Rice Ecotypes Research Articles

Variability in the responses of rice ecotypes to elevated CO2 based on data from FACE studies in China and Japan: Implications for climate change adaptation

Elevated CO2 increases rice yields, and the response level varies across locations and genotypes. Previous analyses of genotypic variations from diverse Free-Air CO2 Enrichment (FACE) studies lacked specificity, limiting their applicability in simulating the responses of crop growth to elevated CO2. Using meta-analysis approach and the ORYZA (v3) model with historical and projected climatic data, this study evaluated the differences in the responses of rice ecotypes to elevated CO2 and identified adaptive measures. Meta-analytical findings indicated that Chinese inbred indica (indicai) and hybrid indica (indicah) rice exhibited comparable yield response rates (28.4% and 31.1%, respectively) to elevated CO2, surpassing those of Chinese japonica rice and Japanese indicai and japonica rice. Achieving higher adaptation to elevated CO2, exemplified by Chinese indicah rice, necessitates the consideration of balanced yield components, with individual contributions to yield responses ranging from 9.8% to 36.2%. This study highlighted the susceptibility of japonica rice to adverse effects of maximum temperatures on yield component responses to elevated CO2 compared to indicai or indicah rice. Strategic adjustments in sowing dates can enhance rice production under climate change, with high-response genotypes benefiting more from optimal sowing periods. Furthermore, for genotypes with less responsiveness to elevated CO2, augmenting nitrogen application in conjunction with sowing date adjustments was beneficial for yield optimization. This research not only advances our understanding of the diverse adaptation strategies of rice genotypes under varying climatic conditions but also enhances the precision of crop growth simulations by accounting for the varied responses to CO2 enrichment. These insights are pivotal for developing targeted breeding and management practices aimed at enhancing climate resilience in rice production.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Independent genetic differentiation between upland and lowland rice ecotypes within japonica and indica subspecies during their adaptations to different soil‐nitrogen conditions

AbstractThe soil‐nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH4+) and dry fields (mainly in the form of nitrate, NO3−), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE‐related traits among rice landraces as well as the genetic differentiation between NUE‐associated genes and quantitative trait loci (QTLs). The japonica upland and lowland rice ecotypes showed large differences in their NUE‐related traits such as the absorption ability for NH4+ and NO3−. The indica upland and lowland rice exhibited similar performances when cultivated in solutions containing NH4+ or NO3− or when planted in paddy or dry fields. However, the indica upland rice possessed a greater ability to absorb NO3−. We identified 76 QTLs for 25 measured traits using genome‐wide association analysis. The highly differentiated NUE‐associated genes or QTLs between ecotypes were rarely shared by japonica and indica subspecies, indicating an independent genetic basis for their soil‐nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil‐nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the japonica and indica subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil‐nitrogen conditions and have implications for the improvement of NUE.

Exploring the genetic basis of pre-harvest sprouting in rice through a genome-wide association study-based haplotype analysis

Pre-harvest sprouting (PHS) poses a significant global challenge to cereal production, impacting both yield and quality. In this study, we employed genome-wide association studies (GWAS) on diverse rice accessions to identify novel PHS-associated haplotypes. An assessment of 127 cultivated accessions for panicle germination (PHS) and detached grain germination (germination rate of detached grains at the 14th day (D14)) revealed considerable phenotypic variation among rice ecotypes. GWAS analysis identified 91 significant signals at –log10(P-value)>5, including 15 SNPs for PHS and 76 SNPs for D14. A subsequent linkage disequilibrium (LD) block-based GWAS analysis detected 227 significant SNPs for both traits, consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes. Further haplotype analysis identified 32 haplotypes, with 10 specific to cultivated accessions, 19 specific to the wild type, and three shared between them. A phenotypic assessment of major haplotypes revealed significant differences between resistant (Hap1 and Hap2) and susceptible haplotypes (Hap5, Hap27, and Hap28), distinguished by a G/A SNP within a novel gene, Os04g0545200. The identified haplotypes offer promising prospects for haplotype-based breeding aimed at enhancing PHS resistance in rice.

Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito

Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis andenvironmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.

Comparative Transcriptome Analysis Reveals OsBGs and OsGSLs Influence Sugar Transport through Callose Metabolism under Heat Stress in Rice

Heat or high temperature stress have caused huge damage to many crops and have become the largest threat in terms of the future. Although a huge amount of research has been conducted to explore the mechanisms of heat tolerance and many achievements were accomplished, the mechanism by which how heat stress (HS) influences the yield is still unclear. In this study, RNA-seq analysis indicated that nine 1,3-β-glucanases (BGs) belonging to the carbohydrate metabolic pathway were expressed differently during heat treatment. Therefore, we identified the BGs and glucan-synthase-likes (GSLs) in three rice ecotypes and processed the analyses of gene gain and loss, phylogenetic relationship, duplication, and syntenic relationship. We found the possibility of an environmental adaption based on BGs and GSLs during evolution. Submicrostructure and dry matter distribution analysis confirmed that HS might block the endoplasmic sugar transport pathway by increasing callose synthesis, which may lead to decreased yield and quality in rice production. This study provides a new clue regarding rice yield and quality under HS and provides guidance to rice cultivation and heat tolerance breeding.

Polymorphisms in alternative oxidase (AOX) genes from ecotypes of Arabidopsis and rice revealed an environment-induced linkage to altitude and rainfall.

We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were defined to detect non-synonymous SNPs in the AOX ORF, which revealed amino acid (AA) changes in AOX1c, AOX1d and AOX2 from Arabidopsis and AOX1c from rice in comparison to AOX references from Columbia-0 and Japonica ecotypes, respectively. Among these AA changes, Arabidopsis AOX1c_A161E&G165R and AOX1c_R242S revealed a link to high rainfall and high altitude, respectively, while all other changes in Arabidopsis and rice AOX were connected to high altitude and rainfall. Comparative 3D modeling showed that all mutant AOX presented structural differences in relation to the respective references. Molecular docking analysis uncovered lower binding affinity values between AOX and the substrate ubiquinol for most of the identified structures compared to their reference, indicating better enzyme-substrate binding affinities. Thus, our in silico data suggest that the majority of the AA changes found in the available ecotypes will confer better enzyme-subtract interactions and thus indicate environment-related, more efficient AOX activity. This article is protected by copyright. All rights reserved.

Divergent taxonomic responses of below-ground microbial communities to silicate fertilizer and biofertilizer amendments in two rice ecotypes

Using silicate fertilizer and bacterial inoculum as biofertilizer is significant for increasing soil silicon (Si) availability and rice agronomic performance. To use microbial technology for sustainable agriculture, it is crucial to have a deeper knowledge of how microbial populations shift among the plant hosts and related compartments, as well as how they respond to various fertilization models. In this study, the effects of silicate fertilizer, a single bacterial strain Bacillus mucilagniosis as biofertilizer, and their integrated application on soil physiochemical properties and soil microbiota structure, composition, and diversity in two eco-geographically diverse races (Indica and Japonica rice) were evaluated. Plant compartment, cultivar type, and fertilizer treatments contributed to microbiome variation. Indica and Japonica harbor different root microbiota; notably, taxa enriched in the rhizosphere soil were more diverse than in the root. Bacterial genera Leptonema, Azospira, Aquabacterium, Fluviicola, Aquabacterium, Leptonema, and fungal genera Metarhizium, Malassezia, and Cladosporium all were found in the rice core microbiome. Both silicate and biofertilizer applications increase the relative abundance of Betaproteobacteria, Deltaproteobacteria, and Actinobacteria, while suppressing fungal pathogens Alternaria and Fusarium. Silicate and bacterial inoculum applications increased the soil pH, available silicon content (ASi), available phosphorous (AP), available potassium (AK), and organic carbon (OC), while reduced the total nitrogen (N). These changes were also associated with major bacterial phyla Spirochaetes, Bacteroidetes, Actinobacteria, and Proteobacteria, except for Acidobacteria, and fungal phyla Ascomycota, Mortierellomycota and unassigned fungi. Several treatment-specific biomarkers were revealed through Linear discriminant analysis effect size (LEfSe) analysis. In conclusion, the change in the structure of root-associated communities driven by plant compartment and genetics suggests dynamic interactions in the host plant microbiome. Short-term silicate and biofertilizer amendments improved soil physiochemical status and altered bacterial and saprotrophic fungal communities, which have important implications for sustainable rice production.

Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS

BackgroundRice is the world’s second largest food crop and accelerated global climate change due to the intensification of human activities has a huge impact on rice. Research on the evolution of different rice ecotypes is essential for enhancing the adaptation of rice to the unpredictable environments.ResultsThe sequencing data of 868 cultivated and 140 wild rice accessions were used to study the domestication history and signatures of adaptation in the distinct rice ecotypes genome. The different populations had formed distinct rice ecotypes by phylogenetic analyses and were domesticated independently in the two subspecies of rice, especially deepwater and upland rice. The domestication history of distinct rice ecotypes was confirmed and the four predicted admixture events mainly involved gene flow between wild rice and cultivated rice. Importantly, we identified numerous selective sweeps that have occurred during the domestication of different rice ecotypes and one candidate gene (LOC_Os11g21804) for deepwater based on transcriptomic evidence. In addition, many regions of genomic differentiation between the different rice ecotypes were identified. Furthermore, the main reason for the increase in genetic diversity in the ecotypes of xian (indica) rice was the high proportion of alternative allele frequency in new mutations. Genome-wide association analysis revealed 28 QTLs associated with flood tolerance which contained 12 related cloned genes, and 20 candidate genes within 13 deepwater QTLs were identified by transcriptomic and haplotype analyses.ConclusionsThese results enhanced our understanding of domestication history in different rice ecotypes and provided valuable insights for genetic improvement and breeding of rice in the current changing environments.

Volatilome evolution during storage and in vitro starch digestibility of high-power ultrasonication pretreated wholegrain Oryza sativa L.

The potential of high-power ultrasonication (HPU) to enhance the physicochemical stability of bran-containing cereal products has been demonstrated, but the information concerning how the wholegrain volatilome and key quality-related chemical reactions evolve responding to HPU remains scarcely reported. The objective of this work was to examine the headspace volatile fingerprinting features of sonicated wholegrain brown rice (WBR; 400 W, 28 kHz, 30 min) following an accelerated storage testing (37 °C, 20 days), and simultaneously to identify the key chemical reactions induced by ultrasonication. A total of 70 aroma compounds were identified by the untargeted headspace GC–MS, including 9 alkanes, 6 alkenes, 15 aldehydes, 6 furans, 12 ketones, 9 alcohols and 13 miscellaneous compounds. Multivariate statistical analysis demonstrated that HPU pretreatments before a storage process significantly influenced the volatilome evolution, as revealed by a clear classification between sonicated and unsonicated grains. Supervised orthogonal partial least squares discriminant analysis identified the volatiles including acetic acid, pentanoic acid, hexanal, ethyl hexanoate and 2-pentyl-furan as HPU-related markers, inferring that HPU mainly modified the chemical reactions involving lipid decomposition, free fatty acids oxidation and esterification. This was further confirmed by targeted monitoring of lipid peroxidation products, with 13.22–14.84 % of MDA contents reduced (p < 0.05) in sonicated samples after storage. Besides, the ultrasonic effects resulted in a slight improvement of in vitro starch digestibility of WBR samples depending on the rice ecotype. This investigation demonstrated the potential of HPU pretreatments for prolonging the oxidative stability of WBR grains, without significantly compromising digestion properties.

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.

