Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

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summary Ceratocystis fimbriata is a serious wilt and canker stain pathogen with a wide geographical distribution and host range that includes both woody and herbaceous plants. Previous studies using hybridization have shown that isolates of C. fimbriata from different hosts and origins differ in colony morphology, pathogenicity and growth rate, as well as conidial state. It has therefore been suggested that distinct strains, linked to host or geographical origin, are encompassed in C. fimbriata. The aim of this study was to develop PCR-based microsatellite markers for population studies on C. fimbriata. ISSR-PCR was used to target specific microsatellite regions of DNA from C. fimbriata. These amplified products were cloned and sequenced. Primer pairs were designed from these sequences to flank the microsatellite regions. From 24 primer pairs, 11 polymorphic primers were selected and tested on a number of C. fimbriata isolates representing a wide host and geographical range. Cluster analyses of the results indicate that these markers clearly distinguish between different geographical and host specific populations of C. fimbriata. The results are concordant with sequence data from the internal transcribed spacer (ITS) region of the rDNA operon of the same isolates. These markers will be useful in future studies of C. fimbriata population structure and diversity.

Quantitative trait loci (QTL) analysis was conducted for pre-harvest sprouting tolerance (PHST) in bread wheat for a solitary chromosome 3A, which was shown to be important for this trait in earlier studies. An inter-varietal mapping population in the form of recombinant inbred lines (RILs) developed from a cross between SPR8198 (a PHS tolerant genotype) and HD2329 (a PHS susceptible cultivar) was used for this purpose. The parents and the RIL population were grown in six different environments and the data on PHS were collected in each case. A framework linkage map of chromosome 3A with 13 markers was prepared and used for QTL analysis. A major QTL (QPhs.ccsu-3A.1) was detected on 3AL at a genetic distance of approximately 183 cM from centromere, the length of the map being 279.1 cM. The QTL explained 24.68% to 35.21% variation in individual environments and 78.03% of the variation across the environments (pooled data). The results of the present study are significant on two counts. Firstly, the detected QTL is a major QTL, explaining up to 78.03% of the variation and, secondly, the QTL showed up in all the six environments and also with the pooled data, which is rather rare in QTL analysis. The positive additive effects in the present study suggest that a superior allele of the QTL is available in the superior parent (SPR8198), which can be used for marker-aided selection for the transfer of this QTL allele to obtain PHS-tolerant progeny. It has also been shown that the red-coloured grain of PHS tolerant parent is not associated with the QTL for PHST identified during the present study, suggesting that PHS tolerant white-grained cultivars can be developed.

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This study demonstrates a dose-dependent response of Trichoderma harzianum Th-56 in improving drought tolerance in rice by modulating proline, SOD, lipid peroxidation product and DHN / AQU transcript level, and the growth attributes. In the present study, the effect of colonization of different doses of T. harzianum Th-56 strain in rice genotypes were evaluated under drought stress. The rice genotypes treated with increasing dose of T. harzianum strain Th-56 showed better drought tolerance as compared with untreated control plant. There was significant change in malondialdehyde, proline, higher superoxide dismutase level, plant height, total dry matter, relative chlorophyll content, leaf rolling, leaf tip burn, and the number of scorched/senesced leaves in T. harzianum Th-56 treated rice genotypes under drought stress. This was corroborated with altered expression of aquaporin and dehydrin genes in T. harzianum Th-56 treated rice genotypes. The present findings suggest that a dose of 30 g/L was the most effective in improving drought tolerance in rice, and its potential exploitation will contribute to the advancement of rice genotypes to sustain crop productivity under drought stress. Interaction studies of T. harzianum with three aromatic rice genotypes suggested that PSD-17 was highly benefitted from T. harzianum colonization under drought stress.

Quantitative trait loci (QTL) analysis for grain weight (GW = 1000 grain weight) in common wheat was conducted using a set of 100 recombinant inbred lines (RILs) derived from a cross 'Rye Selection 111 (high GW) × Chinese Spring (low GW)'. The RILs and their two parental genotypes were evaluated for GW in six different environments (three locations × two years). Genotyping of RILs was carried out using 449 (30 SSRs, 299 AFLP and 120 SAMPL) polymorphic markers. Using the genotyping data of RILs, framework linkage maps were prepared for three chromosomes (1A, 2B, 7A), which were earlier identified by us to carry important/major genes for GW following monosomic analysis. QTL analysis for GW was conducted following genome-wide single marker regression analysis (SMA) and composite interval mapping (CIM) using molecular maps for the three chromosomes. Following SMA, 12 markers showed associations with GW, individual markers explaining 6.57% to 10.76% PV (phenotypic variation) for GW in individual environments. The high grain weight parent, Rye Selection111, which is an agronomically superior genotype, contributed favourable alleles for GW at six of the 12 marker loci identified through SMA. The CIM identified two stable and definitive QTLs, one each on chromosome arms 2BS and 7AS, which were also identified through SMA, and a third suggestive QTL on 1AS. These QTLs explained 9.06% to 19.85% PV for GW in different environments. The QTL for GW on 7AS is co-located with a QTL for heading date suggesting the occurrence of a QTL having a positive pleiotropic effect on the two traits. Some of the markers identified during the present study may prove useful for marker-assisted selection, while breeding for high GW in common wheat.

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals.