Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers.
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ABSTRACT:
SUBMITTER: Mohanavel V
PROVIDER: S-EPMC8446578 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Rice is a staple food crop in Asia and plays a crucial role in the economy of this region. However, production of rice and its cultivating areas are under constant threat of soil salinity. A major QTL, Saltol, responsible for salinity tolerance at seedling stage has been mapped on chromosome 1 using Pokkali/IR29 Recombinant Inbred Lines (RIL) population. The present study was aimed to incorporate Saltol Quantitative Trait Loci (QTL) in two high yielding mega rice varieties i.e. Pusa44 and Sarjoo52 through Marker Assisted Backcross Breeding (MABB). To improve the seedling stage salinity tolerance in these cultivars, we introgressed the Saltol QTL from donor parent FL478 a derivative of Pokkali. A total of three backcrosses (BC3) followed by selfing have led to successful introgression of Saltol QTL. Foreground selection at each breeding cycle was done using micro-satellite markers RM3412 and AP3206 to confirm Saltol QTL. The precise transfer of Saltol region was established using recombinant selection through flanking markers RM493 and G11a. Finally, 10 Saltol near isogenic lines (NILs) of Pusa44 and eight NILs of Sarjoo52 were successfully developed. These NILs (BC3F4) were evaluated for seedling stage salinity under hydroponic system. The NILs PU99, PU176, PU200, PU215, PU229, PU240, PU241, PU244, PU252, PU263 of Pusa44 and SAR17, SAR23, SAR35, SAR39, SAR77, SAR87, SAR123, SAR136 NILs of Sarjoo52 confirmed tolerance to salinity with low salt injury score of 3 or 5. Ratio of Na+/K+ content of Saltol NILs ranged from 1.26 to 1.85 in Pusa44 and 1.08 to 1.69 in Sarjoo52. The successfully developed NILs were further phenotyped stringently for morphological traits to estimate Phenotypic Recovery. Background selection of NILs along with parents was carried out with 50K SNP chip and recovered 94.83-98.38% in Pusa44 NILs and 94.51 to 98.31% in Sarjoo52 NILs of recurrent genome. The present study of MAB has accelerated the development of salt tolerant lines in the genetic background of Pusa44 and Sarjoo52. These NILs could be used for commercial cultivation in saline affected area.
| S-EPMC7300257 | biostudies-literature
Project description:BACKGROUND:Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits. RESULTS:There were 27 accessions performed well (SES < 5.0) under moderate salinity stress (EC12), and 5 accessions were tolerant under both EC12 and EC18. A total of 26 QTLs were identified for 9 measured traits. Eleven of these QTLs were co-located with known salinity tolerance genes. QTL/gene clusters were observed on chromosome 1, 2, 3, 6, 8 and 9. Six candidate genes were identified for five promising QTLs. The alleles of major QTL Saltol and gene O S HKT1;5 (SKC1) for Na+/K+ ratio identified in indica rice accessions were different from those in the temperate japonica rice accessions used in this study. CONCLUSION:Salinity tolerant temperate japonica rice accessions were identified in this study, these accessions are important resources for breeding programs. SNPs located in the promising QTLs and candidate genes could be used for future gene validation and marker assisted selection. This study provided useful information for future studies on genetics and breeding of salinity tolerance in temperate japonica rice.
| S-EPMC5753436 | biostudies-literature
Project description:BackgroundRice (Oryza sativa L.) is one of the major staple food crops consumed globally. However, rice production is severely affected by high salinity levels, particularly at the seedling stage. A good solution would be the development of an efficient screening methodology to identify genotypes possessing genes for salt tolerance.ResultA new salinity tolerance screening technique using rice seedlings in pot-culture was tested. This method controls soil heterogeneity by using pure sand as a growth medium and minimizes unexpected extreme weather conditions with a movable shelter. Seventy-four rice genotypes were screened at three salinity treatments including high salt stress (electrical conductivity (EC) 12 dSm- 1), moderate salt stress (EC 6 dSm- 1), and control (no salt stress), imposed 1 week after emergence. Several shoot and root morpho-physiological traits were measured at 37 days after sowing. A wide range of variability was observed among genotypes for measured traits with root traits being identified as the best descriptors for tolerance to salt stress conditions. Salt stress response indices (SSRI) were used to classify the 74 rice genotypes; 7 genotypes (9.46%) were identified as salt sensitive, 27 (36.48%) each as low and moderately salt tolerant, and 13 (17.57%) as highly salt tolerant. Genotypes FED 473 and IR85427 were identified as the most salt tolerant and salt sensitive, respectively. These results were further confirmed by principal component analysis (PCA) for accuracy and reliability.ConclusionAlthough tolerant genotypes still need to be confirmed in field studies and tolerance mechanisms identified at the molecular level, information gained from this study could help rice breeders and other scientists to accelerate breeding by selecting appropriate donor parents, progenies and potential genotypes at early growth stages necessary for salinity tolerance research.
| S-EPMC6667605 | biostudies-literature
Project description:The success of a rice breeding program in developing salt tolerant varieties depends on genetic variation and the salt stress response of adapted and donor rice germplasm. In this study, we used a combination of morphological and physiological traits in multivariate analyses to elucidate the phenotypic and genetic variation in salinity tolerance of 30 Southern USA rice genotypes, along with 19 donor genotypes with varying degree of tolerance. Significant genotypic variation and correlations were found among the salt injury score (SIS), ion leakage, chlorophyll reduction, shoot length reduction, shoot K(+) concentration, and shoot Na(+)/K(+) ratio. Using these parameters, the combined methods of cluster analysis and discriminant analysis validated the salinity response of known genotypes and classified most of the USA varieties into sensitive groups, except for three and seven varieties placed in the tolerant and moderately tolerant groups, respectively. Discriminant function and MANOVA delineated the differences in tolerance and suggested no differences between sensitive and highly sensitive (HS) groups. DNA profiling using simple sequence repeat markers showed narrow genetic diversity among USA genotypes. However, the overall genetic clustering was mostly due to subspecies and grain type differentiation and not by varietal grouping based on salinity tolerance. Among the donor genotypes, Nona Bokra, Pokkali, and its derived breeding lines remained the donors of choice for improving salinity tolerance during the seedling stage. However, due to undesirable agronomic attributes and photosensitivity of these donors, alternative genotypes such as TCCP266, Geumgangbyeo, and R609 are recommended as useful and novel sources of salinity tolerance for USA rice breeding programs.
| S-EPMC4444739 | biostudies-literature
Project description:Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.
| S-EPMC8228224 | biostudies-literature
Project description:Rice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. To understand the genetic basis of cold tolerance in rice, we evaluated the cold tolerance at the seedling stage (CTS) of 295 rice cultivars in the rice diversity panel 1 (RDP1), these cultivars were collected from 82 countries.The evaluations revealed that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars. Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1, we performed genome-wide association mapping of quantitative trait loci (QTLs) for CTS. The analysis identified 67 QTLs for CTS that are located on 11 chromosomes. Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs.Our study has provided new information on the genetic architecture of rice cold tolerance and has also identified highly cold tolerant cultivars and CTS-associated SNP markers that will be useful rice improvement.
| S-EPMC5110459 | biostudies-other
Project description:Marker assisted backcross breeding was used to transfer Saltol, a major QTL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked to Saltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection. Among the BC3F4 near isogenic lines (NILs) developed, recurrent parent genome recovery ranged from 96.67 to 98.57%. Multi-season evaluation identified some of the NILs showing significantly higher yield with grain and cooking quality comparable to PB 1509. All the NILs exhibited tolerance to salinity with significantly higher relative water content, membrane stability index and proline content as compared to PB 1509. The root and shoot concentration of Na+, K+ and Na+/K+ in NILs was at par with FL478 under stress conditions. The gene OsHKT1;5 located in the Saltol region showed higher expression levels under stress indicating its role in conferring salinity tolerance. Salt tolerant NILs of PB 1509 will be useful in stabilizing production in salt affected areas.
| S-EPMC7474085 | biostudies-literature
Project description:IntroductionThe 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.MethodsThe 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.ResultsThe 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.DiscussionThe 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.
| S-EPMC10266585 | biostudies-literature
Project description:Identification and cloning of cold-tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold-tolerant QTL at the seedling stage, qCTS-9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold-tolerant variety Lijiangxintuanheigu (LTH) and a cold-sensitive variety Shanhuangzhan 2 (SHZ-2). In this study, eight candidate genes within the qCTS-9 interval were identified through integrated analysis of QTL mapping with genomewide differential expression profiling of LTH. The qRT-PCR assay showed that only Os09g0410300 exhibited different expression patterns between LTH and SHZ-2 during cold stress, and significantly positive correlation was found between cold induction of Os09g0410300 and seedling cold tolerance in the RI lines. Five SNPs and one InDel in the promoters of Os09g0410300 were detected between LTH and SHZ-2, and the InDel marker ID410300 designed based on the insertion-deletion polymorphism in the promoter was significantly associated with seedling cold tolerance in RIL population. Further, Os09g0410300 over-expression plants exhibited enhanced cold tolerance at the seedling stage compared with the wild-type plants. Thus, our results suggest that Os09g0410300 is the functional gene underlying qCTS-9. To our knowledge, it is a novel gene contributed to enhance cold tolerance at the seedling stage in rice. Identification of the functional gene underlying qCTS-9 and development of the gene-specific marker will facilitate molecular breeding for cold tolerance at the seedling stage in rice through transgenic approach and marker-assisted selection (MAS).
| S-EPMC5552475 | biostudies-literature
Project description:Soil salinity is a worldwide issue that affects wheat production. A comprehensive understanding of salt-tolerance mechanisms and the selection of reliable screening indices are crucial for breeding salt-tolerant wheat cultivars. In this study, 30 wheat genotypes (obtained from a rapid selection of 96 original varieties) were chosen to investigate the existing screening methods and clarify the salinity tolerance mechanisms in wheat. Ten-day-old seedlings were treated with 150 mM NaCl. Eighteen agronomic and physiological parameters were measured. The results indicated that the effects of salinity on the agronomic and physiological traits were significant. Salinity stress significantly decreased K+ content and K+/Na+ ratio in the whole plant, while the leaf K+/Na+ ratio was the strongest determinant of salinity tolerance and had a significantly positive correlation with salt tolerance. In contrast, salinity stress significantly increased Na+ concentration and relative gene expression (TaHKT1;5, TaSOS1, and TaAKT1-like). The Na+ transporter gene (TaHKT1;5) showed a significantly greater increase in expression than the K+ transporter gene (TaAKT1-like). We concluded that Na+ exclusion rather than K+ retention contributed to an optimal leaf K+/Na+ ratio. Furthermore, the present exploration revealed that, under salt stress, tolerant accessions had higher shoot water content, shoot dry weight and lower stomatal density, leaf sap osmolality, and a significantly negative correlation was observed between salt tolerance and stomatal density. This indicated that changes in stomata density may represent a fundamental mechanism by which a plant may optimize water productivity and maintain growth under saline conditions. Taken together, the leaf K+/Na+ ratio and stomatal density can be used as reliable screening indices for salt tolerance in wheat at the seedling stage.
| S-EPMC8044411 | biostudies-literature