Rice Recombinant Inbred Lines Research Articles

Breeding Rice to Increase Anthocyanin Yield Per Area through Small, Black Grain Size and Three Grains per Spikelet

Rice varieties with high anthocyanin content are often recognized for their vibrant colors and health benefits. The demand for rice with high anthocyanin is increasing domestically and internationally due to consumers becoming more health-conscious. However, the current increase in yield might not raise the anthocyanin content due to its location in the grain pericarp and seed coat, which are relative to the grain surface area. This study aims to develop rice lines to increase anthocyanin yield per production area by improving rice varieties with small, black, and three grains per spikelet. Accordingly, six rice recombinant inbred lines (RILs) were bred by crossing Niaw Dam Chaw Mai Pai 49 (NDCMP49) with Khao Nok (LLR059). The grain color, size, and number of grains per spikelet were selected from the F1 to the F4 population through the pedigree selection method. Six RILs and their parents were assigned in a randomized complete block design (RCBD) with three replications under field conditions during the rainy season of 2021 and 2022 in four locations. The results showed statistically significant differences in environmental conditions, affecting productivity and the yield components of rice lines. Consequently, the rice lines adapted to a specific environment, and there were significant differences in genotype. This study identified three RILs with higher yield performance (13-1 (3842 kg/ha), 374-1 (3699 kg/ha), and 903-3 (3550 kg/ha)) compared with the parent NDCMP49 (1996 kg/ha). However, the grain yields were unstable in the three top-yielding RILs due to varying environmental conditions, indicating that selective breeding requires a specific, narrow environment. Based on grain yield and grain size, the RILs performed better in the grain surface area than in the parent NDCMP49. Moreover, only two RILs (374-1 and 903-3) produced the highest anthocyanin content and yield, although this was lower than in the parent NDCMP49. However, the 374-1 and 903-3 RILs produced more grains, black grains, and three grains per spikelet with high yield and moderate anthocyanin content. They can, therefore, be backcrossed to the parent NDCMP49 to increase the accumulated anthocyanin content with a stable, high yield. This work provides a resource of small grains, black grains, and three grains per spikelet in the rice breeding line for breeding programs in the future.

Variation in Crude Protein Content among Recombinant Inbred Lines of Rice (Oryza sativa L.)

Rice, Oryza sativa L., is the world's most important staple crop, feeding more than half of the world's population, protein plays important role in human nutrition. Protein is the second most abundant storage matter in rice grain. Protein, crucial for growth, antibody production, and immunity, ranks as the second most abundant storage component in rice grains. Various factors, including grain protein content, amino acid composition, and fat content, influence the nutritional quality of rice, with grain protein content being particularly significant. This study conducted screening and evaluation of crude protein content across 200 recombinant inbred lines of rice, derived from an inter-specific cross between BPT5204 and HPR14 parents. Results indicated a range of total crude protein content from 14.99 (mg/g) to 28.11 (mg/g) among samples. Grouping analysis based on available crude protein content categorized the lines into three major groups: approximately 3% (7 lines) exhibited significantly higher protein content (>25mg/g), 59% (119 lines) displayed moderate content (20 mg/g to 25 mg/g), and 38% (76 lines) showed low protein content (<20 mg/g). The identification of high protein content genotypes in this study holds potential for mapping key genomic regions associated with protein content in rice.

Principal Component Analysis of Yield and Its Attributing Traits in Recombinant Inbred Lines of Rice Under Submerged Condition (Oryza sativa L.)

Rice, Oryza sativa L., is the world's most important staple crop, feeding more than half of the world's population. The phenotype of plant is the result of interaction of many factors and final yield is the sum of total effect of several component factors. Therefore evaluation of genetic variability forms the basis for any crop improvement programme, the success of which depends on sufficient genetic variability among genotypes so as to permit effective selection. Hence Evaluation of Principle Component Analysis (PCA)of recombinant inbred lines (RILs) was done at phenotypic level under submerged conditions to reduce a large series of data into smaller number of components by looking for groups that have very strong inter-correlation in a set of variables and each component explained per cent variation to the total variability. The RIL population was derived from an inter-specific cross between BPT5204 and HPR14 parents. A study was conducted using 1256 Recombinant Inbreed Lines submerged condition in the two seasons at College of Agriculture V.C. Farm, Mandya with nine agro-morphological traits and a principle component analysis was carried out. Out of nine principle components, four exhibited Eigenvalue more than one governing 77.74% variance and 69.86% variance in the summer and kharif seasons respectively. The highest positive Eigenvalue was observed for total number of tillers, productive tillers, non-productive tillers and fallowed by single plant yield in PC1 in the summer and kharif season respectively. The highest positive Eigenvalue was observed for five panicle weight, single panicle length, single plant yield and plant height in PC2 of summer and kharif season respectively. Indicating their pronounced effect on the overall variation in the Recombinant Inbreed Lines of Rice.

High-throughput UAV-based rice panicle detection and genetic mapping of heading-date-related traits.

Rice (Oryza sativa) serves as a vital staple crop that feeds over half the world's population. Optimizing rice breeding for increasing grain yield is critical for global food security. Heading-date-related or Flowering-time-related traits, is a key factor determining yield potential. However, traditional manual phenotyping methods for these traits are time-consuming and labor-intensive. Here we show that aerial imagery from unmanned aerial vehicles (UAVs), when combined with deep learning-based panicle detection, enables high-throughput phenotyping of heading-date-related traits. We systematically evaluated various state-of-the-art object detectors on rice panicle counting and identified YOLOv8-X as the optimal detector. Applying YOLOv8-X to UAV time-series images of 294 rice recombinant inbred lines (RILs) allowed accurate quantification of six heading-date-related traits. Utilizing these phenotypes, we identified quantitative trait loci (QTL), including verified loci and novel loci, associated with heading date. Our optimized UAV phenotyping and computer vision pipeline may facilitate scalable molecular identification of heading-date-related genes and guide enhancements in rice yield and adaptation.

Principal Component Analysis of Grain Yield and its Attributing Traits in Recombinant Inbred Lines of Rice (Oryza sativa L.) Developed for Submergence Tolerance

Submergence is an important abiotic stress affecting yield and productivity of rice. There are many landraces such as AC 42088, AC 42087 and AC 38575 which show tolerance to long duration flooding. These landraces can be used as donors in breeding programs for development of improved varieties which show increased yield as well as tolerance to submergence. To study the variability in yield and its attributing traits in the population, principal component analysis was carried out. The present investigation was studied in recombinant inbred lines (RIL) population consisting of 120 lines where principal component analysis was carried out on different agromorphological traits viz. days to fifty percent flowering, plant height, panicle length, total tillers per plant, number of effective tillers per plant, number of filled grains and Spikelet fertility, test weight, grain yield per plant, biomass per plant and harvest index to assess the relative contribution of various traits towards total variability. It was found that first five components with Eigen values greater than 1 accounted for 74.33% of total explained variability. The highest positive eigenvalue was observed for plant height and panicle length in PC1, revealing their maximum contribution to variation in the lines.

Genetic Evaluation of Recombinant Inbred Lines of Rice Derived from Swarna-Sub1 x AC 20431B for Yield Related Traits