Effects of Paclobutrazol on Growth, Yield and Water Use Efficiency of Rice (Oryza sativa L.) under Drought Stress Condition

Paclobutrazol (PBZ) was reported to increase grain yield of different rice ecotypes via improved tillering ability under rainfed condition. In this study, the effects of PBZ on the shoot and root growth, and water use that might have contributed to higher yield under water-limited conditions were further examined. PSB Rc14 and NSIC Rc222 were grown in pots and subjected to continuously waterlogged (CWL) and drought (DR) treatments with soil moisture content maintained at 20% from 14 days after transplanting (DAT) until maturity. PBZ concentrations (0, 250 and 500 ppm) were sprayed at the onset of water treatments (14 DAT). Results showed that drought treatment significantly altered most of the parameters indicating successful imposition of the stress with the two varieties showing almost similar responses under the two water regimes, especially during maturity. PBZ application in CWL improved tiller number and yield components at a lower concentration and consequently increased grain yield. In drought, PBZ improved tiller number (34-39) starting at 35 DAT which contributed to a higher panicle number at maturity. Additionally, PBZ did not affect the shoot and root growth but reduced water use. Furthermore, the panicle number increased which could be linked to more grain numbers per plant leading to higher grain yields. These higher grain yield and lower water use improved water use efficiency, which required higher PBZ concentration (500 ppm). Overall, PBZ improved the panicle number contributing to a higher grain yield while reducing water use, thereby boosting water use efficiency of rice under drought stress condition.

Genetic analysis of root vascular traits in a population from two temperate japonica rice ecotypes

ABSTRACT The genetic basis for root vascular traits in rice, despite its direct impacts on root axial and radial hydraulic conductivity, has not been widely studied compared with deep rooting traits. We used five phenotyping datasets (i.e. from maturity stage grown in upland field in 2013, and from vegetative and maturity stages grown in upland and lowland fields in 2019) to quantify the genotypic variations and genomic regions of root vascular traits in a temperate japonica mapping population (from lowland Otomemochi (OTM) and upland Yumenohatamochi (YHM)). YHM had larger stele transversal area (STA) and total late metaxylem area (LMXA), as well as higher deep root ratio and total root length at deeper layers (>30 cm) than OTM. Root vascular traits were significantly different among progenies in each dataset, and the size of genotype-by-environment interactions was comparable. Root vascular traits were not positively correlated with deep rooting traits. From the multi-environment analysis of all five datasets, four key genomic regions related to STA in both joint and separate analyses were detected on chromosome 2 (RM3703-RM6379, RM6933-RM3857), chromosome 4 (RM1388-RM5503) and chromosome 12 (RM247-RM155), with the first and third collocated with deep rooting traits. QTL-by-environment interaction was comparable to the main additive effect. This study is the first report on genomic regions of root vascular traits in a japonica mapping population.

Root Characterization of Myanmar Upland and Lowland Rice in Relation to Agronomic and Physiological Traits under Drought Stress Condition

Lowland and upland rice are the two most important rice ecotypes and are grown under different ecosystems of contrasting soil water conditions. The study aimed to characterize root morphological, anatomical, and architectural traits and shoot physiological traits related to agronomic traits in Myanmar lowland and upland rice under drought conditions. Drought experiments were conducted in the field and in the greenhouse. The reduction in root traits under drought was observed in both lowland and upland rice except for the stele and xylem area. Stele area and xylem area were increased under drought in lowland rice while stele area in upland rice was decreased and was not changed in the xylem area. A positive relationship between agronomic traits and root traits of lowland rice was observed including the total number of nodal roots, root number per tiller, and a negative relationship in lateral root density more than anatomical traits. While upland rice illustrated the relationship between root anatomical traits and agronomic traits. In addition, a negative contribution to biomass by photosynthesis rate, stomatal conductance, and transpiration rate was observed in lowland and upland rice. These findings can help improve drought tolerance in rice by selecting the optimal root trait for each rice ecosystem.

Androgenesis in indica rice: A comparative competency in development of doubled haploids.

