Gaoneng Shao

Mapping of qGL7-2, a grain length QTL on chromosome 7 of rice

A residual heterozygous line (RHL) carrying a heterozygous segment between two SSR loci RM11 and RM134 on the rice chromosome 7 was selected from a set of recombinant inbred lines from the cross D50 (javanica)/HB277 (indica). The former parent produces much longer grains than the latter. Selfed progenies of this selection were analyzed genotypically (SSRs) and phenotypically (grain length). Grain length was discontinuously variable in the mapping populations, allowing for the placement of this QTL qGL7-2 within a approximately 4.8 cM interval defined by RM351 and RM234. A set of new markers within this region were developed, which narrowed the QTL to a 278 kb region defined by the markers Indel1 and RM21945. This region contains 49 predicted genes. The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.

Allelic variation for a candidate gene for GS7 , responsible for grain shape in rice

Grain shape is an important component of end-use quality in rice. The genomic location of the grain shape QTL GS7 was narrowed to lie within a 4.8-kb segment on chromosome 7. The homologous region in cv. Nipponbare contains no annotated genes, while two open reading frames were predicted, one of which (ORF2) represented a likely candidate for GS7 gene on the basis of correlation between sequence variation and phenotype. Semi-quantitative and quantitative RT-PCR analysis of ORF2 transcription showed that the gene was active in both the leaf and panicle when the cv. D50 allele was present, but not in the presence of the cv. HB277 allele. A microsatellite-based phylogeny and a re-sequencing analysis of ORF2 among a set of 52 diverse rice accessions suggested that the cv. D50 GS7 allele may have originated from the tropical japonica genepool. The effect on grain length of the alternative alleles at GS7and GS3 showed that combination type 3/A was associated with longer grains than type 1/A. An Indel marker developed within the ORF2 sequence was informative for predicting grain length.

The rice nuclear gene WLP1 encoding a chloroplast ribosome L13 protein is needed for chloroplast development in rice grown under low temperature conditions

Plastidial ribosome proteins (PRPs) form the major component of the plastidial ribosome. Here we describe a rice mutant named wlp1 (white leaf and panicles 1) selected from a population of tissue culture regenerants. The early seedling leaves of the mutant were albino, as was the immature panicle at heading, and the phenotype was more strongly expressed in plants exposed to low temperature conditions. Changes in the leaf pigmentation of the mutant were due to altered chlorophyll content and chloroplast development. Positional cloning of WLP1, followed by complementation and knock-down experiments, showed that it encodes a 50S ribosome L13 protein. The WLP1 protein localized to the chloroplast. WLP1 was mainly transcribed in green tissues and particularly abundantly in the early seedling leaves. In addition, the expression level of WLP1 was induced by the low temperature. The transcription pattern of a number of genes involved in plastidial transcription/translation and in photosynthesis was altered in the wlp1 mutants. These results reveal that WLP1 is required for normal chloroplast development, especially under low temperature conditions. This is the first report on the function of PRPs in rice.

Haplotype variation at Badh2, the gene determining fragrance in rice.

Fragrance is an important component of end-use quality in rice. A set of 516 fragrant rice accessions were genotyped and over 80% of them carried the badh2.7 allele. A subset of 144 mostly fragrant accessions, including nine of Oryza rufipogon, was then subjected to a detailed diversity and haplotype analysis. The level of linkage disequilibrium in the Badh2 region was higher among the fragrant accessions. Re-sequencing in the Badh2 region showed that badh2.7, badh2.2 and badh2.4-5 all arose in the japonica genepool, and spread later into the indica genepool as a result of deliberate crossing. However, loss-of-function alleles of Badh2 are also found in the indica genepools, and then transferred into japonica. Evidence for three new possible FNPs was obtained from the Badh2 sequence of 62 fragrant accessions. Based on these data, we have elaborated a model for the evolution of Badh2 and its participation in the rice domestication process.

The cadmium and lead content of the grain produced by leading Chinese rice cultivars

The cadmium (Cd) and lead (Pb) content in both white and wholemeal flour milled from 110 leading rice cultivars was assessed. The white flour Cd content ranged from <0.0025 to 0.2530mg/kg (geometric mean (GM)=0.0150mg/kg), while its Pb content ranged from <0.0250 to 0.3830mg/kg (GM=0.0210mg/kg). The indica types took up higher amounts of Cd and Pb than did the japonica types. Although the heavy metal content of wholemeal flour tended to higher than that of white flour, nevertheless 84.5% (Cd) and 95.4% (Pb) of the entries were compliant with the national maximum allowable concentration of 0.2000mg/kg of each contaminant. An analysis of the Cd content in the white flour of three indica type cultivars grown in two consecutive years at two locations indicated that Cd content may be significantly affected by the conditions prevailing in the growing season.

GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development

Rice grain filling determines grain weight, final yield and grain quality. Here, a rice defective grain filling mutant, gif2, was identified. Grains of gif2 showed a slower filling rate and a significant lower final grain weight and yield compared to wild-type. The starch content in gif2 was noticeably decreased and its physicochemical properties were also altered. Moreover, gif2 endosperm cells showed obvious defects in compound granule formation. Positional cloning identified GIF2 to encode an ADP-glucose pyrophosphorylase (AGP) large subunit, AGPL2; consequently, AGP enzyme activity in gif2 endosperms was remarkably decreased. GIF2 is mainly expressed in developing grains and the coded protein localizes in the cytosol. Yeast two hybrid assay showed that GIF2 interacted with AGP small subunits OsAGPS1, OsAGPS2a and OsAGPS2b. Transcript levels for granule-bound starch synthase, starch synthase, starch branching enzyme and starch debranching enzyme were distinctly elevated in gif2 grains. In addition, the level of nucleotide diversity of the GIF2 locus was extremely low in both cultivated and wild rice. All of these results suggest that GIF2 plays important roles in the regulation of grain filling and starch biosynthesis during caryopsis development, and that it has been preserved during selection throughout domestication of modern rice.

Fine mapping and candidate gene analysis of qTAC8, a major quantitative trait locus controlling tiller angle in rice (Oryza sativa L.)

Rice tiller angle is an important agronomic trait that contributes to crop production and plays a vital role in high yield breeding. In this study, a recombinant inbred line (RIL) population derived from the cross of a glabrous tropical japonica rice D50 and an indica rice HB277, was used to investigate quantitative trait loci (QTLs) controlling rice tiller angle. Two major QTLs, qTAC8 and qTAC9, were detected. While qTAC9 mapped with a previously identified gene (TAC1), using a BC2F2 population qTAC8 was mapped to a 16.5 cM region between markers RM7049 and RM23175. Position of qTAC8 was narrowed to a 92 kb DNA region by two genetic segregating populations. Finally, one opening reading frame (ORF) was regarded as a candidate gene according to genomic sequencing and qRT-PCR analysis. In addition, a set of four near isogenic lines (NILs) were created to investigate the genetic relationship between those two QTLs, and one line carrying qTAC8 and qTAC9 presented additive effect of tiller angle, suggesting that these QTLs are involved in different genetic pathways. Our results provide a foundation for the cloning of qTAC8 and genetic improvement of the rice plant architecture.

Genetic Analysis and Molecular Mapping of Novel White Striped Leaf Mutant Gene in Rice

A new white striped leaf mutant wsl1 was discovered from Nipponbare mutated by ethyl methanesulfonate. The mutant showed white striped leaves at the seedling stage and the leaves gradually turned green after the tillering stage. The chlorophyll content of wsl1 was significantly lower than that of wild-type during the fourth leaf stage, tillering stage and booting stage. The numbers of chloroplast, grana and grana lamella were reduced and the thylakoids were degenerated in wsl1 compared with wild type. Genetic analysis showed that the wsl1 was controlled by a single recessive gene. Molecular mapping of the wsl1 was performed using an F2 population derived from wsl1/Nanjing 11. The wsl1 was finally mapped on the telomere region of chromosome 9 and positioned between simple sequence repeat markers RM23742 and RM23759 which are separated by approximately 486.5 kb. The results may facilitate map-based cloning of wsl1 and understanding of the molecular mechanism of the regulation of leaf-color by WSL1 in rice.

Optimization of Near-Infrared Reflectance Model in Measuring Gelatinization Characteristics of Rice Flour with a Rapid Viscosity Analyzer (RVA) and Differential Scanning Calorimeter (DSC)

This study compared the calibration models generated by combinations of different mathematical and preprocessing treatments as well as regression algorithms to optimize the analysis of gelatinization properties of rice flour by using near-infrared spectroscopy, in comparison with conventional techniques of differential scanning calorimetry (DSC) and rapid viscosity analysis (RVA). A total of 220 milled rice flours were used for model construction. A model generated by the modified partial least squares regression (MPLS) with mathematical treatment “2, 8, 8, 2” (second-order derivative computed based on eight data points, and eight and two data points in the second smoothing, respectively) and detrend preprocessing was identified as the best for simultaneously measuring onset temperature (To), peak temperature (Tp), and conclusion temperature (Tc) of DSC. MPLS/“2, 8, 8, 2”/weighted multiplicative scattering correction preprocessing was identified as the best for RVA properties. The results indicated that n...

White Leaf and Panicle 2, encoding a PEP-associated protein, is required for chloroplast biogenesis under heat stress in rice

WLP2, encoding a PEP-associated protein, and its paralog OsFLN2 can interact with OsTRXz to form a TRX-FLN regulatory module to protect chloroplast development from heat stress in rice.