Genetic Variation for Salinity Tolerance in Pakistani Rice (Oryza sativa L.) Germplasm

Seed Halopriming Improves Salinity Tolerance of Some Rice Cultivars During Seedling Stage

BACKGROUND

Saline land in coastal areas has great potential for crop cultivation. Improving salt tolerance in rice is a key to expanding the available area for its growth and thus improving global food security. Seed priming with salt (halopriming) can enhance plant growth and decrease saline intolerance under salt stress conditions during the subsequent seedling stage. However, there is little known about rice defense mechanisms against salinity at seedling stages after seed halopriming treatment. This study focused on the effect of seed halopriming treatment on salinity tolerance in a susceptible cultivar, IR 64, a resistant cultivar, Pokkali, and two pigmented rice cultivars, Merah Kalimantan Selatan (Merah Kalsel) and Cempo Ireng Pendek (CI Pendek). We grew these cultivars in hydroponic culture, with and without halopriming at the seed stage, under either non-salt or salt stress conditions during the seedling stage.

RESULTS

The SES scoring assessment showed that the level of salinity tolerance in susceptible cultivar, IR 64, and moderate cultivar, Merah Kalsel, improved after seed halopriming treatment. Furthermore, seed halopriming improved the growth performance of IR 64 and Merah Kalsel rice seedlings. Quantitative PCR revealed that seed halopriming induced expression of the OsNHX1 and OsHKT1 genes in susceptible rice cultivar, IR 64 and Merah Kalsel thereby increasing the level of resistance to salinity. The expression levels of OsSOS1 and OsHKT1 genes in resistant cultivar, Pokkali, also increased but there was no affect on the level of salinity tolerance. On the contrary, seed halopriming decreased the expression level of OsSOS1 genes in pigmented rice cultivar, CI Pendek, but did not affect the level of salinity tolerance. The transporter gene expression induction significantly improved salinity tolerance in salinity-susceptible rice, IR 64, and moderately tolerant rice cultivar, Merah Kalsel. Induction of expression of the OsNHX1 and OsHKT1 genes in susceptible rice, IR 64, after halopriming seed treatment balances the osmotic pressure and prevents the accumulation of toxic concentrations of Na⁺, resulting in tolerance to salinity stress.

CONCLUSION

These results suggest that seed halopriming can improve salinity tolerance of salinity-susceptible and moderately tolerant rice cultivars.

Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers

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Rice is a staple food for more than three billion people, and rice cultivars have evolved over thousands of years of adaptation to different environmental stresses in different regions. Domestication of rice cultivation led to the diversity of cultivars though phenotypic selection for desirable characters. India is blessed with great diversity of rice germplasm, and these are still conserved for many reasons. The aim of the study was to show the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu, India. Using a hydroponic system, we studied the different agronomic characters from seedling to plant growth hight 14 days after exposure to six different concentrations of saline solution. Rice genotypes showed significant interaction and differential response towards salinity were assessed at the molecular level using simple sequence repeat (SSR) markers linked with salt-tolerance QTL. We found wide genetic distance among the genotypes studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes. This is, to the best of our knowledge, the first study on the indigenous rice landraces of coastal Tamil Nadu, India.

We evaluated the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu. Using a hydroponic system, we studied the different agronomic characters 14 days after exposure to six different concentrations of saline solution. Shoot and root length as well as plant biomass at seedling stage decreased with increasing salinity. Genotypes showing significant interaction and differential response towards salinity were assessed at the molecular level using 20 simple sequence repeat (SSR) markers linked with salt-tolerance QTL. These genotypes were grouped into eleven clusters based on molecular diversity analysis and eight clusters based on D2 statistical analysis. We found wide genetic distance among the genotypes studied. Simple correlation analysis revealed highly significant associations among the traits studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes viz. Kuzhi adichan, Poonkar, Kallundai, and Sornamugi.

Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice

Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na+ exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na+ in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K+ retention in both root and leaf mesophyll cells; and (4) incorporating Na+ sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.

