Seedling Stage In Rice Research Articles

Transcriptome Analysis of the Responses of Rice Leaves to Chilling and Subsequent Recovery.

Improving chilling tolerance at the seedling stage in rice is essential for agricultural research. We combined a physiological analysis with transcriptomics in a variety Dular subjected to chilling followed by recovery at normal temperature to better understand the chilling tolerance mechanisms of rice. Chilling inhibited the synthesis of chlorophyll and non-structural carbohydrate (NSC) and disrupted the ion balance of the plant, resulting in the impaired function of rice leaves. The recovery treatment can effectively reverse the chilling-related injury. Transcriptome results displayed that 21,970 genes were identified at three different temperatures, and 11,732 genes were differentially expressed. According to KEGG analysis, functional categories for differentially expressed genes (DEGs) mainly included ribosome (8.72%), photosynthesis–antenna proteins (7.38%), phenylpropanoid biosynthesis (11.41%), and linoleic acid metabolism (10.07%). The subcellular localization demonstrated that most proteins were located in the chloroplasts (29.30%), cytosol (10.19%), and nucleus (10.19%). We proposed that some genes involved in photosynthesis, ribosome, phenylpropanoid biosynthesis, and linoleic acid metabolism may play key roles in enhancing rice adaptation to chilling stress and their recovery capacity. These findings provide a foundation for future research into rice chilling tolerance mechanisms.

OsABT Is Involved in Abscisic Acid Signaling Pathway and Salt Tolerance of Roots at the Rice Seedling Stage.

Rice is a staple cereal crop worldwide, and increasing its yields is vital to ensuring global food security. Salinity is a major factor that affects rice yield. Therefore, it is necessary to investigate salt tolerance mechanisms in rice. Proteins containing WD40 repeats play important roles in eukaryotic development and environmental adaptation. Here, we showed that overexpression of OsABT, a gene encoding a WD40-repeat protein, enhanced salt tolerance in rice seedlings by regulating root activity, relative conductivity, malondialdehyde and H2O2 content, and O2•− production rate. Root ion concentrations indicated that OsABT overexpression lines could maintain lower Na+ and higher K+/Na+ ratios and upregulated expression of salt-related genes OsSOS1 and OsHAK5 compared with the wild-type (WT) Nipponbare plants. Furthermore, Overexpression of OsABT decreased the abscisic acid (ABA) content, while downregulating the ABA synthesis genes OsNCED3 and OsNCED4 and upregulating the ABA catabolic gene OsABA8ox2. The yeast two-hybrid and bimolecular fluorescence complementation analyses showed that OsABT interacted with the ABA receptor proteins OsPYL4, OsPYL10, and PP2C phosphatase OsABIL2. A transcriptome analysis revealed that the differentially expressed genes between OsABT overexpression lines and WT plants were enriched in plant hormone signal transduction, including ABA signaling pathway under salt stress. Thus, OsABT can improve the salt tolerance in rice seedling roots by inhibiting reactive oxygen species accumulation, thereby regulating the intracellular Na+/K+ balance, ABA content, and ABA signaling pathway.

Identification of QTL under Brassinosteroid-Combined Cold Treatment at Seedling Stage in Rice Using Genotyping-by-Sequencing (GBS).

Cold stress is a major threat to the sustainability of rice yield. Brassinosteroids (BR) application can enhance cold tolerance in rice. However, the regulatory mechanism related to cold tolerance and the BR signaling pathway in rice has not been clarified. In the current study, the seedling shoot length (SSL), seedling root length (SRL), seedling dry weight (SDW), and seedling wet weight (SWW) were used as the indices for identifying cold tolerance under cold stress and BR-combined cold treatment in a backcross recombinant inbred lines (BRIL) population. According to the phenotypic characterization for cold tolerance and a high-resolution SNP genetic map obtained from the GBS technique, a total of 114 QTLs were identified, of which 27 QTLs were detected under cold stress and 87 QTLs under BR-combined cold treatment. Among them, the intervals of many QTLs were coincident under different treatments, as well as different traits. A total of 13 candidate genes associated with cold tolerance or BR pathway, such as BRASSINAZOLE RESISTANT1 (OsBZR1), OsWRKY77, AP2 domain-containing protein, zinc finger proteins, basic helix-loop-helix (bHLH) protein, and auxin-induced protein, were predicted. Among these, the expression levels of 10 candidate genes were identified under different treatments in the parents and representative BRIL individuals. These results were helpful in understanding the regulation relationship between cold tolerance and BR pathway in rice.