Submergence is the third most important abiotic stress hugely affecting yield and productivity in rice. There are many wild varieties and landraces available which are tolerant to submergence stress. These genotypes can be utilized as donors in different breeding programs. The population derived from such germplasms are subjected to genetic evaluation for yield and yield related attributes for development of lines that are high yielding as well as tolerant to submergence. The present investigation was executed in 120 Recombinant Inbred Lines (RIL) population (F10) derived from Swarna-Sub1 x AC 20431B along with four land races and Swarna-Sub1 to elucidate the association existing between yield and yield attributing characters. Apart from this, Correlation and path analysis was also employed to study direct and indirect effect on grain yield. Observations for agro-morphological traits such as days to 50% flowering, plant height, panicle length, total number of tillers, number of effective tillers per plant, number of filled grains and Spikelet fertility, test weight, grain yield per plant, biomass per plant and harvest index were recorded and analyzed for various variability parameters. Correlation and path coefficient analysis were also carried out. High heritability and genetic advance values were observed for days to 50% flowering, plant height, panicle length, total number of tillers per plant, effective tillers per plant, filled grains per panicle, spikelet fertility, test weight, grain yield and biomass per plant. Among all the characters; filled grains per panicle, biomass and harvest index per plant showed significant correlation with grain yield. Effective number of tillers per plant has the highest positive direct effect on grain yield.

ADDITIVE MAIN EFFECT AND MULTIPLICATIVE INTERACTION ANALYSIS FOR PRODUCTION TRAITS IN RICE RECOMBINANT INBRED LINES USING AMMI BIPLOT TECHNIQUE

The experiment was performed to assess the performance of 87 rice recombinant inbred lines (RILs), identify
 the productive environments and quantify genotype × environment interaction (GEI) effects on yield and yield
 related traits across four locations of the Khyber Pakhtunkhwa Province in Pakistan between 2021 and 2022.
 The pooled ANOVA showed significant differences of GEI for all traits. Across the studied environments, RIL
 AUP-3 took minimum days to heading (139) and produced the highest grain yield (4.1 t ha-1). AUP-3 and AUP30 displayed the highest kernel number in panicle of 214 and 226, respectively. Based on AMMI1 and AMMI2
 biplots, RIL AUP-3 was unanimously declared as the most stable and the highest yielding genotype. AMMI
 biplot analysis cumulatively explained 55.3%, 46.3% and 52.1% of total variation due to GEI for days to
 maturity, grains panicle-1 and grain yield, respectively. The AMMI biplot analysis confirmed the differential
 response of genotypes across environments, suggesting environment-based expression of genes. The AMMI
 biplot also manifested AUP-3 and AUP-30 as ideal genotypes for grains panicle-1 and grain yield, respectively.
 The Peshawar (E-1 and E-5) and Mingora (E-2) were the most discriminating and representative environment
 for grains panicle-1 and grain yield. Application of various stability models in this study identified AUP-3 and
 AUP-30 as the most stable and widely adapted genotype for grain yield and its components. The AMMI analysis
 identified genotypes both for specific and wide adaptation. Based on stability and yield performance, said
 genotypes were identified with superior performance than check cultivars. Therefore, recommended for
 commercialization. Also environments were clustered regardless of their geographical location, which revealed
 unpredictable nature of agro-climatic conditions across four tested locations.

Analysis of Genetic Variability and Correlation in Rice (Oryza sativa L.) Recombinant Inbred Lines (F6) for Yield and Its Component Traits

grain yield and its component traits in 150 rice recombinant inbred lines, their parents and six checks at ICAR-IIRR, Hyderabad and AHRS, Kathalagere in wet 2022. The experiments were laid out in an augmented block design with five blocks. Phenotypic coefficients of variance were higher than genotypic coefficients of variance for all the traits across the locations. A joint consideration of high heritability in broad sense (h2) and genetic advance as per cent mean estimates were obtained for plant height, number of tillers, number of productive tillers, panicle length, number of grains per panicle, test weight, grain yield per plant suggesting that the traits were primarily under genetic control. Furthermore, high heritability (h2) and GAM recorded in these characters could be explained by additive gene action. However, high estimates (h2) combined with moderate GAM recorded for days to 50% flowering could be due to non-additive gene effect. Grain yield per plant recorded positive and significant correlation with the total number of grains per panicle (0.32***, 0.30***) and number of productive tillers per plant (0.21***, 0.26***) at both the locations. This result indicates that selection based on these two traits will be highly effective for yield improvement in rice.

Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1.