Evaluation and clustering on salt-tolerant ability in rice genotypes (Oryza sativa L. subsp. indica) using multivariate physiological indices

Salinity is a major abiotic stress that affects plant growth and development, especially in rice crop as it is a salt susceptible crop. Therefore, a wide range of rice genetic resources are screened in the germplasm banks to identify salt tolerant cultivars. The objective of this investigation was to develop effective indices for the classification of salt tolerant rice genotypes among Pathumthani 1, Khao Dawk Mali 105 (KDML 105), RD31, RD41, Suphanburi 1, RD43, RD49 and Riceberry. Rice seedlings were hydroponically grown with 10 dS m^-1 NaCl treatment or without NaCl treatment (to serve as control) (WP; 2 dS m^-1). Standard evaluation system peaked at a score of 9 in Pathumthani 1 and KDML 105, after 21 days of salt treatment, leading to leaf chlorosis, leaf burns and plant death. Chlorophyll a, chlorophyll b and total carotenoids were maintained better in the salt-stressed leaves of rice cvs. Riceberry and RD43, as compared to other cultivars. Salt stress induced a remarkable increase in the free proline accumulation (by 8.38 folds) in cv. Riceberry. Overall growth performance in rice cv. Riceberry was retained, whereas it declined in other cultivars. After 21 days of NaCl treatment at a concentration of 10 dS m^-1, eight rice cultivars were classified into 3 groups based on multivariate physio-morphological indices, Group I: salt-tolerant rice, including cv. Riceberry; Group II: moderately salt tolerant, consisting of RD31, RD41, Suphanburi 1, RD43 and RD49 cultivars; Group III: salt-sensitive cultivars, namely Pathumthani 1 and KDML 105.

Screening Oat Genotypes for Tolerance to Salinity and Alkalinity

A set of four experiments was conducted to develop methods for screening oat tolerance to salt and alkali and the following results were obtained. (1) In experiment 1, 68.5 mmol L^-1 salt and 22.5 mmol L^-1 alkali were identified as appropriate concentrations for determining oat tolerance to salinity and alkalinity during germination. (2) These concentrations were used in experiment 2 to screen 248 oat genotypes and 21 were identified to be tolerant to salinity and alkalinity in germination. (3) In experiment 3, one salt treatment, 40 L of Na₂SO₄:NaCl (1:1), 150 mmol L^-1, was found to be optimal for screening oat tolerance to salinity during growth and development. For alkalinity tolerance, the optimal treatment was 40 L of Na₂CO₃:NaHCO₃ (1:1) at 75 mmol L^-1. (4) No significant correlation was found between tolerances at the germination and adult stages or between tolerances to salt and alkali. Three lines were found to be tolerant to both salt and alkali in both germination and adult stages. (5) In experiment 4, 25 out of 262 oat genotypes were found to be tolerant to both salinity and alkalinity. (6) GGE biplot analysis was found to be effective in interpreting the multivariate data and the plastic cone-container system was found to be cost-effective system for screening adult plant tolerance to salt and alkali. (7) The symptoms of salt stress and alkali stress were found to be different; alkali stress mainly reduces the chlorophyll content, while salinity mainly disrupts water absorption.

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

The improvement and development of saline–alkali land is of great significance for promoting food production and sustainable development. It is necessary to study the mechanism of saline–alkaline tolerance and breed saline–alkaline tolerant crops to improve the utilization of saline–alkali land. For this study, we conducted a three-year pot experiment to screen the saline–alkaline tolerant germplasm of 72 rice genotypes from hundreds of elite cultivars during the whole growth period using a certain proportion of soda saline–alkali soil. The selected salt-tolerant variety was combined with a salt-sensitive variety to analyze the saline–alkaline tolerance mechanism by using the saline–alkaline soil leachate. We eliminated 36 genotypes with low seedling survival rates under salt–alkali stress, and the salt-tolerant Jiudao-66 (D68) variety had a higher survival rate than most varieties. The membership degree of Jiudao-66, according to the salt tolerance index of multiple agronomic traits, is higher than that of 34 varieties, with a higher survival rate except when compared to D36. The survival rate and these salt tolerance indexes of Jiudao-66 were significantly higher than those of Kitaake (salt-sensitive). Under the stress of leachate, the content of proline and soluble sugars in the shoots of Jiudao-66 were higher than that of Kitaake, and the total antioxidant capacity was stronger than that of Kitaake. However, the content of malondialdehyde was lower than that of Kitaake. Additionally, the Na+/K+ ratios in shoots and roots were not significantly differently between Kitaake and Jiudao-66. The results showed that Jiudao-66, as a salt-tolerant variety, is more tolerant to salt and alkali in a near-natural state due to its stronger tolerance of osmotic stress, and it can accumulate more proline and soluble sugars under stress. At the same time, Jiudao-66 also has a stronger antioxidant capacity. Its ion regulation ability has no obvious advantage.

Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice

Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.