Salicylic acid: To assuage salinity stress at the early seedling stage of rice

Being sessile, plants rely on internal modulation of growth and development to cope up with the changing environmental condition. Among the endogenous regulators, salicylic acid has a major role in restoration of plant growth and providing tolerance towards diverse environmental stresses including salinity stress. Seven genotypes FL 478, ADT 45, ADT 46, ADT 50, CR 1009, KKL(R)1, IW Ponni ) were selected  and treated with 100 ppm SA and sown under saline condition(150 mM NaCl). In this experiment the growth parameters like root length, shoot length, root to shoot ratio and biochemical parameters like total chlorophyll and carotenoids were estimated. When rice seeds treated with 100 ppm of SA, the inhibitory effect of salinity stress on growth parameters were alleviated and significant increase in root to shoot ratio were noticed, which is a very important physiological trait for abiotic stress tolerance. Moreover, there is an increase in both chlorophyll and carotenoid content in seedling stage. This shows that, the increased growth parameters might have attributed to the increase in photosynthetic pigments by exogenous application of salicylic acid under salinity stress in rice.

Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice

Rice is the world’s most important food crop, providing the daily calorie intake for more than half of the world’s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly reduce rice productivity. Salinity, one of the major abiotic stresses, reduces rice yield worldwide. This study was conducted to determine new quantitative trait loci (QTLs) that regulate salt tolerance in rice seedlings. One F2:3 mapping population was derived from a cross between BRRI dhan49 (a popular but sensitive rainfed rice variety) and Akundi (a salt-tolerant rice landrace in Bangladesh used as a donor parent). The 1k-Rice Custom Amplicon (1k-RiCA) single-nucleotide polymorphism (SNP) markers were used to genotype this mapping population. After removing segregation distortion and monomorphic markers, 884 SNPs generated a 1526.8 cM-long genetic linkage map with a mean marker density of 1.7 cM for the 12 linkage groups. By exploiting QGene and ICIM-ADD, a sum of 15 QTLs for nine traits was identified in salt stress on seven chromosomes. Four important genomic loci were identified (qSES1, qSL1, qSUR1 and qRL1) on chromosome 1. Out of these 15 QTLs, 14 QTLs are unique, as no other study has mapped in the same chromosomal location. We also detected 15 putative candidate genes and their functions. The ICIM-EPI approach identified 43 significant pairwise epistasis interactions between regions associated with and unassociated with QTLs. Apart from more well-known donors, Akundi serves as an important new donor source for global salt tolerance breeding initiatives, including Bangladesh. The introgression of the novel QTLs identified in this study will accelerate the development of new salt-tolerant varieties that are highly resistant to salt stress using marker-enabled breeding.

Physiological mechanisms of ABA-induced salinity tolerance in leaves and roots of rice

Abscisic acid (ABA) plays a crucial role in response to abiotic stress as important small molecules in regulating metabolism. This study aimed to evaluate the ability of foliar spraying ABA to regulate growth quality at rice seedling stage under salt stress. Results demonstrated that salt stress strongly reduced all the growth parameters of two rice seedlings (‘Chaoyouqianhao’ and ‘Huanghuazhan’), caused prominent decrease in the levels of photosynthetic pigments (mainly in Huanghuazhan), photosynthesis and fluorescence parameters. Salinity treatment increased the concentration of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in roots, whereas significant decreased H2O2 was found in leaves of Huanghuazhan. Additionally, salinity triggered high Na+ content particularly in leaves and enhanced catalase (CAT) activities, ascorbate peroxidase (APX) and peroxidase (POD) activities of the two rice seedlings. Nevertheless, salinity-induced increased root ascorbic acid (AsA) and glutathione (GSH) levels while decreased in leaves, which depended on treatment time. Conversely, ABA application partially or completely mitigated salinity toxicity on the seedlings. ABA could reverse most of the changed physiological parameters triggered by salt stress. Specially, ABA treatment improved antioxidant enzyme levels and significantly reduced the Na+ content of two varieties as well as increased the K+, Mg2+ and Ca2+ content in leaves and roots. ABA treatment increased the hormone contents of 1-aminocclopropane carboxylic acid (ACC), trans-zeatin (TZ), N6-isopentyladenosine (IPA), Indole-3-acetic acid (IAA), and ABA in leaves of two rice varieties under salt stress. It is suggested that ABA was beneficial to protect membrane lipid peroxidation, the modulation of antioxidant defense systems and endogenous hormonal balance with imposition to salt stress.

Deciphering the Molecular Mechanisms of Chilling Tolerance in Lsi1-Overexpressing Rice.

Improving tolerance to low-temperature stress during the rice seedling stage is of great significance in agricultural science. In this study, using the low silicon gene 1 (Lsi1)-overexpressing (Dular-OE) and wild-type rice (Dular-WT), we showed that Lsi1 overexpression enhances chilling tolerance in Dular-OE. The overexpression of the Lsi1 increases silicon absorption, but it was not the main reason for chilling tolerance in Dular-OE. Instead, our data suggest that the overexpression of a Lsi1-encoding NIP and its interaction with key proteins lead to chilling tolerance in Dular-OE. Additionally, we show that the high-mobility group protein (HMG1) binds to the promoter of Lsi1, positively regulating its expression. Moreover, Nod26-like major intrinsic protein (NIP)’s interaction with α and β subunits of ATP synthase and the 14-3-3f protein was validated by co-immunoprecipitation (Co-IP), bimolecular fluorescent complementary (BiFC), and GST-pulldown assays. Western blotting revealed that the overexpression of NIP positively regulates the ATP-synthase subunits that subsequently upregulate calcineurin B-like interacting protein kinases (CIPK) negatively regulating 14-3-3f. Overall, these NIP-mediated changes trigger corresponding pathways in an orderly manner, enhancing chilling tolerance in Dular-OE.

Jasmonic acid alleviates cadmium toxicity through regulating the antioxidant response and enhancing the chelation of cadmium in rice (Oryza sativa L.)

Cadmium (Cd) is a potentially hazardous element with substantial biological toxicity, adversely affecting plant growth and physiological metabolism. Therefore, it is necessary to explore practical and environment-friendly approaches to reduce toxicity. Jasmonic acid (JA) is an endogenous growth regulator which helps plants defend against biological and abiotic stresses. To determine how JA help relieve Cd toxicity in rice, both laboratory and field experiments were implemented. In the seedling stage, the role of JA in mediating rice Cd tolerance was investigated via a fluorescent probe in vivo localization, Fourier Transform Infrared Spectroscopy (FTIR), and colorimetry. At the mature growth stage of rice, field experiments were implemented to research the effects of JA on the Cd uptake and translocation in rice. In the seedling stage of rice, we found that JA application increased the cell wall compartmentalization of Cd by promoting the Cd combination on chelated-soluble pectin of rice roots and inhibited Cd movement into protoplasts, thereby reducing the Cd content in the roots by 30.5% and in the shoots by 53.3%, respectively. Application of JA reduced H2O2 content and helped relieve Cd-induced peroxidation damage of membrane lipid by increasing the level of catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and glutathione (GSH), but had no significant effect on the superoxide dismutase (SOD) activity. Additionally, field experiments showed that foliar spraying of JA inhibited rice Cd transport from the stalk and root to the grain and reduced Cd concentration in grain by 29.7% in the high-Cd fields and 28.0% in the low-Cd fields. These results improve our understanding of how JA contributes to resistance against Cd toxicity in rice plants and reduces the accumulation of Cd in rice kernels.

Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice

Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean rice. After 10 days of salt stress treatment, salt tolerance was evaluated with a standard evaluation system using a visual salt injury score. With 191 Korean landrace accessions and their genotypes, including 266,040 single-nucleotide polymorphisms (SNPs), using a KNU Axiom Oryza 580K Genotyping Array, GWAS was conducted to detect three QTLs with significant SNPs with a −log10(P) threshold of ≥3.66. The QTL of qSIS2, showed −log10(P) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of qSIS4, showed −log10(P) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of qSIS8 showed −log10(P) = 3.78 and the lead SNP explained 7.83% of total phenotypic variation. Among the annotated genes located in these three QTL regions, five genes were selected as candidates (Os04g0481600, Os04g0485300, Os04g0493000, Os04g0493300, and Os08g0390200) for salt tolerance in rice seedlings based on the gene expression database and their previously known functions.

Transcription factor OsMADS25 improves rice tolerance to cold stress.

Cold stress is the limiting factor of rice growth and production, and it is important to clone cold stress tolerant genes and cultivate cold tolerance rice varieties. The MADS transcription factors play an important role in abiotic stress signaling in rice. This study showed that OsMADS25 was up-regulated by low temperature and abscisic acid (ABA), suggesting that OsMADS25 may be involved in ABA-dependent signaling. The OsMADS25 overexpression vector, pCambia1300-221-OsMADS25-Flag, was constructed and introduced into the rice variety Zhonghua 11 (ZH11) through Agrobacterium tumefacian-mediated genetic transformation. Two homozygous lines with high expression levels were selected for phenotypic identification. OsMADS25 overexpression lines show significantly improved cold stress tolerance and the sensitivity to ABA at the seedling stage of rice. Reactive oxygen species (ROS) was detected by diaminobenzidine (DAB) staining and nitroblue tetrazolium (NBT) staining. After treatment with cold stress, little ROS accumulation was observed in OsMADS25 overexpression lines compared to wild-type ZH11. In conclusion, OsMADS25 plays a role in scavenging reactive oxygen species (ROS) and could improve rice tolerance to cold stress involved in ABA-dependent pathway.

The phosphatidylinositol transfer gene Os08PTS regulating the development and nitrogen metabolism in rice seedling stage

The phosphatidylinositol transfer gene Os08PTS regulating the development and nitrogen metabolism in rice seedling stage

Effects of humidity-cold combined stress at the seedling stage in direct-seeded indica rice

Low temperature (LT) and extreme humidity constantly threaten direct-seeded early indica rice production during the seedling stage. However, the physiological mechanism and damage induced by LT combined with high/low humidity are still unclear. A pot experiment was conducted to study seedling growth performance and physiological traits of two indica rice cultivars (i.e., the cold-sensitive cultivar Zhongjiazao17 and the cold-tolerant cultivar Xiangzaoxian6) under LT plus low humidity treatment (LL, 8°C; relative humidity, 25 %), LT plus high humidity treatment (LH, 8°C; relative humidity, 95 %) and a control treatment (CK, 25 °C; relative humidity, 75 %). The results showed that seedling height, rubisco concentration, and APX, PDH and α-KGDH activity significantly decreased under LL and LH compared to CK, and large decreases were found under LH, especially for the cold-sensitive cultivar Zhongjiazao17. However, LH significantly increased the reactive oxygen species O2− and the soluble protein, GSH and ABA concentrations. Moreover, the APX, PDH and α-KGDH activities, rubisco and chlorophyll concentrations, and GA3 induced by LH also significantly decreased after treatment. The differences in physiological traits of Zhongjiazao17 after LL and LH were significant. During three days of recovery, the physiological activity of the two cultivars under LL tended to recover to the level of CK, and the cold-tolerant cultivar showed reduced damage caused by humidity-cold combined stress. The results suggested that the double stress of low temperature plus high humidity rather than low temperature plus low humidity could decrease the growth performance by hampering photosynthetic and respiratory systems and altering the endogenous hormonal regulation of direct-seeded early indica rice, whereas it could significantly enhance the antioxidant protective system derived from the osmotic damage of leaves.

