High-yielding Rice Research Articles

Curling Leaf 1, Encoding a MYB-Domain Protein, Regulates Leaf Morphology and Affects Plant Yield in Rice.

The leaf is the main site of photosynthesis and is an important component in shaping the ideal rice plant architecture. Research on leaf morphology and development will lay the foundation for high-yield rice breeding. In this study, we isolated and identified a novel curling leaf mutant, designated curling leaf 1 (cl1). The cl1 mutant exhibited an inward curling phenotype because of the defective development of sclerenchymatous cells on the abaxial side. Meanwhile, the cl1 mutant showed significant reductions in grain yield and thousand-grain weight due to abnormal leaf development. Through map-based cloning, we identified the CL1 gene, which encodes a MYB transcription factor that is highly expressed in leaves. Subcellular localization studies confirmed its typical nuclear localization. Transcriptome analysis revealed a significant differential expression of the genes involved in photosynthesis, leaf morphology, yield formation, and hormone metabolism in the cl1 mutant. Yeast two-hybrid assays demonstrated that CL1 interacts with alpha-tubulin protein SRS5 and AP2/ERF protein MFS. These findings provide theoretical foundations for further elucidating the mechanisms of CL1 in regulating leaf morphology and offer genetic resources for practical applications in high-yield rice breeding.

Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties

The development of salt-tolerant rice has become urgent due to climate change and rising global rice consumption. A large-scale analysis using different but related platforms has become imperative to filter out candidate genes responsible for salinity tolerance and salinity stress-responsive pathways. Such genes can be used to find prospective candidate salt resistance genes in donor rice genotypes and transfer them to high-yielding rice varieties. We performed a meta-analysis to screen out candidate genes using stress-related three microarray and one RNASeq datasets from NCBI. As different genotypes of rice and different salinity stress conditions were considered in our analysis, the sensitivity of the results is expected to be multi-fold higher. Our analysis revealed the differentially expressed genes (DEGs) OsbZIP52 and OsLTP2.5 to be common between leaf and root tissues. These genes were further compared with those of the wild halophytic rice Oryza coarctata expression data in stress conditions to understand the significance of these genes. The OsbZIP52 gene homolog of Oryza coarctata was the only one found to be differentially expressed. The expression level of OsbZIP52 was quantified using RT-qPCR and observed downregulated expression in salt stress in root and leaf tissues of four rice cultivars (2 salt-tolerant and 2 salt-sensitive). Promoter and motif analysis revealed a high number of variations in promoter and motif regions of the gene in IR29 salt-sensitive rice. Expression correlation analysis and Gene Ontology study suggested that OsbZIP52 interacts with genes that are engaged in stress response and participate in stress-responsive pathways. Collectively this study increases our understanding of the differential gene expression in various stress conditions in root and leaf tissues. It also helped identify a critical regulatory transcription factor in assisting the plant in combating salinity stress.

Assessment of agronomic performances of aromatic varieties in stations in the senegal river valley (vfs)

Senegal is one of the largest rice importing countries in West Africa with rice production that still fails to meet consumer demands. The State has made great efforts to make up for the deficit in local production by setting up the Program for the Acceleration of the Agricultural Cadence in Senegal (PRACAS) and the National Program for Self-sufficiency in Rice (PNAR), whose objective is to satisfy national demand with a halt in imports. To support this dynamic, the Senegalese Institute for Agricultural Research (ISRA) has revised these research activities with the introduction of a major selection component for new high-yielding rice varieties with good grain quality. It is within this framework, in partnership with BAYER, that the ISRA of Saint Louis is evaluating new varieties of hybrid rice. This study attempts to evaluate the behavior of new hybrid varieties according to two sowing methods in the Senegal River Valley. The material is composed of two hybrid varieties 6444 GOLD and TEJ GOLD and a control Sahel 108. The device is in split-plot with the sowing methods in large plots and the varieties in small plots. The effect of the sowing method on the behavior of the varieties was only noted to be significant on the cycle at maturity; the hybrids have longer cycles than the control Sahel 108 both in direct sowing and in transplanting. The varieties have different agronomic behaviors only on the weight of 1000 seeds, the length of the panicle and the duration of cycles at 50% flowering. The TEJ GOLD variety has a long panicle and a good grain load per panicle. The best performances such as very good tillering ability (6444 GOLD) and good panicle load (TEJ GOLD) were recorded in the hybrids. These hybrids would behave better in direct seeding in terms of yield, unlike the control Sahel 108. From the above, we can say that the introduction of these hybrid varieties could significantly increase rice production and productivity and contribute to achieve our self-sufficiency in rice.