Rice is critical to global food security which demands immediate attention to meet the ever-growing population. Development of improved variety is the major focus area of research, in which doubled haploid (DH) technology plays a vital role. Since, androgenesis shows its potential in DH production, this method was not capitalized specially in indica rice due to due to its recalcitrant nature to tissue culture. Success of androgenesis is governed by many important factors such as stage of anther, pre-treatment conditions, accurate concentrations of media, and plant growth regulators. Though reports of androgenesis are abundant in rice, most of them either used japonica or a specific cultivar of indica rice ecotypes. In this study, a media combination was established which is successful in producing doubled haploids from F1s of Savitri x Pokkali, IR20 x Mahulata along with the popular indica hybrids of Arize 8433DT, Arize 6453, Arize Bold, and Swift Gold. Out of 12 different media combinations tested, and 5 different durations of cold-treatments studied, N6 media with 2,4-D (2.0 mg/l) and BAP (0.5 mg/l) with 7th day cold pre-treatment was found to be most effective in all of the F1s for callus induction. Among all the F1s, rice hybrid, Arize 8433DT showed highest of 52% callus induction. In case of green shoot regeneration, MS media with NAA (0.5 mg/l), BAP (2.0 mg/l) and Kn (1.0 mg/l) (MS+C4) was found to be the most efficient of six treatments studied with highest of 58.25% regeneration in Arize 8433DT. Further, MS+C4 in combination with proline (5.0 mg/l) increased the regeneration rate to 85.99%. Besides, MS media with NAA (1.0 mg/l), Kn (0.1 mg/l) and 50 g/l sucrose was found to be most efficient for supporting root induction in all F1s. This study claims the establishment of genotype independent androgenic protocol for indica rice which could be capitalized in indica rice improvement.

Display of distinct endogenous phenolic contents in different rice ecotypes grown under normal conditions: a potent biomarker system for sensing growth, stress and adaptability

Phenolic compounds are important bioactive components in plant kingdoms with ubiquitous distribution amid immense structural diversity. They are indispensable in developmental and physiological stages of a plant besides having specific response in protection, adaptability, environmental and climatic resilience. In the present study, total phenolic content (TPC) was evaluated in 9 different rice ecotypes (PB- 1, PB-1121, PB-1509, Pusa-RH-10, CSR-30, PR-126, HKR-47, Govind and Sharbati) belonging to basmati and non-basmati rice varieties. TPC distribution was measured in both shoot and root system at 14 days old seedling stage. In shoot, the average TPC distribution was 254.38 μg of GAE/gm FW, ranged from 170.33 μg to 357.62 μg of GAE/gm FW. For root, the TPC ranged from 64.58 μg to 105.27 μg of GAE/gm Fw with an average of 84.82 μg of GAE/gm FW. Hence, increased TPC was observed in shoots compared to roots, also there was a positive correlation in TPC distribution between shoot and root. Furthermore, the TPC distribution was more profound in shoot and root of basmati varieties compared to non-basmati varieties. Therefore, differential TPC distribution represents significant physiological feature during the developmental process for optimum growth and metabolism within the rice varieties according to their ecological behavior.

Kam Sweet Rice (Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis.

Kam Sweet Rice (KSR) is a special kind of rice landrace that has been domesticated for thousands of years by the local Dong people in southeast Guizhou province, China. KSR has many distinguishing characteristics including strong fragrance; high resistance to diseases, pests, and adverse abiotic conditions; difficulty of threshing; and glutinous texture. There is a lack of systematic research on its genetic diversity. In this study, we analyzed the levels and patterns of genetic diversity and nucleotide variation in 1,481 rice germplasm using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The accessions included 315 KSR resources from southeast Guizhou, 578 rice landraces from six rice-growing ecological zones in Guizhou, 546 rice landraces from nine provinces around Guizhou, and 42 wild rice sources. Genetic diversity and heterozygosity of KSR were both low, and thus KSR might be close to a pure rice line. Population structure analysis showed that KSR was isolated into a single type of rice, which had a large genetic distance and a unique genetic background compared to the local varieties in Guizhou province, indicating that KSR is a special rice ecotype. Haplotype analysis of the target genes showed that the population of KSR was rich in haplotypes for resistance to bacterial blight (Xa23) and rice blast (Pid3), and identified unique haplotypes that were different from those of the six rice ecotypes in Guizhou. This study shows that KSR is an excellent rice germplasm resource, provides important information for the improvement and utilization of rice landraces, and serves as a reference for formulating effective rice conservation measures.