Effects of Coconut Chaff Biochar Amendment on Methane and Nitrous Oxide Emissions from Paddy Fields in Hot Areas

Based on the rice-vegetable crop rotation model, in-situ measurements of nitrous oxide (N2O) and methane (CH4) emissions were conducted in double-cropping rice fields in Hainan to determine the impact of coconut chaff biochar on greenhouse gas emissions. The experiment involved four treatments:conventional farming fertilization (CON), nitrogen fertilizer combined with 20 t ·hm-2 biochar (B1), nitrogen fertilizer combined with 40 t ·hm-2 biochar (B2), and no nitrogen fertilizer, as the control (CK). The N2O and CH4 emissions were measured using static chamber-gas chromatography during the two paddy seasons, and the global warming potential (GWP) and greenhouse gas intensity (GHGI) were also estimated. The results show that N2O emission dynamics during the early rice season are closely related to the mineral nitrogen content of the soil. The N2O is emitted at the rice seedling and tillering stages after fertilization. The cumulative N2O emission during the early rice season was 0.18-0.76 kg ·hm-2. Compared with the CON treatment, the biochar treatments reduced N2O by 18%-43%, and the B2 treatment resulted in a significant reduction. The addition of biochar may promote the reduction of N2O at the early rice seedling stage and increase N2O emissions by improving the soil NO3--N content at the early rice tillering stage. During the late rice season, N2O is emitted during the heading and maturity stages, and the cumulative N2O emission was 0.17-0.34 kg ·hm-2. The B1 treatment reduced emissions by 37%, and B2 increased emission by only 3%, which is not a significant difference. The peak of CH4 emissions from rice fields appeared in the late phase of the early rice season and prophase of the late rice season. The cumulative emission of CH4 in the early rice season was 3.11-14.87 kg ·hm-2. Compared with CON, the CK treatment increased emission by 39%. The biochar treatment may increase soil aeration and limit the ability of CH4 production in the early rice season, as B1 and B2 treatments reduced CH4 emissions by 28% and 71%. The cumulative CH4 emission in late rice season was 53.1-146.3 kg ·hm-2, and the emission dynamics were significantly positively correlated with NH4+-N content. CK and B1 treatments increased CH4 emissions by 52% and 99%, respectively compared with CON, and the B2 treatment significantly increased CH4 emissions by 176%. Compared with CON, the B1 and B2 treatments increased the yield by 12.0% and 14.3% when applied in the early rice season and by 7.6% and 0.4% when applied in the late rice season, respectively. Due to the increased methane emissions in the late rice season, biochar amendment increased the GWP of the double-cropping rice field, in which the high amount of biochar reached a significant level; different amounts of biochar had no significant effect on the GHGI of the double-cropping rice field. Thus, the application of coconut chaff biochar for the reduction of greenhouse gas emission, from rice fields in hot areas, requires further research.

Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

BackgroundCold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding.ResultsIn this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice.ConclusionWe identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45\u20131 at the Seedling Stage in Rice

BackgroundCold stress is the main abiotic stress in rice, which seriously affects the growth and yield of rice. Identification of cold tolerance genes is of great significance for rice to solve these problems. GATA-family transcription factors involve diverse biological functions, however, their role in cold tolerance in rice remains unclear.ResultsIn this study, a GATA-type zinc finger transcription factor OsGATA16, which can improve cold tolerance, was isolated and characterized from rice. OsGATA16 belongs to OsGATA subfamily-II and contains 11 putative phosphorylation sites, a nuclear localization signal (NLS), and other several conserved domains. OsGATA16 was expressed in all plant tissues, with the strongest in panicles. It was induced by cold and ABA treatments, but was repressed by drought, cytokinin and JA, and acted as a transcriptional suppressor in the nucleus. Overexpression of OsGATA16 improves cold tolerance of rice at seedling stage. Under cold stress treatments, the transcription of four cold-related genes OsWRKY45–1, OsSRFP1, OsCYL4, and OsMYB30 was repressed in OsGATA16-overexpressing (OE) rice compared with wild-type (WT). Interestingly, OsGATA16 bound to the promoter of OsWRKY45–1 and repressed its expression. In addition, haplotype analysis showed that OsGATA16 polarized between the two major rice subspecies japonica and indica, and had a non-synonymous SNP8 (336G) associated with cold tolerance.ConclusionOsGATA16 is a GATA transcription factor, which improves cold tolerance at seedling stage in rice. It acts as a positive regulator of cold tolerance by repressing some cold-related genes such as OsWRKY45–1, OsSRFP1, OsCYL4 and OsMYB30. Additionally, OsGATA16 has a non-synonymous SNP8 (336G) associated with cold tolerance on CDS region. This study provides a theoretical basis for elucidating the mechanism of cold tolerance in rice and new germplasm resources for rice breeding.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress

BackgroundRice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.ResultThree main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research.ConclusionsThe results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

Dissipation kinetics and harvest time residues of pyrazosulfuron-ethyl + pretilachlor in rice

The study on dissipation and harvest time residues of pyrazosulfuron-ethyl 0.75% and pretilachlor 30% WG after foliar application at seedling stage in rice at two doses 2000 g/ha (15 + 600 g/ha) and 4000 g/ha (30.0 + 1200 g/ha) was conducted at Integrated Farming System Research Station, Kerala Agricultural University, Thiruvananthapuram, Kerala. The pyrazosulfuron-ethyl and pretilachlor residues were estimated using LCMS/MS. The mean initial deposit of pyrazosulfuron-ethyl at recommended and double the recommended doses were 0.18 and 0.48 mg/kg, respectively. The residue dissipated with time and reached below limit of quantification (LOQ) of 0.01 mg/kg after 5 days in the recommended dose and 7 days in double the recommended dose. The mean initial deposit of pretilachlor at recommended and double the recommended dose were 8.84 and 15.50 mg/kg, respectively. The residue dissipated with time and reached below LOQ of 0.05 mg/kg within 15 days both in the recommended and double the recommended dose. The half-life values (days) were 1.29 and 1.80 for pyrazosulfuron-ethyl and 1.88, 1.37 for pretilachlor at recommended and double the recommended doses, respectively. In addition, the harvest time residues of pyrazosulfuron-ethyl 0.75% + pretilachlor 30% WG were estimated in samples of rice grain, husk, straw and cropped soil and were found below LOQ.

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice.

Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium (LD) decay identified a 230 kb exploratory range for detection of candidate root-related genes. Candidates were filtered using RNA-seq data, gene annotations, and quantitative real-time PCR (qRT-PCR), and five previously characterized genes related to root development were identified, as well as four novel candidate genes. Promoter analysis of candidate genes showed that LOC_Os03g08880 and LOC_Os06g13060 contained SNPs with the potential to impact gene expression in root-related promoter motifs. Haplotype analysis of candidate genes revealed diverse haplotypes that were significantly associated with phenotypic variation. Taken together, these results indicate that LOC_Os03g08880 and LOC_Os06g13060 are strong candidate genes for root development functions. The significant haplotypes identified in this study will be beneficial in future breeding programs for root improvement.

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel.

Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.

Mapping QTLs for tolerance to salt stress at the early seedling stage in rice (Oryza sativa L.) using a newly identified donor \u2018Madina Koyo\u2019

Salt stress is a menace to rice production and a threat to food security worldwide. We evaluated 308 F4 families from Sahel 317/Madina Koyo for tolerance to salt stress at the early seedling stage. To better understand genomic regions controlling tolerance in the population, we genotyped the progenies and the two parents using single nucleotide polymorphism (SNP) markers and regressed the genotypic data on their phenotype to detect QTLs. An average reduction of 63.4% was observed for all fitness-related traits among the F4 families. A total of 46 progenies recorded an average salt injury score (SIS) between 1–3 and were rated as tolerant to salt stress at the early seedling stage. A high-density genetic map was constructed for the 12 rice chromosomes using 3698 SNP markers. Multiple interval mapping identified 13 QTLs for SIS, shoot length, shoot dry weight and root length on chromosomes 2, 3, 4, 6, 7, 10 and 12, with trait increasing alleles coming from both parents. Two (qSDW2 and qRL2.2) and three (qSL2, qRL2.1 and qSIS2) QTLs at different regions on chromosome 2 and another two on chromosome 7 (qSDW7 and qSL7) were tightly linked. These QTLs could facilitate breeding for salt tolerance at the early seedling stage as direct selection for one, would mean indirectly selecting for the other. Fine mapping of these novel QTLs in a different genetic background is necessary to confirm their stability and usefulness in breeding for tolerance to salinity in rice.