Rice domestication-associated transcription factor PROSTRATE GROWTH 1 controls plant and panicle architecture by regulating the expression of LAZY 1 and OsGIGANTEA, respectively

Plant architecture and panicle architecture are two critical agronomic traits that greatly affect the yield of rice (Oryza sativa). PROSTRATE GROWTH 1 (PROG1) encodes a key C2H2-type zinc-finger transcription factor and has pleiotropic effects on the regulation of both plant and panicle architecture, thereby influencing the grain yield. However, the molecular mechanisms through which PROG1 controls plant and panicle architecture remain unclear. In this study, we showed that PROG1 directly binds the LAZY 1 (LA1) promoter and acts as a repressor to inhibit LA1 expression. Conversely, LA1 acts as a repressor of PROG1 by directly binding to the PROG1 promoter. These two genes play antagonistic roles in shaping plant architecture by regulating both tiller angle and tiller number. Interestingly, our data showed that PROG1 controls panicle architecture through direct binding to the intragenic regulatory regions of OsGIGANTEA (OsGI) and subsequent activation of its expression. Collectively, we have identified two crucial targets of PROG1, LA1 and OsGI, shedding light on the molecular mechanisms underlying plant and panicle architecture control by PROG1. Our study provides valuable insights into the regulation of key domestication-related traits in rice and identifies potential targets for future high-yield rice breeding.

GR5 acts in the G protein pathway to regulate grain size in rice

Grain size is an important determinant of grain yield in rice. Although dozens of grain size genes have been reported, the molecular mechanisms that control grain size remain to be fully clarified. Here, we report the cloning and characterization of GR5 (GRAIN ROUND 5), which is allelic to SMOS1/SHB/RLA1/NGR5 and encodes an AP2 transcription factor. GR5 acts as a transcriptional activator and determines grain size by influencing cell proliferation and expansion. We demonstrated that GR5 physically interacts with five Gγ subunit proteins (RGG1, RGG2, DEP1, GS3, and GGC2) and acts downstream of the G protein complex. Four downstream target genes of GR5 in grain development (DEP2, DEP3, DRW1, and CyCD5;2) were revealed and their core T/CGCAC motif identified by yeast one-hybrid, EMSA, and ChIP–PCR experiments. Our results revealed that GR5 interacts with Gγ subunits and cooperatively determines grain size by regulating the expression of downstream target genes. These findings provide new insight into the genetic regulatory network of the G protein signaling pathway in the control of grain size and provide a potential target for high-yield rice breeding.

Co-Incorporating Chinese Milk Vetch and Rice Straw Increases Rice Yield by Improving Nutrient Uptake during Rice Growth

In the past ten years, in paddy rice systems in southern China, the co-incorporation of Chinese milk vetch (MV) and rice straw (RS) has become a new and effective practice in which the advantages of the two species are combined to improve rice yields. However, more studies are needed to better understand the mechanisms by which rice productivity is improved through this practice. In this study, a pot experiment was performed to investigate the effects of different residue management treatments on rice productivity and soil properties. Five treatments were tested: (i) CK (no residue and no chemical fertilizer); (ii) CF (chemical fertilizer); (iii) FM (CF with MV returning); (iv) FR (CF with RS returning); and (v) FMR (CF with a mixture of MV and RS returning). The results showed that the application of MV and/or RS returning improved grain yields by between 13.7% and 31.5%, compared with CF treatment alone. In addition, the application of MV significantly improved rice yield relative to RS returning. However, co-incorporation of MV and RS resulted in the highest yield productivity of all. FMR treatment significantly increased shoot biomass and shoot N, P, and K uptake, compared with FR treatment, at all three growth stages, and compared with FM treatment at the jointing and maturity stages. Moreover, FMR treatment significantly improved grain N, P, and K uptake, relative to FM and FR treatments. These results clearly demonstrated that co-incorporation management promotes nitrogen and phosphorus nutrient uptake at jointing and maturity stages of the rice growth process, compared to application of single residues alone, resulting in higher rice yields. Because incorporation of MV and/or RS increases the available nutrients in the soil and enhances nutrient uptake by the crop, wide-scale adoption of the co-incorporation of residues would significantly increase rice yields and improve soil fertility.

Influence of Organic Nitrogen Sources on Aromatic Rice (Oryza sativa L.) Cultivation in the Eastern Plateau and Hill Region of India

The field experiment was conducted at farm of Divyayan Krishi Vigyan Kendra, Ramakrishna Mission Ashrama, Ranchi, Jharkhand, India during kharif season of 2021 following the three times replicated randomized block design with 7 organic N sources (control, 100% FYM, 100% vermicompost (VC), 100% Karanj cake (KC), 50% FYM +50% VC, 50% VC +50% KC, 50% FYM +50% KC) to study the response of transplanted aromatic rice to various organic N sources. The results expressed that N applied through manures ensured higher plant response over control and specifically, that through 50% VC +50% KC recorded the maximum plant height, tillers/m2 and leaves/plant. Further, this combined application of VC and KC also recorded maximum productive tillers/m2 (199.3), panicle length (24.1 cm), filled grains/panicle (172.8), test weight (22.9 g), grain yield (7.37 t/ha), straw yield (9.08 t/ha) and harvest index (44.8%) resulting in higher gross return (₹4,83,590/ha), net return (₹3,37,079/ha) and B:C (3.30). 100% N applied through KC remained as the second-best alternative in ensuring high growth, yield and profitability in aromatic rice.

Knocking out OsNAC050 Expression Causes Low-Temperature Tolerance in Rice by Regulating Photosynthesis and the Sucrose Metabolic Pathway

Because rice is native to tropical and subtropical regions, it is generally more sensitive to cold stress compared to other cereals. Low-temperature stress has a strong influence on the growth, development, and yield of rice. Plant NAM, ATAF1/2 and CUC(NAC) transcription factors (TFs) play significant regulatory roles in stress response. In our research, we found that OsNAC050 (LOC_Os03g60080) is mainly expressed in leaves. Cold (4 °C), heat (42 °C), PEG 6000 (20%, w/v), NaCl (200 mM), H2O2 (1%), IAA (100 μM), ABA (100 μM) and GA3 (100 μM) were used to treat wild type (WT) plants. A low temperature further up-regulated OsNAC050 expression. OsNAC050 mutants created using CRISPR-Cas9 gene editing technology showed significantly enhanced tolerance to the low-temperature treatment. The measurement of enzyme activities related to the redox pathway also showed that mutants have stronger viability under low-temperature stress. Comparative transcriptome analysis showed that photosynthesis and soluble sugar metabolism were significantly affected in OsNAC050 mutant lines, suggesting that OsNAC050 may participate in the above molecular pathways in response to low-temperature stress. The results expand our understanding of the molecular mechanisms underlying the responses to cold stress in rice and can provide new strategies for engineering cold tolerance in high-yielding rice varieties.

RESISTANCE OF DOUBLED HAPLOID RICE LINES TO BACTERIAL LEAF BLIGHT (Xanthomonas oryzae pv. oryzae)

Developing new high-yielding rice varieties resistant to bacterial leaf blight (BLB) is an effective strategy for controlling BLB. Several advanced doubled haploid rice lines derived from anther culture previously selected need assessment for BLB resistance. This study aimed to evaluate the resistance of these lines to BLB pathotypes III, IV, and VIII in the vegetative and generative phases. The experiment took place in a greenhouse using 16 rice genotypes comprising 12 doubled haploid rice lines, two commercial check varieties (Inpari 18 and Inpari 34), and a BLB-resistant and susceptible check variety (Code and TN-1, respectively). Inoculation began with the leaf clipping method using a suspension of the pathogen Xanthomonas oryzae pv. oryzae (Xoo) at a concentration of 109 cfu/ml. The results indicated significant influences on disease severity and intensity of BLB of pathotype, genotype, and the interactions between pathotype and genotype, finding their values higher in the vegetative phase. Six doubled haploid lines ranged from resistant to moderately resistant (disease severity 2.0%–10.7%, disease intensity 6.7%–36.8%) to pathotypes III and IV in two growth phases, i.e., HS1-35-1-4, HS4-15-1-9, HS4-15-1-16, HS4-15-1-24, HS4-15-1-26, and HS4-15-1-28. All those doubled haploid lines were susceptible to BLB pathotype VIII in the vegetative phase and moderately susceptible in the generative phase.

Optimum Cultivation Model Increased the Grain Yield of Ratoon Rice and Nitrogen Agronomic Efficiency by Improving Root Morphological Traits and Stubble Character of the Main Rice

The present study investigated the effects of different integrated cultivation treatments on the yield, nitrogen agronomic efficiency (AEN), and growth performance of a ratoon rice system. A two-year field experiment was carried out during 2021–2022 using a randomized block design. Cultivation treatments included the farmers’ practice model (control, CK), high-yield and high-efficiency model (T1), enhanced-high-yield and high-efficiency model (T2), and the no-N model (N0). The grain yield, yield components, root traits, and stubble characteristics were determined. The results showed that T2 treatment significantly increased the grain yield and AEN by 53% and 236%, respectively, compared with CK. Similarly, the stubble weight, non-structure carbohydrate contents, and the root attributes were significantly improved under T2 treatment. The correlation analysis suggested that ratoon rice yield and AEN was significantly and positively correlated with root weight (p < 0.01) and the stubble parameters including stubble weight (p < 0.01), starch content (p < 0.01), and soluble sugar content (p < 0.01). Additionally, a significant and positive correlation between root weight and stubble weight (p < 0.05) was determined in our study. Consequently, our work highlights the benefits of integrating planting density, nitrogen/water management, and other practices to achieve high AEN and grain yield of the ratoon rice by improving root trait and stubble characteristics of the main rice.

RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice.

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

Detection of QTL for High-Temperature Tolerance in Rice Using a High-Density Bin Map

Rice is sensitive to high-temperature stress during almost all stages of growth and development. High-temperature stress has become one of the main factors restricting high yield and superior quality of rice. In this study, recombinant inbred lines (RILs) derived from an indica rice cross between two restorer lines were planted in two years. One sowing date was applied in 2019, and four sowing dates were set in 2020 according to the period of local high temperatures in recent years. Two traits closely related to high-temperature tolerance, heading date (HD), and spikelet fertility (SF) were measured. In each trial, the HD showed a bimodal distribution, whereas SF had a continuous and left-skewed distribution. QTL analysis was performed using a high-density bin map. For HD, a total of six QTL were detected. All of them correspond in position to the cloned genes, among which qHD8 in the DTH8/Ghd8 region showed the largest genetic effect. For SF, a total of eight QTL were detected. Five of them, qSF1, qSF2, qSF3.1, qSF3.2, and qSF8, showed high-temperature tolerance and had an important potential in rice breeding.

Introgression of SUB1 aggravates the susceptibility of the popular rice cultivars Swarna and Savitri to stagnant flooding

Identification of the Sub1 gene for tolerance to flash flooding and its introgression into high-yielding rice cultivars are major targets in rice breeding for flood-prone rice agro-ecosystems for ensuring yield stability. However, knowledge is scant on the response of the modified genotypes under stagnant flooding (SF) to meet the challenge of finding a superior allele that may confer greater resilience to the plant under a stress-prone environment. In pursuance, we have tested the response of Sub1-introgression in two popular rice varieties, Swarna and Savitri to SF by comparing the biochemical factors in the control of flag leaf senescence and its primary production mechanisms of the parental lines’ versus Sub1-introgressed lines. The activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GR), and ascorbate peroxidase (APX) increased while various parameters of primary production like total chlorophyll content, stomatal conductance (gs), normalized difference vegetation index (NDVI) and photosynthetic activity (Pn) decreased progressively with passage of time in the flag leaf of the cultivars during the post-anthesis period and SF-treatment increased the enzyme activity while depressing primary production further. Introgression of Sub1 had no influence on these activities under control conditions but widened the margin of effects under SF. It was concluded that the functional ability of flag leaf in mega rice cultivars like Swarna and Savitri decreased significantly by SF because of an ethylene-mediated promotion of senescence of the flag leaf. The enhancement of antioxidant enzyme activity by SF could not sustain the stability of primary production in the flag leaf. The introgression of the Sub1 gene made the cultivars more vulnerable to SF because the gene induced overexpression of ethylene.

Mild Hydrothermal Treatment for Improving Outturn of Basmati Rice

Hydrothermal treatment of rice, called “Parboiling”, is an ancient traditional process in Asian countries. It consists of soaking rough rice in water and steaming it, and it both reduces the level of grain breakage and increases head yield of rice during milling. However, parboiling of rice is associated with some drawbacks regarding consumer preferences: the loss of its aroma, reduced rice-kernel whiteness and increased kernel hardness. This research study was carried out to develop a mild hydrothermal treatment that could be applied to basmati paddy by controlling hydrothermal treatment, i.e., soaking water temperature, steaming pressure and time. The Basmati 370 paddy variety was used for this study. The results revealed that, by soaking the paddy in hot water (70 ± 2 °C) for 75 min and steaming the soaked paddy for 20 min with non-pressurized steam at atmospheric pressure, and soaking the paddy for 120 min in hot water (70 ± 2 °C) and steaming the soaked paddy for 4 min with pressurized steam (4 kg/cm2), the optimum treatments are achieved. These optimum hydrothermal treatments were able to produce high head rice yield and preserve the basmati aroma, colour, hardness and palatability characteristics similar to non-parboiled basmati rice. Further, nutritional values such as vitamin B and protein content were also significantly preserved by these mild hydrothermal treatments. These optimized treatment combinations achieved minimized grain breakage while increasing head rice yield during milling and, at the same time, preserved basmati aroma, kernel whiteness, cooking and palatability characteristics similar to non-parboiled rice.

The underlying mechanism of variety–water–nitrogen–stubble damage interactions on yield formation in ratoon rice with low stubble height under mechanized harvesting

Agronomic measures are the key to promote the sustainable development of ratoon rice by reducing the damage from mechanical crushing to the residual stubble of the main crop, thereby mitigating the impact on axillary bud sprouting and yield formation in ratoon rice. This study used widely recommended conventional rice Jiafuzhan and hybrid rice Yongyou 2640 as the test materials to conduct a four-factor block design field experiment in a greenhouse of the experimental farm of Fujian Agricultural and Forestry University, China from 2018 to 2019. The treatments included fertilization and no fertilization, alternate wetting and drying irrigation and continuous water flooding irrigation, and plots with and without artificial crushing damage on the rice stubble. At the same time, a 13C stable isotope in-situ detection technology was used to fertilize the pot experiment. The results showed significant interactions among varieties, water management, nitrogen application and stubble status. Relative to the long-term water flooding treatment, the treatment with sequential application of nitrogen fertilizer coupled with moderate field drought for root-vigor and tiller promotion before and after harvesting of the main crop, significantly improved the effective tillers from low position nodes. This in turn increased the effective panicles per plant and grains per panicle by reducing the influence of artificial crushing damage on rice stubble and achieving a high yield of the regenerated rice. Furthermore, the partitioning of 13C assimilates to the residual stubble and its axillary buds were significantly improved at the mature stage of the main crop, while the translocation rate to roots and rhizosphere soil was reduced at the later growth stage of ratooning season rice. This was triggered by the metabolism of hormones and polyamines at the stem base regulated by the interaction of water and fertilizer at this time. We therefore suggest that to achieve a high yield of ratoon rice with low stubble height under mechanized harvesting, the timely application of nitrogen fertilizer is fundamental, coupled with moderate field drying for root-vigor preservation and tiller promotion before and after the mechanical harvesting of the main crop.

The Effects of Paclobutrazol Seed Soaking on Biomass Production and Yield Formation in Direct-Seeded Rice

Direct-seeded rice has been widely adopted in Asia in recent years. However, its low and unstable yields severely limit the increase in rice production and directly affect food security. The aim of this research was to investigate the effects of different concentrations of paclobutrazol seed soaking on the biomass production and yield formation of direct-seeded rice and to find the optimal concentrations to provide a theoretical basis for the high-yielding cultivation of direct-seeded rice. Two rice varieties, Jiyujing and Jijing305, were used in this experiment, and the seeds were soaked in paclobutrazol at concentrations of 0, 50, 100, 150, and 200 mg L−1. The appropriate concentration of paclobutrazol seed soaking increased the yield of direct-seeded rice; this was attributed to the increase in the spikelet per unit area and the seed setting rate. However, the too-high paclobutrazol concentration was not conducive to a yield increase. Regression analysis showed that the appropriate concentration of paclobutrazol seed soaking was 100–105 mg L−1. The appropriate concentration of paclobutrazol for seed soaking ensured the seedling emergence rate; improved the seedling quality, stem tillers, and productive tillers; increased the efficient leaf area, chlorophyll content, and net photosynthetic rate, resulting in an increase in dry matter accumulation; coordinated the source-sink relationship and dry matter distribution; and promoted the material translocation from the “source” to the “sink”. In conclusion, using the appropriate concentration of paclobutrazol for seed soaking is an effective means of obtaining high yields of direct-seeded rice.

An ecological economic comparison between integrated rice-fish farming and rice monocultures with low and high dikes in the Mekong Delta, Vietnam.

This study makes an ecological economic comparison between three different rice farming strategies in the Mekong Delta. Interviews were made with 30 farmers with two crops of rice and low dikes (2RLd), 30 farmers with three crops of rice and high dikes (3RHd) and 18 farmers with two crops of rice and one crop of fish (2RF). 2RF farmers had the highest annual net income and benefit cost ratio, because oflow production costs and high yields of rice and fish. 2RLd farmers had the lowest annual net income. 3RHd had the highest annual rice yield, but also used the highest amount of rice seeds and agrochemicals, generating the lowest benefit cost ratio. Most farmers (70%) preferred two crops because of a higher production efficiency. High dikes and frequent use of pesticidesand fertilizers were seen to decrease the water and rice quality, connectivity and biodiversity in farms with three crops. It is concluded that rice farming with two crops, and especially if integrated with fish and applying IPM, provides a sustainable alternative to rice farming with three crops and high dikes, because it makes use of the high connectivity within the rice-field ecosystem for an efficient production of healthy food through increasedrecycling of nutrients and natural pest control mechanisms.

Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers.

Rice (Oryza sativa L.) is a staple food for more than 50% of the world's population. Rice cultivar improvement is critical in order to feed the world's growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.

Enhanced rice plant (BRRI-28) growth at lower doses of urea caused by diazinon mineralizing endophytic bacterial consortia and explorations of relevant regulatory genes in a Klebsiella sp. strain HSTU-F2D4R

Endophytic biostimulant with pesticide bioremediation activities may reduce agrochemicals application in rice cultivation. The present study evaluates diazinon-degrading endophytic bacteria, isolated from rice plants grown in the fields with pesticide amalgamation, leading to increased productivity in high-yielding rice plants. These endophytes showed capabilities of decomposing diazinon, confirmed by FT-IR spectra analysis. Growth promoting activities of these endophytes can be attributed to their abilities to produce an increased level of IAA content and to demonstrate high level ACC-deaminase activities. Furthermore, these endophytes demonstrated enhanced level of extracellular cellulase, xylanase, amylase, protease and lignin degrading activities. Five genera including Enterobacter, Pantoea, Shigella, Acinetobacter, and Serratia, are represented only by the leaves, while four genera such as Enterobacter, Escherichia, Kosakonia, and Pseudomonas are represented only by the shoots. Five genera including, Klebsiella, Enterobacter, Pseudomonas, Burkholderia, and Bacillus are represented only by the roots of rice plants. All these strains demonstrated cell wall hydrolytic enzyme activities, except pectinase. All treatments, either individual strains or consortia of strains, enhanced rice plant growth at germination, seedling, vegetative and reproductive stages. Among four (I-IV) consortia, consortium-III generated the maximum rice yield under 70% lower doses of urea compared to that of control (treated with only fertilizer). The decoded genome of Klebsiella sp. HSTU-F2D4R revealed nif-cluster, chemotaxis, phosphates, biofilm formation, and organophosphorus insecticide-degrading genes. Sufficient insecticide-degrading proteins belonging to strain HSTU-F2D4R had interacted with diazinon, confirmed in molecular docking and formed potential catalytic triads, suggesting the strains have bioremediation potential with biofertilizer applications in rice cultivation.

Effect of Sowing Date on the Growth Characteristics and Yield of Growth-Constrained Direct-Seeding Rice.

To investigate changes in the yield and physiological characteristics of indica hybrid rice varieties sown on different dates, we evaluated appropriate hybrid rice varieties and their optimal sowing dates in the hilly areas of Sichuan. Three popular indica rice varieties were used as experimental materials, and five sowing dates were set uniformly locally [16 May (SD1), 23 May (SD2), 30 May (SD3), 6 June (SD4), and 13 June (SD5)] to investigate differences in the yield characteristics, growth period, and dry matter accumulation. The results showed that, over the two years, the sowing-to-heading period and overall growth period of the three varieties shortened as the sowing date was delayed, and the difference in yield between the SD1 and SD2 treatments was not significant, owing to higher material accumulation after flowering and higher assimilative material transport capacity. These varieties are both photosensitive and tolerant to low temperatures. Among the three varieties tested, the Huangyouyuehesimiao (V3) cultivar had the highest yield, with 10.75 t ha-1 under the SD2 treatment. The impact of shifting the sowing date on yield components varied. Delaying the sowing date increased and then decreased the number of effective panicles, and the number of grains per panicle and the seed setting rate decreased by differing degrees. In summary, a high yield of indica hybrid rice can be maintained by sowing between 16 and 23 May each year in the study area. It indicated that indica hybrid rice in the hilly rice-producing region of Sichuan is highly adaptable to different sowing dates.