BPH (brown planthopper) and WBPH (white backed planthopper) are significant rice pests that often co-occur as sympatric species and cause substantial yield loss. Despite their genetic similarities, different host-resistance genes confer resistance against these two hoppers. The defense mechanisms in rice against these pests are complex, and the molecular processes regulating their responses remain largely unknown. This study used specific recombinant inbred lines (RILs) derived from a cross between rice varieties RP2068-18-3-5 (BPH- and WBPH-resistant) and TN1 (BPH- and WBPH-susceptible) to investigate the mechanisms of interaction between these planthoppers and their rice hosts. WBPH and BPH were allowed to feed on specific RILs, and RNA-Seq was carried out on WBPH insects. Transcriptome profiling and qRT-PCR results revealed differential expression of genes involved in detoxification, digestion, transportation, cuticle formation, splicing, and RNA processing. A higher expression of sugar transporters was observed in both hoppers feeding on rice with resistance against either hopper. This is the first comparative analysis of gene expressions in these insects fed on genetically similar hosts but with differential resistance to BPH and WBPH. These results complement our earlier findings on the differential gene expression of the same RILs (BPH- or WBPH-infested) utilized in this study. Moreover, identifying insect genes and pathways responsible for countering host defense would augment our understanding of BPH and WBPH interaction with their rice hosts and enable us to develop lasting strategies to control these significant pests.

Narrow root cone angle promotes deeper rooting, cooler canopy temperatures and higher grain yield in a rice (Oryza sativa L.) recombinant inbred line population grown under different water availabilities in aerobic production systems

Rice crops are one of the world’s major consumers of irrigation water. With water becoming more limited, water-saving aerobic production (AP) systems may provide an alternative to traditional flooded culture. Genotypes with narrow root cone angle (RCA) and subsequently deeper rooting systems are hypothesised as key for AP adaptation ensuring water uptake at depth. Using a recombinant inbred line (RIL) population and differential genotypes (narrow and wide RCA groups) derived from a Sherpa/IRAT109 cross, a glasshouse experiment and four field experiments with different water inputs in well-watered (WW, in two seasons), mild water deficit (MWD), and intermittent water deficit (IWD) conditions were carried out to characterise the relationship of RCA with grain yield (GY) and key physiological traits. Significant genotypic variation and group differences were found in root traits, canopy temperature and GY. Expression of genotypes with narrow RCA were found to be consistent across experiments and water availability conditions. Genotypes in the narrow RCA group produced a greater proportion of roots below 20 cm (7.4–17.7%), longer total root length (69.7%), cooler canopies (0.3–1.0 °C) and higher GY (14–62%) compared with wide RCA group. Two promising RILs were identified which expressed high GY in WW (12.0–13.4 t/ha) conditions while maintaining GY in IWD (up to 9.4 t/ha). Higher GY was obtained in genotypes with cooler canopies (r = −0.72) and narrow RCA (r = −0.39) in IWD. Narrower RCA was associated with higher total root length (r = −0.70) and higher stomatal conductance (r = −0.71) in the glasshouse and proportion of deep roots (r = −0.65) and cooler canopies (r = 0.66) in the field. To our knowledge, this was one of the foremost studies exploring and demonstrating such relationships in rice AP systems. Root traits determined in the field were congruent with the other root-related traits driving differences between RCA groups measured in the glasshouse providing confidence with the field phenotyping methods. This work demonstrated the advantage conferred by the development of narrow RCA in aerobic conditions, presented improved physiological understanding of RCA and with genomics assisted breeding, is considered valuable for the development of AP-adapted, sustainably produced rice.

Whole-genome analysis of recombinant inbred rice lines reveals a quantitative trait locus on chromosome 3 with genotype-by-environment interaction effects.