Yield Response of Different Rice Ecotypes to Meteorological, Agro‐Chemical, and Soil Physiographic Factors for Interpretable Precision Agriculture Using Extreme Gradient Boosting and Support Vector Regression

The food security of more than half of the world’s population depends on rice production which is one of the key objectives of precision agriculture. The traditional rice almanac used astronomical and climate factors to estimate yield response. However, this research integrated meteorological, agro‐chemical, and soil physiographic factors for yield response prediction. Besides, the impact of those factors on the production of three major rice ecotypes has also been studied in this research. Moreover, this study found a different set of those factors with respect to the yield response of different rice ecotypes. Machine learning algorithms named Extreme Gradient Boosting (XGBoost) and Support Vector Regression (SVR) have been used for predicting the yield response. The SVR shows better results than XGBoost for predicting the yield of the Aus rice ecotype, whereas XGBoost performs better for forecasting the yield of the Aman and Boro rice ecotypes. The result shows that the root mean squared error (RMSE) of three different ecotypes are in between 9.38% and 24.37% and that of R‐squared values are between 89.74% and 99.13% on two different machine learning algorithms. Moreover, the explainability of the models is also shown in this study with the help of the explainable artificial intelligence (XAI) model called Local Interpretable Model‐Agnostic Explanations (LIME).

Finding a breather for Oryza sativa: Understanding hormone signalling pathways involved in rice plants to submergence stress.

During the course of evolution, different ecotypes of rice (Oryza sativa L.) have evolved distinct strategies to cope with submergence stress. Such contrasting responses are mediated by plant hormones that are principle regulators of growth, developmentand responses to various biotic and abiotic stresses. These hormones act cooperatively and show extensive crosstalk which is mediated by key regulatory genes that serve as nodes of molecular communication. The presence or absence of such genes leads to significant changes in hormone signalling pathways and hence, governs the type of response that the plant will exhibit. As flooding is one of the leading causes of crop loss across all the major rice-producing countries, it is crucial to deeply understand the molecular nexus governing the response to submergence to produce flood resilient varieties. This review focuses on the hormonal signalling pathways that mediate two contrasting responses of the rice plant to submergence stress namely, rapid internode elongation to escape flood waters and quiescence response that enables the plant to survive under complete submergence. The significance of several key genes such as Sub1A-1, SLR1, SD1and SK1/SK2, in defining the ultimate response to submergence has also been discussed.

Relative contribution of different members of OsDREB gene family to osmotic stress tolerance in indica and japonica ecotypes of rice.

Drought/osmotic stress is the single largest production constraint in rain-fed rice cultivation. Different members of the DREB gene family are known to contribute to osmotic stress tolerance. In this study, an attempt was made to understand their relative contribution towards osmotic stress tolerance in indica and japonica ecotypes of rice. Two genotypes (one tolerant and one susceptible) from each ecotype were grown hydroponically, and 21-day-old seedlings were subjected to polyethylene glycol-induced osmotic stress (15% PEG-6000, equivalent to -3.0 bars osmotic potential). The tolerant genotypes CR143 and Moroberekan were found to have superior root traits (total root length, surface area and volume), better plant water status and increased total dry biomass as compared to their susceptible counterparts after 10 days of osmotic stress. Different members of the DREB gene family were differentially induced in response to osmotic shock (1 h after stress) and osmotic stress (24 h after stress), which also differed between the two rice ecotypes. From the gene expression profiles of 10 DREB genes (both DREB1 and DREB2 families), in indica two DREB genes, DREB1B and DREB1G, were significantly correlated with stress tolerance indices, whereas in japonica significant correlations with five DREB genes (DREB1A, DREB1B, DREB1D, DREB1E and DREB2B) were observed. We found that only one member, i.e. DREB1B, showed a significant correlation with drought tolerance indices in both indica and japonica ecotypes. This study provides an overview of the relative contribution of different members of the DREB gene family and their association with drought/osmotic stress tolerance in rice.