Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

Key message Reproductive stage salinity tolerance is most critical for rice as it determines the yield under stress. Few studies have been undertaken for this trait as phenotyping was cumbersome, but new methodology outlined in this review seeks to redress this deficiency. Sixty-three meta-QTLs, the most important genomic regions to target for enhancing salinity tolerance, are reported. Abstract Although rice has been categorized as a salt-sensitive crop, it is not equally affected throughout its growth, being most sensitive at the seedling and reproductive stages. However, a very poor correlation exists between sensitivity at these two stages, which suggests that the effects of salt are determined by different mechanisms and sets of genes (QTLs) in seedlings and during flowering. Although tolerance at the reproductive stage is arguably the more important, as it translates directly into grain yield, more than 90% of publications on the effects of salinity on rice are limited to the seedling stage. Only a few studies have been conducted on tolerance at the reproductive stage, as phenotyping is cumbersome. In this review, we list the varieties of rice released for salinity tolerance traits, those being commercially cultivated in salt-affected soils and summarize phenotyping methodologies. Since further increases in tolerance are needed to maintain future productivity, we highlight work on phenotyping for salinity tolerance at the reproductive stage. We have constructed an exhaustive list of the 935 reported QTLs for salinity tolerance in rice at the seedling and reproductive stages. We illustrate the chromosome locations of 63 meta-QTLs (with 95% confidence interval) that indicate the most important genomic regions for salt tolerance in rice. Further study of these QTLs should enhance our understanding of salt tolerance in rice and, if targeted, will have the highest probability of success for marker-assisted selections

Development of a phenotyping protocol for combined drought and salinity stress at seedling stage in rice

Introduction: The case of combined drought and salinity stress is increasingly becoming a constraint to rice production, especially in coastal areas and river deltas where low rainfall not only reduces soil moisture levels but also reduces the flow of river water, resulting in intrusion of saline sea-water. A standardized screening method is needed in order to systematically evaluate rice cultivars under combined drought+salinity at the same time because sequential stress of salinity followed by drought or vice-versa is not similar to simultaneous stress effects. Therefore, we aimed to develop a screening protocol for combined drought+salinity stress applied to soil-grown plants at seedling stage. Methods: The study system used 30-L soil-filled boxes, which allowed a comparison of plant growth under control conditions, individual drought and salinity stress, as well as combined drought+salinity. A set of salinity tolerant and drought tolerant cultivars were tested, together with several popular but salinity and drought-susceptible varieties that are grown in regions prone to combined drought+salinity. A range of treatments were tested including different timings of the drought and salinity application, and different severities of stress, in order to determine the most effective that resulted in visible distinction among cultivars. The challenges related to determining a protocol with repeatable seedling stage stress treatment effects while achieving a uniform plant stand are described here. Results: The optimized protocol simultaneously applied both stresses by planting into saline soil at 75% of field capacity which was then allowed to undergo progressive drydown. Meanwhile, physiological characterization revealed that chlorophyll fluorescence at seedling stage correlated well with grain yield when drought stress was applied to vegetative stage only. Discussion: The drought+salinity protocol developed here can be used for screening rice breeding populations as part of a pipeline to develop new rice varieties with improved adaptation to combined stresses

Development of early maturing salt-tolerant rice variety KKL(R) 3 using a combination of conventional and molecular breeding approaches

Introduction: Soil salinity poses a severe threat to rice production, resulting in stunted growth, leaf damage, and substantial yield losses. This study focuses on developing an early maturing seedling stage salinity tolerant rice variety by integrating conventional breeding methods with marker assisted breeding (MAB) approaches.Methods: Seedling-stage salinity tolerance Quantitative Trait Locus (QTL) “Saltol” from the salt-tolerant parent FL478 was introduced into the high-yielding but salt-sensitive rice variety ADT 45. This was achieved through a combination of conventional breeding and MAB. The breeding process involved rigorous selection, screening, and physiological parameter assessments.Results: KKL(R) 3 (KR 15066) identified as the top performing Recombinant Inbred Line (RIL), consistently demonstrating maximum mean grain yields under both salinity (3435.6 kg/ha) and normal (6421.8 kg/ha) conditions. In comparison to the early maturing, salt-tolerant national check variety CSR 10, KKL(R) 3 exhibited a substantial yield increase over 50%.Discussion: The notable improvement observed in KKL(R) 3 positions it as a promising variety for release, offering a reliable solution to maximize yields, ensure food security, and promote agricultural sustainability in both saline and non-saline environments. The study highlights the effectiveness of MAB in developing salt-tolerant rice varieties and emphasizes the significance of the Saltol QTL in enhancing seedling stage salinity tolerance. The potential release of KKL(R) 3 has the capacity to revolutionize rice production in salt affected regions, providing farmers with a reliable solution to maximize yields and contribute to food security while ensuring agricultural sustainability

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Not AvailableTwenty three new plant type (NPT) wheat derivatives with three checks were evaluated for grain yield and stability under timely (TSI) and late-sown irrigated environments (LSI).The experiment was conducted in six environments at two locations in 2006-07 and 2007-08. Analysis of variance of stability for grain yield through Eberhart and Russell’s model and AMMI analysis revealed highly significant differences among genotypes and environments and significant genotype x environment (G x E) interaction (GEI). Highly significant mean squares due to environment + genotype x environment interactions (E + G x E) in the Eberhart and Russell model revealed that genotype interacted considerably with environmental conditions that existed under TSI and LSI condition. Further partitioning of E + G x E effects indicated that E (linear), G x E (linear) component, and pooled deviation were highly significant for grain yield. Some genotypes showed linear effects over environments, while others showed significant deviation from a linear relationship. Partitioning of G x E interaction into principal components in AMMI analysis revealed that the two interaction principal component axes accounted for 90.4% of the total GEI variation. Genotypes DL 893, DL 901, DL 966 and PBW 343 exhibited high per se performance under TSI, whereas DL 880, DL 882, DL 886, DL 892, DL 893, DL 901 and DL 927 recorded high per se performance under LSI at both locations. Based on per se performance, regression coefficient, and deviations from regression as well as AMMI analysis, genotypes DL 886, DL 901, DL 924, DL 927, DL 966 and DL 960 were found to be stable and are adaptable to both TSI and LSI. Both Eberhart and Russell and AMMI results are comparable in identifying stable genotypes for the test environments.Not Availabl

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Not AvailableSUMMARY Twenty three new plant type (NPT) wheat derivatives with three checks were evaluated for grain yield and stability under timely (TSI) and late-sown irrigated environments (LSI).The experiment was conducted in six environments at two locations in 2006-07 and 2007-08. Analysis of variance of stability for grain yield through Eberhart and Russell's model and AMMI analysis revealed highly significant differences among genotypes and environments and significant genotype x environment (G x E) interaction (GEI). Highly significant mean squares due to environment + genotype x environment interactions (E + G x E) in the Eberhart and Russell model revealed that genotype interacted considerably with environmental conditions that existed under TSI and LSI condition. Further partitioning of E + G x E effects indicated that E (linear), G x E (linear) component, and pooled deviation were highly significant for grain yield. Some genotypes showed linear effects over environments, while others showed significant deviation from a linear relationship. Partitioning of G x E interaction into principal components in AMMI analysis revealed that the two interaction principal component axes accounted for 90.4% of the total GEI variation. Genotypes DL 893, DL 901, DL 966 and PBW 343 exhibited high per se performance under TSI, whereas DL 880, DL 882, DL 886, DL 892, DL 893, DL 901 and DL 927 recorded high per se performance under LSI at both locations. Based on per se performance, regression coefficient, and deviations from regression as well as AMMI analysis, genotypes DL 886, DL 901, DL 924, DL 927, DL 966 and DL 960 were found to be stable and are adaptable to both TSI and LSI. Both Eberhart and Russell and AMMI results are comparable in identifying stable genotypes for the test environments.Not Availabl

Screening of Rice (Oryza sativa L.) Genotypes for Anaerobic Germination

The present investigation was carried out to screen the set of 2000 rice genotypes including germplasm, released varieties, INGER nurseries and elite lines for anaerobic germination trait. Based on initial screening of 2000 genotypes, five hundred lines were selected for further to study the trait based on parameters namely germination percentage, seedling length and vigour index. Frequency distribution was calculated for the three observations under study. Out of five hundred genotypes under study, 16 genotypes were not germinated, while 100 % germination was recorded by 17 genotypes. The seedling length of the germinated seeds was in the range of 1 cm (E 199 and E 282) to 62 cm (E 480), While vigour index was ranged from 20 (E199, E282 and E532) to 4880 (E1777). After repeated screening, 13 entries namely E775, E1810, E596, E1786, E 753, E773, E1846, E1195, E1049, E1772, E1723, E1701 and E1777 were recorded 100% anaerobic germination with high seed vigour index, was identified as tolerant genotypes for the anaerobic germination. These genotypes could be used as parents to introduce anaerobic germination tolerance into improved cultivars to utilize under direct seeded condition

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Not AvailableGlobally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.NASF/CRISPR-Cas-7003/2018-19/GATES/Bill & Melinda Gates Foundation/United State

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency

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Not AvailableBacterial blight (BB) is a major production threat to Basmati, the aromatic rice prized for its unique quality. In order to improve the BB resistance of two elite, traditional BB-susceptible Basmati varieties (Taraori Basmati and Basmati 386), we utilized the strategy of limited marker-assisted backcrossing for introgression of two major BB resistance genes, Xa21 and xa13, coupled with phenotype-based selection for improvement of their plant type and yield. Improved Samba Mahsuri, an elite high-yielding, fine-grain-type BB-resistant rice variety served as donor for BB resistance. Backcross-derived improved Basmati lines at BC1F5 possessing a single resistance gene (i.e. either Xa21 or xa13) displayed moderate resistance to BB, while lines possessing both Xa21 and xa13 showed significantly higher levels of resistance. Two-gene pyramid lines (Xa21 + xa13) possessing good grain and cooking quality similar to their respective traditional Basmati parents, short plant stature (<110 cm plant height) and higher grain yield than the recurrent parent(s) were identified and advanced. This work demonstrates the successful application of marker-assisted selection in conjunction with phenotype-based selection for targeted introgression of multiple resistance genes into traditional Basmati varieties along with improvement of their plant stature and yield.Not Availabl

Assessment of reproductive stage drought tolerance using stress indices in improved restorer lines of KMR-3R in rice

Drought stress during the reproductive stage is an evident limitation of rice grain yield. The present study aimed to assess the reproductive stage drought tolerance of eight promising backcross inbred lines (BILs) with complete fertility restoration in the genetic background of KMR-3R. Various stress indices based on grain yield under Non-stress (NS) and drought-stress (DS) conditions were used to assess BILs drought tolerance potential. Based on correlation analysis, the best indices for determining drought-tolerant genotypes were K2STI, YI, HM, SNPI, GMP, and DTI. By ensuring stable performance, the indices K2STI and YI were crucial criteria in identifying DS genotypes. The stress-tolerant and susceptible genotypes were best differentiated under DS using the susceptible indices TOL and ATI, which had considerably low values. The IL-1, IL-2, and IL-7 (RP6340-NRR-5, RP6340-NRR-11, and RP 6340-NPVR-25) were identified as promising drought-tolerant genotypes based on lower grain yield reduction under DS. The improved restorers with drought tolerance performed well under DS in terms of agronomy, and it may be exploited in hybridization programs to develop elite drought-tolerant rice hybrids for unfavorable ecologies