Elucidating genotype-by-environment (GxE) interactions is fundamental for understanding the interplay between genetic and environmental factors that shape complex traits in crops. GxE interactions are of practical importance, as they determine the performance of cultivars grown in different environments, prompting the need for an efficient approach for evaluating GxE interactions. Here, we describe a method for GxE detection that involves comparing linear mixed models. This method successfully detected GxE interactions in rice (Oryza sativa) recombinant inbred lines grown at three locations. We identified a quantitative trait locus (QTL) on chromosome 3 that was associated with heading date, grain number, and leaf length. The effect of this QTL on plant growth-related traits varied with environmental conditions, indicating the presence of GxE interactions. Therefore, our method enables a powerful GxE detection pipeline that should facilitate the production of high-yielding crops in a given environment.

Imaging Sensor-Based High-Throughput Measurement of Biomass Using Machine Learning Models in Rice

Phenomics technologies have advanced rapidly in the recent past for precision phenotyping of diverse crop plants. High-throughput phenotyping using imaging sensors has been proven to fetch more informative data from a large population of genotypes than the traditional destructive phenotyping methodologies. It provides accurate, high-dimensional phenome-wide big data at an ultra-super spatial and temporal resolution. Biomass is an important plant phenotypic trait that can reflect the agronomic performance of crop plants in terms of growth and yield. Several image-derived features such as area, projected shoot area, projected shoot area with height constant, estimated bio-volume, etc., and machine learning models (single or multivariate analysis) are reported in the literature for use in the non-invasive prediction of biomass in diverse crop plants. However, no studies have reported the best suitable image-derived features for accurate biomass prediction, particularly for fully grown rice plants (70DAS). In this present study, we analyzed a subset of rice recombinant inbred lines (RILs) which were developed from a cross between rice varieties BVD109 × IR20 and grown in sufficient (control) and deficient soil nitrogen (N stress) conditions. Images of plants were acquired using three different sensors (RGB, IR, and NIR) just before destructive plant sampling for the quantitative estimation of fresh (FW) and dry weight (DW). A total of 67 image-derived traits were extracted and classified into four groups, viz., geometric-, color-, IR- and NIR-related traits. We identified a multimodal trait feature, the ratio of PSA and NIR grey intensity as estimated from RGB and NIR sensors, as a novel trait for predicting biomass in rice. Among the 16 machine learning models tested for predicting biomass, the Bayesian regularized neural network (BRNN) model showed the maximum predictive power (R2 = 0.96 and 0.95 for FW and DW of biomass, respectively) with the lowest prediction error (RMSE and bias value) in both control and N stress environments. Thus, biomass can be accurately predicted by measuring novel image-based parameters and neural network-based machine learning models in rice.

Evaluation of Rice Recombinant Inbred Lines Developed from the Cross Rasi × Improved Samba Mahsuri for Drought Tolerance

Drought has been one of the most important limiting factors for rice productivity, particularly in the rainfed ecosystem. It is important to understand the genetic basis of drought tolerance in donor lines and develop drought tolerant rice cultivars, based on this information. We earlier identified the rice line, Rasi as tolerant to drought and developed a recombinant inbred line (RIL) mapping population consisting of 209 lines. These lines along with their parents were grown under well-watered and drought stress conditions in a two-year experiment (wet season 2020 and 2021) with drought stress imposed during reproductive stage. The study revealed high genetic variability for 12 key agro morphological traits associated with drought tolerance among the RILs. Of the 209 RILs, 59 showed superior performance over the checks and even the tolerant parent, Rasi under severe drought condition. Two RILs, RIL-33 and RIL-58 showed exceptional drought tolerance along with greater plot yield and grain weight under drought condition and they possessed medium slender grain type. These two lines can be a new novel genetic resource for drought tolerance in breeding programmes.

Phloem Unloading in Developing Rice Caryopses and its Contribution to Non-Structural Carbohydrate Translocation from Stems and Grain Yield Formation.

Phloem unloading plays an important role in photoassimilate partitioning and grain yield improvements in cereal crops. The phloem unloading strategy and its effects on photoassimilate translocation and yield formation remain unclear in rice. In this study, plasmodesmata were observed at the interface between the sieve elements (SEs) and companion cells (CCs), and between the SE-CC complex and surrounding parenchyma cells (PCs) in phloem of the dorsal vascular bundle in developing caryopses. Carboxyfluorescein (CF) signal was detected in the phloem of caryopses, which showed that CF was unloaded into caryopses. These results indicated that the SE-CC complex was symplasmically connected with adjacent PCs by plasmodesmata. Gene expression for sucrose transporter (SUT) and cell wall invertase (CWI), and OsSUT1 and OsCIN1 proteins were detected in developing caryopses, indicating that rice plants might actively unload sucrose into caryopses by the apoplasmic pathway. Among three rice recombinant inbred lines, R201 exhibited lower plasmodesmal densities at the boundaries between cell types (SE-CC, SE-PC and CC-PC) in developing caryopses than R91 and R156. R201 also had lower expression of SUT and CWI genes and lower protein levels of OsSUT1 and OsCIN1, as well as CWI activity, than R91 and R156. These data agreed with stem non-structural carbohydrate (NSC) translocation and grain yields for the three lines. The nitrogen application rate had no significant effect on plasmodesmal densities at the interfaces between different cells types, and did not affect CF unloading in the phloem of developing caryopses. Low nitrogen treatment enhanced expression levels of OsSUT and OsCIN genes in the three lines. These results suggested that nitrogen application had no substantial effect on symplasmic unloading but affected apoplasmic unloading. Therefore, we concluded that poor symplasmic and apoplasmic unloading in developing caryopses might result in low stem NSC translocation and poor grain yield formation of R201.

Analyses and identifications of quantitative trait loci and candidate genes controlling mesocotyl elongation in rice

Rice direct seeding has the significant potential to save labor and water, conserve environmental resources, and reduce greenhouse gas emissions tremendously. Therefore, rice direct seeding is becoming the major cultivation technology applied to rice production in many countries. Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice (DSR) production. This study used a permanent mapping population with 144 recombinant inbred lines (RILs) and 2 828 bin-markers to detect quantitative trait loci (QTLs) associated with mesocotyl length in 2019 and 2020. The mesocotyl lengths of the rice RILs and their parents, Lijiangxintuanheigu (LTH) and Shennong 265 (SN265), were measured in a growth chamber at 30°C in a dark environment. A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2), 2(4), 3(2), 4, 5, 6, 7, 9, 11(2), and 12. Seven of these QTLs, including qML1a, qML1b, qML2d, qML3a, qML3b, qML5, and qML11b, were reproducibly detected in both years via the interval mapping method. The major QTL, qML3a, was reidentified in two years via the composite interval mapping method. A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb, respectively. Thirteen predicted genes within a relatively small genetic interval (88.18 kb) of the major mesocotyl elongation QTL, qML3a, were more thoroughly analyzed. Finally, the coding DNA sequence variations among SN265, LTH, and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation. This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase. Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265. In conclusion, these results further strengthen our knowledge about rice's genetic mechanisms of mesocotyl elongation. This investigation's discoveries will help to accelerate breeding programs for new DSR variety development.

Higher CO2 Assimilation in Selected Rice Recombinant Inbred Lines Is Driven by Higher CO2 Diffusion and Light Use Efficiency Related to Leaf Anatomy and Mesophyll Cell Density.

Leaf anatomy determining the light distribution within the leaf and exerting influence on CO2 diffusion is considered to have dramatic potential for photosynthesis performance increase. In this study, we observed that two rice recombinant inbred lines, H138 and H217 (RILF11 plants from Sasanishiki × IRAT10), have higher net CO2 assimilation (An) than their parent Sasanishiki due mainly to the improvement of leaf anatomy. Our results showed that An positively correlated with anatomy traits’ mesophyll cell number per cross-sectional area (NO.mescell/Acros) and mesophyll area (Ames). NO.mescell/Acros exert direct and indirect effects on An. Compared to Sasanishiki flag leaves, IRAT10, H138, and H217 have higher mesophyll cell numbers. Simultaneously, higher chlorophyll content and expression of genes encoding the light-harvesting protein of PSII and PSI (Lhcb1, 2, 3 and Lhca1, 2, 3) were recorded in IRAT10, H138, and H217, which facilitates light use efficiency. Higher electron transport rate and RuBP concentration were recorded in IRAT10, H138, and H217 flag leaves. Retinoblastoma-related gene (OsRBR1), exerting effects on mesophyll cell density, can be used to modify leaf anatomy for improving leaf photosynthesis. Additionally, higher stomatal conductance and mesophyll conductance were also recorded in H138 and H217 than in Sasanishiki. Furthermore, we modeled mesophyll conductance through anatomical traits, and the results revealed that chloroplast thickness was the dominant factor restricting CO2 diffusion within mesophyll cells rather than cell wall thickness. Higher RuBP content accompanied by higher CO2 concentration within the carboxylation set in H138 and H217 flag leaves contributed to higher CO2 assimilation.

Stem small vascular bundles have greater accumulation and translocation of non-structural carbohydrates than large vascular bundles in rice.

Phloem unloading and loading are associated with stem non-structural carbohydrates (NSCs) accumulation and remobilization in rice (Oryza sativa L.). Four rice recombinant inbred lines (R032, R191, R046, and R146) derived from a cross between Zhenshan 97 and Minghui 63 were used to investigate the contributions of stem large and small vascular bundles (SVBs) to NSCs accumulation and translocation. Before heading, the parenchyma cells in stem cortex tissues (PCs) surrounding SVBs had higher starch density than those surrounding large vascular bundles (LVBs). Moreover, the protein levels of sucrose transporters (SUTs), cell wall invertase, sucrose synthase, and adenosine diphosphate glucose pyrophosphorylase, as well as the phloem plasmodesma densities were higher in SVBs than those in LVBs. After heading, starch density decreased more in PCs surrounding SVBs than in LVBs. Also, the protein levels of SUTs, α-amylase, sucrose phosphate synthase and sucrose synthase, the phloem plasmodesma densities in SVBs were higher than those in LVBs. The correlations of the number and total cross-sectional area of SVBs with mass and contribution to yield of transferred NSCs were higher than those of LVBs. Our results suggest that SVBs may have higher contributions to pre-anthesis stem NSCs accumulation and post-anthesis translocation than LVBs, which is potentially attributed to the high level of protein and enzyme involved in stem unloading and loading via apoplastic and symplastic pathways.

Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice (Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109.

Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.

Comparative Analysis of Heat-Tolerant and Heat-Susceptible Rice Highlights the Role of OsNCED1 Gene in Heat Stress Tolerance.

To elucidate the mechanism underlying the response of rice to heat stress (HS), the transcriptome profile of panicles was comparatively analyzed between the heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082), two rice recombinant inbred lines (RILs). Our differentially expressed gene (DEG) analysis revealed that the DEGs are mainly associated with protein binding, catalysis, stress response, and cellular process. The MapMan analysis demonstrated that the heat-responsive (HR) genes for heat shock proteins, transcription factors, development, and phytohormones are specifically induced in HTL252 under HS. Based on the DEG analysis, the key gene OsNCED1 (Os02g0704000), which was induced under HS, was selected for further functional validation. Moreover, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key rate-limiting enzyme in the ABA biosynthetic pathway. Overexpression of OsNCED1 improved the HS tolerance of rice at the heading and flowering stage. OsNCED1-overexpression plants exhibited significant increases in pollen viability, seed setting rate, superoxide dismutase (SOD) and peroxidase (POD) activities, while significantly lower electrolyte leakage and malondialdehyde (MDA) content relative to the wild type (WT). These results suggested that OsNCED1 overexpression can improve the heat tolerance of rice by enhancing the antioxidant capacity. Overall, this study lays a foundation for revealing the molecular regulatory mechanism underlying the response of rice to prolonged HS.

Identification of Expression QTL by QTLtools in a Rice Recombinant Inbred Line Population

Identification of Expression QTL by QTLtools in a Rice Recombinant Inbred Line Population