The kinesin-13 protein BR HYPERSENSITIVE 1 is a negative brassinosteroid signaling component regulating rice growth and development.

Phytohormones performed critical roles in regulating plant architecture and thus determine grain yield in rice. However, the roles of brassinosteroids (BRs) compared to other phytohormones in shaping rice architecture are less studied. In this study, we report that BR hypersensitive1 (BHS1) plays a negative role in BR signaling and regulate rice architecture. BHS1 encodes the kinesin-13a protein and regulates grain length. We found that bhs1 was hypersensitive to BR, while BHS1-overexpression was less sensitive to BR compare to WT. BHS1 was down-regulated at RNA and protein level upon exogenous BR treatment, and proteasome inhibitor MG132 delayed the BHS1 degradation, indicating that both the transcriptional and posttranscriptional regulation machineries are involved in BHS1-mediated regulation of plant growth and development. Furthermore, we found that the BR-induced degradation of BHS1 was attenuated in Osbri1 and Osbak1 mutants, but not in Osbzr1 and Oslic mutants. Together, these results suggest that BHS1 is a novel component which is involved in negative regulation of the BR signaling downstream player of BRI1.

A ß-ketoacyl carrier protein reductase confers heat tolerance via the regulation of fatty acid biosynthesis and stress signaling in rice.

Heat stress is a major environmental threat affecting crop growth and productivity. However, the molecular mechanisms associated with plant responses to heat stress are poorly understood. Here, we identified a heat stress-sensitive mutant, hts1, in rice. HTS1 encodes a thylakoid membrane-localized ß-ketoacyl carrier protein reductase (KAR) involved in de novo fatty acid biosynthesis. Phylogenetic and bioinformatic analysis showed that HTS1 probably originated from streptophyte algae and is evolutionarily conserved in land plants. Thermostable HTS1 is predominantly expressed in green tissues and strongly induced by heat stress, but is less responsive to salinity, cold and drought treatments. An amino acid substitution at A254T in HTS1 causes a significant decrease in KAR enzymatic activity and, consequently, impairs fatty acid synthesis and lipid metabolism in the hts1 mutant, especially under heat stress. Compared to the wild-type, the hts1 mutant exhibited heat-induced higher H2 O2 accumulation, a larger Ca2+ influx to mesophyll cells, and more damage to membranes and chloroplasts. Also, disrupted heat stress signaling in the hts1 mutant depresses the transcriptional activation of HsfA2s and the downstream target genes. We suggest that HTS1 is critical for underpinning membrane stability, chloroplast integrity and stress signaling for heat tolerance in rice.

The ell1 mutation disrupts tryptophan metabolism and induces cell death.

Tryptophan metabolism pathways are important components of the plant immune system; for example, serotonin is derived from tryptophan, and plays a vital role in rice (Oryza sativa) innate immunity. Recently, we isolated a rice mutant, early lesion leaf 1 (ell1), which exhibits lesions. RNA-seq analysis revealed that KEGG pathways related to amino acid metabolism were significantly enriched in the transcripts differentially expressed in this mutant. Furthermore, measurements of free amino acid contents revealed the accumulated tryptophan of ell1 mutant. In addition, the transcript levels of genes related to tryptophan biosynthesis were significantly enhanced in the ell1 mutant. These results revealed that ELL1 plays a critical role in tryptophan metabolism. Based on these findings, it is revealed that loss of ELL1 function may disrupt tryptophan metabolism, thereby inducing cell death and forming lesions in rice.

Disruption of EARLY LESION LEAF 1, encoding a cytochrome P450 monooxygenase, induces ROS accumulation and cell death in rice.

Lesion-mimic mutants (LMMs) provide a valuable tool to reveal the molecular mechanisms determining programmed cell death (PCD) in plants. Despite intensive research, the mechanisms behind PCD and the formation of lesions in various LMMs still remain to be elucidated. Here, we identified a rice (Oryza sativa) LMM, early lesion leaf 1 (ell1), cloned the causal gene by map-based cloning, and verified this by complementation. ELL1 encodes a cytochrome P450 monooxygenase, and the ELL1 protein was located in the endoplasmic reticulum. The ell1 mutant exhibited decreased chlorophyll contents, serious chloroplast degradation, upregulated expression of chloroplast degradation-related genes, and attenuated photosynthetic protein activity, indicating that ELL1 is involved in chloroplast development. RNA sequencing analysis showed that genes related to oxygen binding were differentially expressed in ell1 and wild-type plants; histochemistry and paraffin sectioning results indicated that hydrogen peroxide (H2 O2 ) and callose accumulated in the ell1 leaves, and the cell structure around the lesions was severely damaged, which indicated that reactive oxygen species (ROS) accumulated and cell death occurred in the mutant. TUNEL staining and comet experiments revealed that severe DNA degradation and abnormal PCD occurred in the ell1 mutants, which implied that excessive ROS accumulation may induce DNA damage and ROS-mediated cell death in the mutant. Additionally, lesion initiation in the ell1 mutant was light dependent and temperature sensitive. Our findings revealed that ELL1 affects chloroplast development or function, and that loss of ELL1 function induces ROS accumulation and lesion formation in rice.

Rice EARLY SENESCENCE 2, encoding an inositol polyphosphate kinase, is involved in leaf senescence.

BACKGROUND: Early leaf senescence influences yield and yield quality by affecting plant growth and development. A series of leaf senescence-associated molecular mechanisms have been reported in rice. However, the complex genetic regulatory networks that control leaf senescence need to be elucidated. RESULTS: In this study, an early senescence 2 (es2) mutant was obtained from ethyl methanesulfonate mutagenesis (EMS)-induced mutational library for the Japonica rice cultivar Wuyugeng 7 (WYG7). Leaves of es2 showed early senescence at the seedling stage and became severe at the tillering stage. The contents of reactive oxygen species (ROS) significantly increased, while chlorophyll content, photosynthetic rate, catalase (CAT) activity significantly decreased in the es2 mutant. Moreover, genes which related to senescence, ROS and chlorophyll degradation were up-regulated, while those associated with photosynthesis and chlorophyll synthesis were down-regulated in es2 mutant compared to WYG7. The ES2 gene, which encodes an inositol polyphosphate kinase (OsIPK2), was fine mapped to a 116.73-kb region on chromosome 2. DNA sequencing of ES2 in the mutant revealed a missense mutation, ES2 was localized to nucleus and plasma membrane of cells, and expressed in various tissues of rice. Complementation test and overexpression experiment confirmed that ES2 completely restored the normal phenotype, with chlorophyll contents and photosynthetic rate increased comparable with the wild type. These results reveal the new role of OsIPK2 in regulating leaf senescence in rice and therefore will provide additional genetic evidence on the molecular mechanisms controlling early leaf senescence. CONCLUSIONS: The ES2 gene, encoding an inositol polyphosphate kinase localized in the nucleus and plasma membrane of cells, is essential for leaf senescence in rice. Further study of ES2 will facilitate the dissection of the genetic mechanisms underlying early leaf senescence and plant growth.

Isolation of TSCD11 Gene for Early Chloroplast Development under High Temperature in Rice.

BACKGROUND: Chloroplasts are essential for photosynthesis and play key roles in plant development. High temperature affects structure of chloroplasts and metabolism in plants. The seryl-tRNA synthetase plays an important role in translation of proteins. Although seryl-tRNA synthetase has been widely studied in microbes and animals, few studies have reported about its role in chloroplast development under high temperature in rice. RESULTS: In this study, we isolated a novel temperature-sensitive chlorophyll-deficient 11 (tscd11) mutant by ethyl methane sulfonate (EMS) mutagenesis of japonica variety Wuyujing7. The tscd11 mutant developed albino leaves at the 3-leaf stage under high temperature (35 °C), but had normal green leaves under low temperature (25 °C). Consistent with the albino phenotype, impaired chloroplasts, decreased chlorophyll content and increased ROS accumulation were found in the tscd11 mutant at 35 °C. Fine mapping and DNA sequencing of tscd11 revealed a missense mutation (G to A) in the eighth exon of LOC_Os11g39670 resulted in amino acid change (Glu374 to Lys374). The TSCD11 gene encodes a seryl-tRNA synthetase localized to chloroplast. Complementation test confirmed that the point mutation in TSCD11 is responsible for the phenotype of tscd11. TSCD11 is highly expressed in leaves. Compared with the wild type (WT), mutation in TSCD11 led to significant alteration in expression levels of genes associated with chlorophyll biosynthesis, photosynthesis and chloroplast development under high temperature. CONCLUSIONS: TSCD11, encoding a seryl-tRNA synthetase localized to chloroplast, is vital to early chloroplast development at high temperature in rice, which help to further study on the molecular mechanism of chloroplast development under high temperature.

Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency.

Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC4F2 population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.

Natural variation in the promoter of TGW2 determines grain width and weight in rice.

Understanding the genetic basis of natural variation in grain size among diverse rice varieties can help breeders develop high-yielding rice cultivars. Here, we report the discovery of qTGW2, a new semidominant quantitative trait locus for grain width and weight. The corresponding gene, TGW2, encodes CELL NUMBER REGULATOR 1 (OsCNR1) localized to the plasma membrane. A single nucleotide polymorphism (SNP) variation 1818 bp upstream of TGW2 is responsible for its different expression, leading to alteration in grain width and weight by influencing cell proliferation and expansion in glumes. TGW2 interacts with KRP1, a regulator of cell cycle in plants, to negatively regulate grain width and weight. Genetic diversity analysis of TGW2 in 141 rice accessions revealed it as a breeding target in a selective sweep region. Our findings provide new insights into the genetic mechanism underlying grain morphology and grain weight, and uncover a promising gene for improving rice yield.

Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding.

Enriching zinc (Zn) and selenium (Se) levels, while reducing cadmium (Cd) concentration in rice grains is of great benefit for human diet and health. Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Se-biofortification and Cd-minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci (QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSLGCC7 with the PA64s-derived GCC7 allele in the 93-11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93-11. This elite chromosome segment substitution line (CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSLGZC6 for grain Zn concentration and CSSLGSC5 for grain Se concentration. The CSSLGCC7+GZC6 and CSSLGCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains.

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.

The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency.

The indica and japonica rice (Oryza sativa) subspecies differ in nitrate (NO3-) assimilation capacity and nitrogen (N) use efficiency (NUE). Here, we show that a major component of this difference is conferred by allelic variation at OsNR2, a gene encoding a NADH/NADPH-dependent NO3- reductase (NR). Selection-driven allelic divergence has resulted in variant indica and japonica OsNR2 alleles encoding structurally distinct OsNR2 proteins, with indica OsNR2 exhibiting greater NR activity. Indica OsNR2 also promotes NO3- uptake via feed-forward interaction with OsNRT1.1B, a gene encoding a NO3- uptake transporter. These properties enable indica OsNR2 to confer increased effective tiller number, grain yield and NUE on japonica rice, effects enhanced by interaction with an additionally introgressed indica OsNRT1.1B allele. In consequence, indica OsNR2 provides an important breeding resource for the sustainable increases in japonica rice yields necessary for future global food security.

Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits.

BACKGROUND: Detecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait. CSSLs are also powerful tools for studying the effects of quantitative trait loci (QTLs) pyramiding and interaction on phenotypic variation. RESULTS: Here, we developed three sets of CSSLs consisting of 81, 55, and 61 lines, which were derived from PA64s × 9311, Nipponbare × 9311 and PA64s × Nipponbare crosses, respectively. All of the 197 CSSLs were subjected to high-throughput genotyping by whole-genome resequencing to obtain accurate physical maps for the 3 sets of CSSLs. The 3 sets of CSSLs were used to analyze variation for 11 major agronomic traits in Hangzhou and Shenzhen and led to the detection of 71 QTLs with phenotypic effect that ranged from 7.6% to 44.8%. Eight QTLs were commonly detected under two environments for the same phenotype, and there were also 8 QTL clusters that were found. Combined with GWAS on grain length and expression profiles on young panicle tissues, qGL1 detected in CSSLs was fine mapped within a 119 kb region on chromosome 1 and LOC_Os01g53140 and LOC_Os01g53250 were the two most likely candidate genes. CONCLUSIONS: Our results indicate that developing CSSLs genotyped by whole-genome resequencing are powerful tools for basic genetic research and provide a platform for the rational design of rice breeding. Meanwhile, the conjoint analysis of different CSSLs, natural population and expression profiles can facilitate QTL fine mapping.

