Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice.

Rice is a major source of cadmium (Cd) intake for Asian people. Indica rice usually accumulates more Cd in shoots and grains than Japonica rice. However, underlying genetic bases for differential Cd accumulation between Indica and Japonica rice are still unknown. In this study, we cloned a quantitative trait locus (QTL) grain Cd concentration on chromosome 7 (GCC7) responsible for differential grain Cd accumulation between two rice varieties by performing QTL analysis and map-based cloning. We found that the two GCC7 alleles, GCC7PA64s and GCC793-11 , had different promoter activity of OsHMA3, leading to different OsHMA3 expression and different shoot and grain Cd concentrations. By analyzing the distribution of different haplotypes of GCC7 among diverse rice accessions, we discovered that the high and low Cd accumulation alleles, namely GCC793-11 and GCC7PA64s , were preferentially distributed in Indica and Japonica rice, respectively. We further showed that the GCC7PA64s allele can be used to replace the GCC793-11 allele in the super cultivar 93-11 to reduce grain Cd concentration without adverse effect on agronomic traits. Our results thus reveal that the QTL GCC7 with sequence variation in the OsHMA3 promoter is an important determinant controlling differential grain Cd accumulation between Indica and Japonica rice.

Reproduction and In-Depth Evaluation of Genome-Wide Association Studies and Genome-Wide Meta-analyses Using Summary Statistics.

In line with open-source genetics, we report a novel linear regression technique for genome-wide association studies (GWAS), called Open GWAS algoriTHm (OATH). When individual-level data are not available, OATH can not only completely reproduce reported results from an experimental model, but also recover underreported results from other alternative models with a different combination of nuisance parameters using naïve summary statistics (NSS). OATH can also reliably evaluate all reported results in-depth (e.g., p-value variance analysis), as demonstrated for 42 Arabidopsis phenotypes under three magnesium (Mg) conditions. In addition, OATH can be used for consortium-driven genome-wide association meta-analyses (GWAMA), and can greatly improve the flexibility of GWAMA. A prototype of OATH is available in the Genetic Analysis Repository (https://github.com/gc5k/GEAR).

LSCHL4 from Japonica Cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11.

The basic premise of high yield in rice is to improve leaf photosynthetic efficiency and coordinate the source-sink relationship in rice plants. Quantitative trait loci (QTLs) related to morphological traits and chlorophyll content of rice leaves were detected at the stages of heading to maturity, and a major QTL (qLSCHL4) related to flag leaf shape and chlorophyll content was detected at both stages in recombinant inbred lines constructed using the indica rice cultivar 93-11 and the japonica rice cultivar Nipponbare. Map-based cloning and expression analysis showed that LSCHL4 is allelic to NAL1, a gene previously reported in narrow leaf mutant of rice. Overexpression lines transformed with vector carrying LSCHL4 from Nipponbare and a near-isogenic line of 93-11 (NIL-9311) had significantly increased leaf chlorophyll content, enlarged flag leaf size, and improved panicle type. The average yield of NIL-9311 was 18.70% higher than that of 93-11. These results indicate that LSCHL4 had a pleiotropic function. Exploring and pyramiding more high-yield alleles resembling LSCHL4 for super rice breeding provides an effective way to achieve new breakthroughs in raising rice yield and generate new ideas for solving the problem of global food safety.

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.

The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang-You-Pei-Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93-11 and maternal cultivar PA64s of Liang-You-Pei-Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice.

Synthesis, characterization, and antibacterial activity of cross-linked chitosan-glutaraldehyde.

This present study deals with synthesis, characterization and antibacterial activity of cross-linked chitosan-glutaraldehyde. Results from this study indicated that cross-linked chitosan-glutaraldehyde markedly inhibited the growth of antibiotic-resistant Burkholderia cepacia complex regardless of bacterial species and incubation time while bacterial growth was unaffected by solid chitosan. Furthermore, high temperature treated cross-linked chitosan-glutaraldehyde showed strong antibacterial activity against the selected strain 0901 although the inhibitory effects varied with different temperatures. In addition, physical-chemical and structural characterization revealed that the cross-linking of chitosan with glutaraldehyde resulted in a rougher surface morphology, a characteristic Fourier transform infrared (FTIR) band at 1559 cm⁻¹, a specific X-ray diffraction peak centered at 2θ = 15°, a lower contents of carbon, hydrogen and nitrogen, and a higher stability of glucose units compared to chitosan based on scanning electron microscopic observation, FTIR spectra, X-ray diffraction pattern, as well as elemental and thermo gravimetric analysis. Overall, this study indicated that cross-linked chitosan-glutaraldehyde is promising to be developed as a new antibacterial drug.

Characterization of physiological response and identification of associated genes under heat stress in rice seedlings.

Global warming, which is caused by greenhouse gas emissions, makes food crops more vulnerable to heat stress. Understanding the heat stress-related mechanisms in crops and classifying heat stress-related genes can increase our knowledge in heat-resistant molecular biology and propel developments in molecular design breeding, which can help rice cope with unfavorable temperatures. In this study, we carried out a physiological analysis of rice plants after heat stress. The results show a dramatic increase in malondialdehyde contents and SOD activities. We successfully isolated 11 heat-related rice genes with known function annotation through DNSH, which is an improved SSH method for screening long cDNA fragments. The reanalysis of microarray data from public database revealed that all these genes displayed various expression patterns after heat stress, drought, cold and salt. Quantitative real-time reverse transcription PCR was also performed to validate the expression of these genes after heat stress. The expressions in 10 genes were all significantly changed except for contig 77, which is a CBL-interacting protein kinase. Several reports have been published about the members of the same gene family.

Rice leaf inclination2, a VIN3-like protein, regulates leaf angle through modulating cell division of the collar.

As an important agronomic trait, inclination of leaves is crucial for crop architecture and grain yields. To understand the molecular mechanism controlling rice leaf angles, one rice leaf inclination2 (lc2, three alleles) mutant was identified and functionally characterized. Compared to wild-type plants, lc2 mutants have enlarged leaf angles due to increased cell division in the adaxial epidermis of lamina joint. The LC2 gene was isolated through positional cloning, and encodes a vernalization insensitive 3-like protein. Complementary expression of LC2 reversed the enlarged leaf angles of lc2 plants, confirming its role in controlling leaf inclination. LC2 is mainly expressed in the lamina joint during leaf development, and particularly, is induced by the phytohormones abscisic acid, gibberellic acid, auxin, and brassinosteroids. LC2 is localized in the nucleus and defects of LC2 result in altered expression of cell division and hormone-responsive genes, indicating an important role of LC2 in regulating leaf inclination and mediating hormone effects.

[Genetic analysis of two extremely segregation distorted populations in rice (Oryza sativa L.)].

Segregation distortion is a quite common phenomenon in living species and thought to be a potent evolutional force. The main reasons of distorted segregation ratios are responsible for the selection of gametes or sporophytes. In this study, two extreme segregation distortions from the progenies of lmi x 02428 and d6 x 93-11 were identified. The segregation ratio of molecular markers tightly linked with LMI and D6 genes were analyzed and skew segregation were found in the markers tested which were indicated by significant deviation from the expected Mendelian segregation ratio(1:2:1). The segregation distorted regions were detected between molecular markers ST8 and ST8-2 near the centromere of chromosome 8, and ST7-1 and ST7-3 near telomere of chromosome 7, respectively. Meanwhile, the results indicated that segregation distortion had related with the different crossed combinations.

Genetic dissection for leaf correlative traits of rice (Oryza sativa L.) under drought stress.

Water is becoming a restricted factor of agricultural development owing to the global shortage of water resources. Screening and improving drought tolerant rice cultivars would be helpful for increasing and stabilizing yield, economizing water and reducing environmental pollution. In this study, 127 rice lines of DII population derived from an indica variety Zhaiyeqing 8 (ZYQ8) and a japonica variety Jingxi 17 (JX17) were used to locate QTLs for leaf rolling, relative water content and rate of electric conductivity under drought stress. The results showed that significant differences between the parents were detected for all measured traits. The tremendous transgressive segregations for these traits were observed in the population. The frequency of all traits in the population was approximately normally distributed with slight skew. A total of six QTLs for the three traits were detected with molecular linkage map of 234 markers, including three QTLs (qLR-1, qLR-5 and qLR-11) for leaf rolling, two QTLs (qRWC-1 and qRWC-6) for relative water content and one QTL (qREC-6) for rate of electric conductivity. Visual measurement for leaf rolling can be used to screen a large number of rice germplasm resources or varieties, which is of importance to screening and utilization of drought tolerant rice varieties.

[Genetic dissection of cooked rice elongation in rice (Oryza sativa L.)].

QTLs for milled rice length (MRL), cooked rice length (CRL) and cooked rice elongation (CRE) were identified by using a population of 127 DH lines derived from a cross between ZYQ8 and JX17. Totally, 14 QTLs for rice elongation traits were detected on chromosomes 1, 2, 3, 5, 6, 7, 10, 11 and 12. Two putative QTLs for MRL were mapped on chromosomes 2. Seven putative QTLs for CRL were mapped on chromosomes 1, 6, 7, 10, 11 and 12. Five putative QTLs for CRE were mapped on chromosomes 5, 6, and 10. The regions of G249-G164 on chromosome 3, G30-RZ516 on chromosome 6 and G1082-GA223 on chromosome 10 were detected simultaneously for affecting cooked rice length and cooke rice elongation. LODs of the QTLs related to rice elongation varied from 2.26 to 9.25, and their explained variations from 5.31% to 17.21% . It is indicated that cooked rice elongation was controlled by polygene and Wx-gene located on the same region with qCRE-6 was important to cooked rice elongation.

[QTL analysis for percentage of exserted stigma in rice (Oryza sativa L.)].

Percentage of exserted stigmas (PES) was investigated in Hainan by using a population of 127 DH population derived from a cross between a high-PES indica variety Zaiyeqing 8 (ZYQ 8) and a low-PES japonica variety Jingxi 17(JX 17) and its molecular linkage map of 234 markers. Two QTLs (qPES-2, qPES-3) for PES were located on chromosome 2 and 3, respectively. There is no difference between the QTLs for single stigma exsertation and total PES, but the only QTL for dual stigma exsertation located on chromosome 2, whose positive additive effect was from ZYQ 8. Simultaneously the detected QTLs for spikelets per panicle located on chromosome 6,8, respectively and had no linkage relation with the QTLs for PES.

[Molecular mapping of QTLs for rice milling yield traits].

QTLs of three milling yield traits, including brown rice (BR,%), milled rice (MR,%) and head milled rice (HR,%), were mapped using a set of 212 Lemont/Teqing RI population, an RFLP linkage map with 182 markers and a mixed model approach(QTLMapper V1.0). The population showed continuous distributions with transgressive segregation on both sides for all traits while HR had a wider variation than BR and MR. One and four main effect QTLs were detected for MR and HR. Two QTLs for HR(QHr6 and QHr7) had large additive effects. Twelve, five and sixteen pairs of digenic epistatic loci were associated with BR, MR and HR respectively. Epistasis was more important than main effect QTLs according to the mapping result. A complex relationship was observed for epistatic pairs mapped in same trait or among different traits by sharing intervals.