traits examined. A set of 122 RFLP and microsatellite markers was used to identify QTL. A total of 68 significant QTL were identified, and of these, 35 (51%) had beneficial alleles derived from the phenotypically inferior O. rufipogon parent. Nineteen (54%) of these beneficial QTL alleles were free of deleterious effects on other characters. O. rufipogon alleles at two QTL on chromosomes 1 and 2 were associated with an 18 and 17% increase in grain yield per plant, respectively, without delaying maturity or increasing plant height. This discovery suggests that the innovative use of molecular maps and markers can alter the way geneticists utilize wild and exotic germplasm.

Nitrogen (N) is a major limiting factor in crop production, and plant adaptive responses to low N are involved in many post-transcriptional regulation. Recent studies indicate that miRNAs play important roles in adaptive responses. However, miRNAs in soybean adaptive responses to N limitation have been not reported. We constructed sixteen libraries to identify low N-responsive miRNAs on a genome-wide scale using samples from 2 different genotypes (low N sensitive and low N tolerant) subjected to various periods of low nitrogen stress. Using high-throughput sequencing technology (Illumina-Solexa), we identified 362 known miRNAs variants belonging to 158 families and 90 new miRNAs belonging to 55 families. Among these known miRNAs variants, almost 50% were not different from annotated miRNAs in miRBase. Analyses of their expression patterns showed 150 known miRNAs variants as well as 2 novel miRNAs with differential expressions. These differentially expressed miRNAs between the two soybean genotypes were compared and classified into three groups based on their expression patterns. Predicted targets of these miRNAs were involved in various metabolic and regulatory pathways such as protein degradation, carbohydrate metabolism, hormone signaling pathway, and cellular transport. These findings suggest that miRNAs play important roles in soybean response to low N and contribute to the understanding of the genetic basis of differences in adaptive responses to N limitation between the two soybean genotypes. Our study provides basis for expounding the complex gene regulatory network of these miRNAs.

A set of 194 F7 lines derived from a subspecific rice cross showing strong F1 heterosis was backcrossed to the two parents. The materials (388 BC1F7 lines, 194 F8 lines, two parents, F1) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD > or = 2.0) was detected through 141 RFLP markers in the BC1F7 populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC1F7 populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC1F7 populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F8 population having phenotypic values superior to the F1 for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident.