Natural variation of Alfin-like family affects seed size and drought tolerance in rice.

The Alfin-like (AL) family is a group of small plant-specific transcriptional factors involved in abiotic stresses in dicotyledon. In an early study, we found an AL gene in rice that was associated with grain yield under drought stress. However, little information is known about the AL family in rice. In this study, AL genes in the rice genome were identified, and the OsAL proteins were found to locate in the nucleus and have no transcriptional self-activation activity. The expression of the OsALs was regulated by different environmental stimulations and plant hormones. Association and domestication analysis revealed that natural variation of most OsALs was significantly associated with yield traits, drought resistance and divergence in grain size in indica and japonica rice varieties. Hap1 of OsAL7.1 and Hap7 of OsAL11 were favorable haplotypes of seed weight and germination under osmotic stress. Furthermore, osal7.1 and osal11 mutants have larger seeds and are more sensitive to abscisic acid and mannitol during germination stage. Overexpressing of OsAL7.1 and OsAL11 in rice weakened the tolerance to drought in the adult stage. Thus, our work provides informative knowledge for exploring and harnessing haplotype diversity of OsALs to improve yield stability under drought stress.

Overexpression of a novel small auxin-up RNA gene, OsSAUR11, enhances rice deep rootedness.

BACKGROUND: Deep rooting is an important factor affecting rice drought resistance. However, few genes have been identified to control this trait in rice. Previously, we identified several candidate genes by QTL mapping of the ratio of deep rooting and gene expression analysis in rice. RESULTS: In the present work, we cloned one of these candidate genes, OsSAUR11, which encodes a small auxin-up RNA (SAUR) protein. Overexpression of OsSAUR11 significantly enhanced the ratio of deep rooting of transgenic rice, but knockout of this gene did not significantly affect deep rooting. The expression of OsSAUR11 in rice root was induced by auxin and drought, and OsSAUR11-GFP was localized both in the plasma membrane and cell nucleus. Through an electrophoretic mobility shift assay and gene expression analysis in transgenic rice, we found that the transcription factor OsbZIP62 can bind to the promoter of OsSAUR11 and promote its expression. A luciferase complementary test showed that OsSAUR11 interacts with the protein phosphatase OsPP36. Additionally, expression of several auxin synthesis and transport genes (e.g., OsYUC5 and OsPIN2) were down-regulated in OsSAUR11-overexpressing rice plants. CONCLUSIONS: This study revealed a novel gene OsSAUR11 positively regulates deep rooting in rice, which provides an empirical basis for future improvement of rice root architecture and drought resistance.

Coordination of growth and drought responses by GA-ABA signaling in rice.

The drought caused by global warming seriously affects the crop growth and agricultural production. Plants have evolved distinct strategies to cope with the drought environment. Under drought stress, energy and resources should be diverted from growth toward stress management. However, the molecular mechanism underlying coordination of growth and drought response remains largely elusive. Here, we discovered that most of the gibberellin (GA) metabolic genes were regulated by water scarcity in rice, leading to the lower GA contents and hence inhibited plant growth. Low GA contents resulted in the accumulation of more GA signaling negative regulator SLENDER RICE 1, which inhibited the degradation of abscisic acid (ABA) receptor PYL10 by competitively binding to the co-activator of anaphase-promoting complex TAD1, resulting in the enhanced ABA response and drought tolerance. These results elucidate the synergistic regulation of crop growth inhibition and promotion of drought tolerance and survival, and provide useful genetic resource in breeding improvement of crop drought resistance.

Ubiquitin ligase OsRINGzf1 regulates drought resistance by controlling the turnover of OsPIP2;1.

Water is crucial for plant growth and survival. The transcellular water movement is facilitated by aquaporins (AQPs) that rapidly and reversibly modify water permeability. The abundance of AQPs is regulated by its synthesis, redistribution and degradation. However, the molecular mechanism of proteasomal degradation of AQPs remains unclear. Here, we demonstrate that a novel E3 ligase, OsRINGzf1, mediated the degradation of AQPs in rice. OsRINGzf1 is the candidate gene from a drought-related quantitative trait locus (QTL) on the long arm of chromosome 4 in rice (Oryza sativa) and encodes a Really Interesting New Gene (RING) zinc finger protein 1. OsRINGzf1 possesses the E3 ligase activity, ubiquitinates and mediates OsPIP2;1 degradation, thus reducing its protein abundance. The content of OsPIP2;1 protein was decreased in OsRINGzf1 overexpression (OE) plants. The degradation of OsPIP2;1 was inhibited by MG132. The OsRINGzf1 OE plants, with higher leaf-related water content (LRWC) and lower leaf water loss rate (LWLR), exhibited enhanced drought resistance, whereas the RNAi and knockout plants of OsRINGzf1 were more sensitive to drought. Together, our data demonstrate that OsRINGzf1 positively regulates drought resistance through promoting the degradation of OsPIP2;1 to enhance water retention capacity in rice.

A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population.

Increasing agricultural productivity is one of the most important goals of plant science research and imperative to meet the needs of a rapidly growing population. Rice (Oryza sativa L.) is one of the most important staple crops worldwide. Grain size is both a major determinant of grain yield in rice and a target trait for domestication and artificial breeding. Here, a genome-wide association study of grain length and grain width was performed using 996,722 SNP markers in 270 rice accessions. Five and four quantitative trait loci were identified for grain length and grain width, respectively. In particular, the novel grain size gene OsSNB was identified from qGW7, and further results showed that OsSNB negatively regulated grain size. Most notably, knockout mutant plants by CRISPR/Cas9 technology showed increased grain length, width, and weight, while overexpression of OsSNB yielded the opposite. Sequencing of this gene from the promoter to the 3'-untranslated region in 168 rice accessions from a wide geographic range identified eight haplotypes. Furthermore, Hap 3 has the highest grain width discovered in japonica subspecies. Compared to other haplotypes, Hap 3 has a 225 bp insertion in the promoter. Based on the difference between Hap 3 and other haplotypes, OsSNB_Indel2 was designed as a functional marker for the improvement of rice grain width. This could be directly used to assist selection toward an improvement of grain width. These findings suggest OsSNB as useful for further improvements in yield characteristics in most cultivars.

An APETALA2/ethylene responsive factor, OsEBP89 knockout enhances adaptation to direct-seeding on wet land and tolerance to drought stress in rice.

Water stress is the most important adverse factor limiting rice production. Too much water leads to flood and too little leads to drought. Floods and droughts can severely damage crop at different times of the rice life cycle. So the research on submergence tolerance and drought resistance of rice is particularly urgent. In this study, we reported that OsEBP89 (Oryza sativa Ethylene-responsive element binding protein, clone 89), a member of the AP2/ERF subfamily, is involved in a novel signal transduction associated with the tolerance to drought and submergence stress. OsEBP89 was found to be strongly inhibited by drought stress and promoted by submergence. The OsEBP89 protein was located at the nucleus in the rice protoplast. Loss of OsEBP89 was found to improve the seed germination under submerged conditions and also enhanced the tolerance to drought stress throughout growth stage. Additionally, OsEBP89 knockout rice plants increased the accumulation of proline, improved the ability to scavenge ROS compared to overexpression lines and wild type after PEG treatment. Transcriptome data indicates that knockout of OsEBP89 improved the expression of specific genes in response to adverse factors, such as OsAPX1, OsHsfA3, and OsP5CS. Further results indicate that OsEBP89 can interact with and be phosphorylated by SnRK1α (sucrose non-fermenting-1-related protein kinase-1 gene). These findings provide insight into the mechanism of abiotic stress tolerance, and suggest OsEBP89 as a new genetic engineering resource to improve abiotic stress tolerance in rice.

A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative tolerance in rice.

BACKGROUND: Drought is a major abiotic stress factor that influences the yield of crops. Basic leucine zipper motif (bZIP) transcription factors play an important regulatory role in plant drought stress responses. However, the functions of a number of bZIP transcription factors in rice are still unknown. RESULTS: In this study, a novel drought stress-related bZIP transcription factor, OsbZIP62, was identified in rice. This gene was selected from a transcriptome analysis of several typical rice varieties with different drought tolerances. OsbZIP62 expression was induced by drought, hydrogen peroxide, and abscisic acid (ABA) treatment. Overexpression of OsbZIP62-VP64 (OsbZIP62V) enhanced the drought tolerance and oxidative stress tolerance of transgenic rice, while osbzip62 mutants exhibited the opposite phenotype. OsbZIP62-GFP was localized to the nucleus, and the N-terminal sequence (amino acids 1-68) was necessary for the transcriptional activation activity of OsbZIP62. RNA-seq analysis showed that the expression of many stress-related genes (e.g., OsGL1, OsNAC10, and DSM2) was upregulated in OsbZIP62V plants. Moreover, OsbZIP62 could bind to the promoters of several putative target genes and could interact with stress/ABA-activated protein kinases (SAPKs). CONCLUSIONS: OsbZIP62 is involved in ABA signalling pathways and positively regulates rice drought tolerance by regulating the expression of genes associated with stress, and this gene could be used for the genetic modification of crops with improved drought tolerance.

Neutrophil to Lymphocyte Ratio as a Novel Predictor of Outcome in Patients With Severe Traumatic Brain Injury.

OBJECTIVE: The neutrophil to lymphocyte ratio (NLR) has been reported to be a predictor of outcome in critical illness. Objective of this study was to investigate the changes of the NLR in patients with severe traumatic brain injury (TBI) and analyze the relationship between the NLR and TBI outcome. SETTING: China. PARTICIPANTS: A total of 855 patients with severe TBI from January 2007 to April 2012. DESIGN: Retrospective. MAIN MEASUREMENT: Data on the NLR and other indicators were collected. After follow-up until death or 1 year, the relationship between the NLR and TBI outcome was analyzed retrospectively. RESULTS: The final analysis included 688 patients. There were 508 (73.8%) who had an unfavorable outcome by 1 year after head trauma. The value of the NLR on admission was significantly higher in the unfavorable outcome group than in the favorable outcome group (P < .001). Multivariate logistic analysis showed that higher NLR was associated with an unfavorable outcome (odds ratio, 1.100; P < .001). Receiver operating characteristic curve analysis showed that the NLR had a sensitivity of 60.2% and a specificity of 71.1% for predicting unfavorable outcome at 1 year on the basis of the best threshold. CONCLUSION: The NLR might be useful as a novel predictor for 1-year outcome and mortality in severe TBI.

OsGRAS23, a rice GRAS transcription factor gene, is involved in drought stress response through regulating expression of stress-responsive genes.

BACKGROUND: Drought is a major abiotic stress factors that reduces agricultural productivity. GRAS transcription factors are plant-specific proteins that play diverse roles in plant development. However, the functions of a number of GRAS genes identified in rice are unknown, especially the GRAS genes related to rice drought resistance have not been characterized. RESULTS: In this study, a novel GRAS transcription factor gene named OsGRAS23, which is located in a drought-resistant QTL interval on chromosome 4 of rice, was isolated. The expression of OsGRAS23 was induced by drought, NaCl, and jasmonic acid treatments. The OsGRAS23-GFP fused protein was localized in the nucleus of tobacco epidermal cells. A trans-activation assay in yeast cells demonstrated that the OsGRAS23 protein possessed a strong transcriptional activation activity. OsGRAS23-overexpressing rice plants showed improved drought resistance and oxidative stress tolerance as well as less H2O2 accumulation compared with the wild-type plants. Furthermore, microarray analysis showed that several anti-oxidation related genes were up-regulated in the OsGRAS23-overexpressing rice plants. The yeast one hybrid test indicated that OsGRAS23 could bind to the promoters of its potential target genes. CONCLUSIONS: Our results demonstrate that OsGRAS23 encodes a stress-responsive GRAS transcription factor and positively modulates rice drought tolerance via the induction of a number of stress-responsive genes.

Micro-polluted water source purification of root channel wetland in Jiaxing, China.

Root channel wetlands, as a new type of nature-imitating wetland system, provide a paradigm for micro-polluted water source purification; however, there is a knowledge gap on root channel wetlands' pollution removal effects and their main influencing factors after longtime operation. This study collected the turbidity, ammonia nitrogen (NH3-N), total nitrogen (TN), total phosphorus (TP), permanganate index (CODMn), dissolved oxygen (DO), and chemical oxygen demand (COD) at the inlet and outlet of Shijiuyang (SJY) wetland and Guanjinggang (GJG) wetland in Jiaxing City, China, from 2019 to 2021. The results showed that root channel wetlands had better water quality improvement effects. The SJY wetland had larger removal rates for DO, CODMn, and turbidity compared with the GJG wetland. In contrast, other water quality indexes have similar removal rates at both wetlands. The influencing factor analysis showed that water purification agent, flow, pH, and water temperature have large influences on the removal rates of pollutants for both wetlands. To address high turbidity and excessive DO, which are the primary pollutants affecting the two wetlands, implementing the diversion river before the pretreatment area and incorporating ecological floating beds in the deep purification area are recommended solutions to mitigate these issues. Compared with conventional general constructed wetlands, root channel wetlands are a more cost-effective and sustainable technology. The research is conducive to improving understanding of root channel wetland purification for micro-polluted water sources and enhancing water supply security capability in the plains water network area of the Yangtze River Delta region. PRACTITIONER POINTS: Compared with conventional general constructed wetlands, root channel wetlands are more cost-effective and sustainable technology. The SJY wetland demonstrated better removal rates for DO, CODMn, and turbidity, indicating a higher purification capacity compared to GJG wetland. Flow rate and pH are the primary factors influencing the GJG wetland, while the waterpurification agent and water temperature are the main factors affecting water quality in the SJY wetland.

Autotetraploidy of rice does not potentiate the tolerance to drought stress in the seedling stage.

Polyploid is considered an advantage that has evolved to be more environmentally adaptable than its diploid. To understand if doubled chromosome of diploid rice can improve drought tolerance, we evaluated the diploid (2X) and autotetraploid (4X) plants of three indica and three japonica varieties. Drought stress in the plastic bucket of four-leaf stage revealed that the drought tolerance of 4X plants was lower than that of its diploid donor plants. The assay of photosynthetic rate of all varieties showed that all 4X varieties had lower rates than their diploid donors. The capacity for reactive oxygen species production and scavenging varied among different 2X and 4X varieties. Further, transcriptomic analysis of 2X and 4X plants of four varieties under normal and drought condition showed that the wide variation of gene expression was caused by difference of varieties, not by chromosome ploidy. However, weighted gene co-expression network analysis (WGCNA) revealed that the severe interference of photosynthesis-related genes in tetraploid plants under drought stress is the primary reason for the decrease of drought tolerance in autotetraploid lines. Consistently, new transcripts analysis in autotetraploid revealed that the gene transcription related with mitochondrion and plastid of cell component was influenced most significantly. The results indicated that chromosome doubling of diploid rice weakened their drought tolerance, primarily due to disorder of photosynthesis-related genes in tetraploid plants under drought stress. Maintain tetraploid drought tolerance through chromosome doubling breeding in rice needs to start with the selection of parental varieties and more efforts.

Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations.

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log10(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.

Pentatricopeptide Repeat Gene-Mediated Mitochondrial RNA Editing Impacts on Rice Drought Tolerance.

Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.

Elevated cerebrospinal fluid protein levels associated with poor short-term outcomes after spinal cord stimulation in patients with disorders of consciousness.

Background: Spinal cord stimulation (SCS) is a promising treatment for patients with disorders of consciousness (DoC); however, the laboratory examinations and different electrodes (permanent #39286 vs. temporary percutaneous #3777, Medtronic, USA) that are associated with postoperative outcomes are unclear. The study aims to study the association between the change in postoperative cerebrospinal fluid (CSF) protein level and improvement in consciousness after SCS in DoC patients and to explore whether different electrodes were associated with elevated CSF protein levels. Materials and methods: A total of 66 DoC patients who received SCS treatment from December 2019 to December 2021 were retrospectively analyzed. Patients were grouped according to their elevated CSF protein level. The clinical characteristics of the patients and SCS stimulation parameters were compared. The preoperative sagittal diameter of the spinal canal is the distance from the midpoint of the posterior border of the vertebral body to the midpoint of the posterior wall of the spinal canal at the level of the superior border of C3. The postoperative sagittal diameter of the spinal canal is the distance from the midpoint of the posterior edge of the vertebral body to the anterior edge of the stimulation electrode. Patients with improved postoperative CRS-R scores greater than 3 or who progressed to the MCS + /eMCS were classified as the improved group and otherwise regarded as poor outcome. Results: We found that more DoC patients had elevated CSF protein levels among those receiving SCS treatment with permanent electrodes than temporary percutaneous electrodes (P = 0.001), and elevated CSF protein levels were significantly associated with a reduced sagittal diameter (P = 0.044). In DoC patients receiving SCS treatment, we found that elevated CSF protein levels (P = 0.022) and preoperative diagnosis (P = 0.003) were significantly associated with poor outcomes at 3 months. Logistic regression analysis showed that elevated CSF protein levels were significantly associated with poor outcomes (OR 1.008, 95% CI 1.001-1.016, P = 0.032). Conclusion: The results suggest that reducing the effect of electrode pads on anatomical changes may help improve the outcomes of DoC patients receiving SCS treatment. CSF protein levels are associated with poor postoperative outcomes and whether they are potential biomarkers in DoC patients receiving SCS treatment remain further exploration.

Overexpressing PpBURP2 in Rice Increases Plant Defense to Abiotic Stress and Bacterial Leaf Blight.