OsACL-A2 negatively regulates cell death and disease resistance in rice.

ATP-citrate lyases (ACL) play critical roles in tumour cell propagation, foetal development and growth, and histone acetylation in human and animals. Here, we report a novel function of ACL in cell death-mediated pathogen defence responses in rice. Using ethyl methanesulphonate (EMS) mutagenesis and map-based cloning, we identified an Oryza sativa ACL-A2 mutant allele, termed spotted leaf 30-1 (spl30-1), in which an A-to-T transversion converts an Asn at position 343 to a Tyr (N343Y), causing a recessive mutation that led to a lesion mimic phenotype. Compared to wild-type plants, spl30-1 significantly reduces ACL enzymatic activity, accumulates high reactive oxygen species and increases degradation rate of nuclear deoxyribonucleic acids. CRISPR/Cas9-mediated insertion/deletion mutation analysis and complementation assay confirmed that the phenotype of spl30-1 resulted from the defective function of OsACL-A2 protein. We further biochemically identified that the N343Y mutation caused a significant degradation of SPL30N343Y in a ubiquitin-26S proteasome system (UPS)-dependent manner without alteration in transcripts of OsACL-A2 in spl30-1. Transcriptome analysis identified a number of up-regulated genes associated with pathogen defence responses in recessive mutants of OsACL-A2, implying its role in innate immunity. Suppressor mutant screen suggested that OsSL, which encodes a P450 monooxygenase protein, acted as a downstream key regulator in spl30-1-mediated pathogen defence responses. Taken together, our study discovered a novel role of OsACL-A2 in negatively regulating innate immune responses in rice.

OsHAK1 controls the vegetative growth and panicle fertility of rice by its effect on potassium-mediated sugar metabolism.

Plant growth and reproduction are both energy-requiring processes; the necessary energy is supplied by the products of photosynthesis. Both the vegetative growth and reproductive success of rice are compromised by the absence of a functional copy of the gene OsHAK1. Here, a comparison between wild type rice and OsHAK1 knockout mutants not only confirmed the known detrimental effect of the absence of OsHAK1 on root growth, pollen viability and fertility, but also showed that sucrose phosphate synthase activity was lowered, and the sucrose content of the leaves was markedly increased, due to a partial block on the up-loading of sucrose into the phloem. The impaired allocation of sugar to the roots and spikelets caused by the knocking out of OsHAK1 was accompanied by a down-regulation in the leaf sheaths and panicle axes of genes encoding sucrose transporters (SUT genes), which are active in the phloem, as well as in the roots and spikelets of those encoding monosaccharide transporters (MST genes), which transport hexose sugars across the plant plasma membrane. The activity of sucrose synthase, acid invertase and neutral invertase in the roots of mutant plants assayed at the tillering stage, and in their spikelets, assayed during grain-filling, was significantly lower than in the equivalent organs of wild type plants. As a result, the supply of total soluble sugar, glucose and fructose to sink organs was reduced, consistent with the effect of the mutation on root growth and panicle fertility. Compared to wild type plants, the mutants accumulated less potassium (K) throughout the plant. The conclusion was that the failure to fully supply the demand of the mutant's sink organs for assimilate was responsible for its compromised phenotype, and that the deficiency in K uptake induced by the loss of OsHAK1 functionality was responsible for the disruption of sugar metabolism.

Characterization of a major QTL for manganese accumulation in rice grain.

Some diets lack sufficient manganese (Mn), an essential mineral. Increasing Mn in grain by biofortification could prevent Mn deficiency, but may increase levels of the toxic element cadmium (Cd). Here, we investigated Mn in rice (Oryza sativa) grains in recombinant inbred lines (RILs) from the cross of 93-11 (low grain Mn) with PA64s (high grain Mn). Quantitative trait locus (QTL) analysis to identify loci controlling grain Mn identified a major QTL, qGMN7.1, on the short arm of chromosome 7; qGMN7.1 explained 15.6% and 22.8% of the phenotypic variation in the RIL populations grown in two distinct environments. We validated the QTL with a chromosome segment substitution line (CSSL), CSSL-qGMN7.1, in the 93-11 background harboring qGMN7.1 from PA64s. Compared to 93-11, CSSL-qGMN7.1 grain had increased Mn and decreased Cd concentrations; CSSL-qGMN7.1 roots also showed enhanced Mn uptake. Fine mapping delimited qGMN7.1 to a 49.3-kb region containing OsNRAMP5, a gene responsible for Mn and Cd uptake. Sequence variations in the OsNRAMP5 promoter caused changes in its transcript level, and in grain Mn levels. Our study thus cloned a major QTL for grain Mn concentration in rice, and identified materials for breeding rice for high Mn and low Cd concentrations in the grain.

Genetic analysis for rice seedling vigor and fine mapping of a major QTL qSSL1b for seedling shoot length.

Seedling vigor is an important agricultural trait as direct-seeded rice technology becomes widely applied. In order to investigate the genetic mechanisms underlying seedling vigor in rice, seeds of 132 recombinant inbred lines (RILs) derived from 93-11 and PA64s, harvested from Lingshui and Hangzhou were cultivated in the nutrient solution, and four indices for seedling vigor were measured including seedling shoot length (SSL), seedling root length (SRL), seedling wet weight (SWW) and seedling dry weight (SDW). Significant correlations were observed among the indices, and also between 1000-seed weight (TSW) and SWW or SDW. Combined with a high-resolution genetic map generated from sequencing of the RILs, 65 quantitative trait loci (QTLs) were detected on all chromosomes with interval of 1.93 Mb on average. Among 57 QTLs for seedling vigor, 28 were detected from seeds harvested in both sites and 33 were first identified. With BC3F2 derived from 93-11 and a CSSL harboring segments from PA64s in 93-11 background, a major QTL for SSL, qSSL1b was fine mapped within 80.5 kb between two InDel markers. Our study provides a platform for further cloning of the QTL and dissecting the molecular basis for seedling vigor at early seedling stage in rice.

Fine Mapping of a Novel defective glume 1 (dg1) Mutant, Which Affects Vegetative and Spikelet Development in Rice.

In cereal crops, vegetative and spikelet development play important roles in grain yield and quality, but the genetic mechanisms that control vegetative and spikelet development remain poorly understood in rice. Here, we identified a new rice mutant, defective glume 1 (dg1) mutant from cultivar Zhonghua11 after ethyl methanesulfonate treatment. The dg1 mutant displayed the dwarfism with small, rolled leaves, which resulted from smaller cells and more bulliform cells. The dg1 mutant also had an enlarged leaf angle and defects in brassinosteroid signaling. In the dg1 mutant, both the rudimentary glume and sterile lemma (glumes) were transformed into lemma-like organ and acquired the lemma identity. Additionally, the dg1 mutant produced slender grains. Further analysis revealed that DG1 affects grain size by regulating cell proliferation and expansion. We fine mapped the dg1 locus to a 31-kb region that includes eight open reading frames. We examined the DNA sequence and expression of these loci, but we were not able to identify the DG1 gene. Therefore, more work will be needed for cloning and functional analysis of DG1, which would contribute to our understanding of the molecular mechanisms behind whole-plant development in rice.

QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9.

BACKGROUND: An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far. RESULTS: In this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5.1 to 30.6 % of phenotypic variations. A novel major QTL qACE9 for the area of chalky endosperm (ACE) was detected in Hainan and Hangzhou, both mapped in the overlapping region on chromosome 9. It was further fine mapped to an interval of 22 kb between two insertion-deletion (InDel) markers IND9-4 and IND9-5 using a BC4F2 population. Gene prediction analysis identified five putative genes, among which only one gene (OsAPS1), whose product involved in starch synthesis, was detected two nucleotide substitutions causing amino acid change between the parents. Significant difference was found in apparent amylose content (AAC) between NILqACE9 and 9311. And starch granules were round and loosely packed in NILqACE9 compared with 9311 by scanning electron microscopy (SEM) analysis. CONCLUSIONS: OsAPS1 was selected as a novel candidate gene for fine-mapped qACE9. The candidate gene not only plays a critical role during starch synthesis in endosperm, but also determines the area of chalky endosperm in rice. Further cloning of the QTL will facilitate the improvement of quality in hybrid rice.

Functional Inactivation of Putative Photosynthetic Electron Acceptor Ferredoxin C2 (FdC2) Induces Delayed Heading Date and Decreased Photosynthetic Rate in Rice.

Ferredoxin (Fd) protein as unique electron acceptor, involved in a variety of fundamental metabolic and signaling processes, which is indispensable for plant growth. The molecular mechanisms of Fd such as regulation of electron partitioning, impact of photosynthetic rate and involvement in the carbon fixing remain elusive in rice. Here we reported a heading date delay and yellowish leaf 1 (hdy1) mutant derived from Japonica rice cultivar "Nipponbare" subjected to EMS treatment. In the paddy field, the hdy1 mutant appeared at a significantly late heading date and had yellow-green leaves during the whole growth stage. Further investigation indicated that the abnormal phenotype of hdy1 was connected with depressed pigment content and photosynthetic rate. Genetic analysis results showed that the hdy1 mutant phenotype was caused by a single recessive nuclear gene mutation. Map-based cloning revealed that OsHDY1 is located on chromosome 3 and encodes an ortholog of the AtFdC2 gene. Complementation and overexpression, transgenic plants exhibited the mutant phenotype including head date, leaf color and the transcription levels of the FdC2 were completely rescued by transformation with OsHDY1. Real-time PCR revealed that the expression product of OsHDY1 was detected in almost all of the organs except root, whereas highest expression levels were observed in seeding new leaves. The lower expression levels of HDY1 and content of iron were detected in hdy1 than WT's. The FdC2::GFP was detected in the chloroplasts of rice. Real-time PCR results showed that the expression of many photosynthetic electron transfer related genes in hdy1 were higher than WT. Our results suggest that OsFdC2 plays an important role in photosynthetic rate and development of heading date by regulating electron transfer and chlorophyll content in rice.

Genetic analysis of flag leaf size and candidate genes determination of a major QTL for flag leaf width in rice.

BACKGROUND: Flag leaf is the most essential organ for photosynthesis in rice and its size plays an important role in rice breeding for ideal plant-type. Flag leaf size affect photosynthesis to a certain extent, thereby influencing rice production. Several genes controlling leaf size and shape have been identified with mutants. Although a number of quantitative trait loci (QTLs) for leaf size and shape have been detected on 12 chromosomes with different populations of rice, few of them were cloned. RESULTS: The pair-wise correlation analysis was conducted on length, width and length-width ratio of the flag leaf, and yield per plant in the core recombinant inbred lines of Liang-You-Pei-Jiu (LYP9) developed in Hainan and Hangzhou. There were significant correlations among the three flag leaf size and shape traits. Interestingly, a positive correlation was found between flag leaf width and yield per plant. Based on the high-resolution linkage map we constructed before, 43 QTLs were detected for three flag leaf size and shape traits and yield per plant, among which 31 QTLs were unreported so far. Seven QTLs were identified common in two environments. And qFLW7.2, a new major QTL for flag leaf width, was fine mapped within 27.1 kb region on chromosome 7. Both qFLW7.2 and qPY7 were located in the interval of 45.30 ~ 53.34 cM on chromosome 7, which coincided with the relationship between yield per plant (PY) and flag leaf width (FLW). CONCLUSION: qFLW7.2, which explained 14% of the phenotypic variation, increased flag leaf width with 93-11 allele. Two candidate genes were selected based on sequence variation and expression difference between two parents, which facilitated further QTL cloning and molecular breeding in super rice.