Mosses are one of the earliest diverging land plants that adapted to living on land. The BURP domain-containing proteins (BURP proteins) are plant-specific proteins that appeared when plants shifted from aquatic environments to land. Phylogenetic analysis revealed that the BURP domain of higher plants is originated from lower land plants and divergent because of motif conversion. To discover the function of BURP protein in moss, rice transgenics with ectopic expression of PpBURP2 were subjected to different abiotic stresses treatments. The results revealed that the ectopic expression of PpBURP2 enhanced the tolerance to osmotic and saline stresses at the seedling stage and drought stress at the adult stage. Further ectopic expression of PpBURP2 improved the cadmium (2+) (Cd2+) tolerance and reduced Cd2+ accumulation in rice leaves. Transcriptomic analysis of the transgenic PpBURP2 plants showed that the differentially expressed genes were involved in the metabolism of secondary metabolites, energy, oxidation-reduction process, and defense-related genes. Further experiments showed that the photosynthetic efficiency and resistance against bacterial leaf blight were obviously improved in transgenic plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays revealed the physical interaction of BURP domain protein from rice and moss with mitogen-activated protein kinase kinase (MKK) from rice. Therefore, our findings demonstrate that overexpressing PpBURP2 in rice confers resistance to abiotic stresses and bacterial leaf blight. They also suggested that the regulatory role of BURP-like proteins across lower and higher plants was evolutionary conservation of responses of different classes of plants to different environmental challenges.

Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression.

Drought stress adversely affects crop growth and productivity worldwide. In response, plants have evolved several strategies in which numerous genes are induced to counter stress. High mobility group (HMG) proteins are the second most abundant family of chromosomal proteins. They play a crucial role in gene transcriptional regulation by modulating the chromatin/DNA structure. In this study, we isolated a novel HMG gene, OsHMGB707, one of the candidate genes localized in the quantitative trait loci (QTL) interval of rice drought tolerance, and examined its function on rice stress tolerance. The expression of OsHMGB707 was up-regulated by dehydration and high salt treatment. Its overexpression significantly enhanced drought tolerance in transgenic rice plants, whereas its knockdown through RNA interference (RNAi) did not affect the drought tolerance of the transgenic rice plants. Notably, OsHMGB707-GFP is localized in the cell nucleus, and OsHMGB707 is protein-bound to the synthetic four-way junction DNA. Several genes were up-regulated in OsHMGB707-overexpression (OE) rice lines compared to the wild-type rice varieties. Some of the genes encode stress-related proteins (e.g., DREB transcription factors, heat shock protein 20, and heat shock protein DnaJ). In summary, OsHMGB707 encodes a stress-responsive high mobility group protein and regulates rice drought tolerance by promoting the expression of stress-related genes.

Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene.

Salinity is one of the most important abiotic stress affecting the world rice production. The cultivation of salinity-tolerant cultivars is the most cost-effective and environmentally friendly approach for salinity control. In recent years, CRISPR/Cas9 systems have been widely used for target-site genome editing; however, their application for the improvement of elite rice cultivars has rarely been reported. Here, we report the improvement of the rice salinity tolerance by engineering a Cas9-OsRR22-gRNA expressing vector, targeting the OsRR22 gene in rice. Nine mutant plants were identified from 14 T0 transgenic plants. Sequencing showed that these plants had six mutation types at the target site, all of which were successfully transmitted to the next generations. Mutant plants without transferred DNA (T-DNA) were obtained via segregation in the T1 generations. Two T2 homozygous mutant lines were further examined for their salinity tolerance and agronomic traits. The results showed that, at the seedling stage, the salinity tolerance of T2 homozygous mutant lines was significantly enhanced compared to wild-type plants. Furthermore, no significantly different agronomic traits were found between T2 homozygous mutant lines and wild-type plants. Our results indicate CRISPR/ Cas9 as a useful approach to enhance the salinity tolerance of rice.

A novel gene OsAHL1 improves both drought avoidance and drought tolerance in rice.

A novel gene, OsAHL1, containing an AT-hook motif and a PPC domain was identified through genome-wide profiling and analysis of mRNAs by comparing the microarray of drought-challenged versus normally watered rice. The results indicated OsAHL1 has both drought avoidance and drought tolerance that could greatly improve drought resistance of the rice plant. Overexpression of OsAHL1 enhanced multiple stress tolerances in rice plants during both seedling and panicle development stages. Functional studies revealed that OsAHL1 regulates root development under drought condition to enhance drought avoidance, participates in oxidative stress response and also regulates the content of chlorophyll in rice leaves. OsAHL1 specifically binds to the A/T rich sequence region of promoters or introns, and hence directly regulates the expression of many stress related downstream genes.

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes.

Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.