Dataset Information

Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'.

ABSTRACT: Salinity is a major threat to rice production worldwide. Several studies have been conducted to elucidate the molecular basis of salinity tolerance in rice. However, the genetic information such as quantitative trait loci (QTLs) and molecular markers, emanating from these studies, were rarely exploited for marker-assisted breeding. To better understand salinity tolerance and to validate previously reported QTLs at seedling stage, a set of introgression lines (ILs) of a salt tolerant donor line 'Pokkali' developed in a susceptible high yielding rice cultivar 'Bengal' background was evaluated for several morphological and physiological traits under salt stress. Both SSR and genotyping-by-sequencing (GBS) derived SNP markers were utilized to characterize the ILs and identify QTLs for traits related to salinity tolerance. A total of eighteen and thirty-two QTLs were detected using SSR and SNP markers, respectively. At least fourteen QTLs detected in the RIL population developed from the same cross were validated in IL population. Analysis of phenotypic responses, genomic composition, and QTLs present in the tolerant ILs suggested that the mechanisms of tolerance could be Na+ dilution in leaves, vacuolar Na+ compartmentation, and possibly synthesis of compatible solutes. Our results emphasize the use of salt injury score (SIS) QTLs in marker-assisted breeding to improve salinity tolerance. The tolerant lines identified in this study will serve as improved breeding materials for transferring salinity tolerance without the undesirable traits of Pokkali. Additionally, the lines will be useful for fine mapping and map-based cloning of genes responsible for salinity tolerance.

SUBMITTER: De Leon TB

PROVIDER: S-EPMC5384751 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'.

De Leon Teresa B TB Linscombe Steven S Subudhi Prasanta K PK

PloS one 20170407 4

Salinity is a major threat to rice production worldwide. Several studies have been conducted to elucidate the molecular basis of salinity tolerance in rice. However, the genetic information such as quantitative trait loci (QTLs) and molecular markers, emanating from these studies, were rarely exploited for marker-assisted breeding. To better understand salinity tolerance and to validate previously reported QTLs at seedling stage, a set of introgression lines (ILs) of a salt tolerant donor line ' ...[more]

PMID: 28388633

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Project description:BACKGROUND:Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace, whereas IR29 is a salt-sensitive but widely cultivated genotype. Comparative analysis of these genotypes may offer a better understanding of the salinity tolerance mechanisms in rice. Although most stress-responsive genes are regulated at the transcriptional level, in many cases, changes at the transcriptional level are not always accompanied with the changes in protein abundance, which suggests that the transcriptome needs to be studied in conjunction with the proteome to link the phenotype of stress tolerance or sensitivity. Published reports have largely underscored the importance of transcriptional regulation during salt stress in these genotypes, but the regulation at the translational level has been rarely studied. Using RNA-Seq, we simultaneously analyzed the transcriptome and translatome from control and salt-exposed Pok and IR29 seedlings to unravel molecular insights into gene regulatory mechanisms that differ between these genotypes. RESULTS:Clear differences were evident at both transcriptional and translational levels between the two genotypes even under the control condition. In response to salt stress, 57 differentially expressed genes (DEGs) were commonly upregulated at both transcriptional and translational levels in both genotypes; the overall number of up/downregulated DEGs in IR29 was comparable at both transcriptional and translational levels, whereas in Pok, the number of upregulated DEGs was considerably higher at the translational level (544 DEGs) than at the transcriptional level (219 DEGs); in contrast, the number of downregulated DEGs (58) was significantly less at the translational level than at the transcriptional level (397 DEGs). These results imply that Pok stabilizes mRNAs and also efficiently loads mRNAs onto polysomes for translation during salt stress. CONCLUSION:Under salt stress, Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis. The present study confirmed the known salt stress-associated genes and also identified a number of putative new salt-responsive genes. Most importantly, the study revealed that the translational regulation under salinity plays an important role in salt-tolerant Pok, but such regulation was less evident in the salt-sensitive IR29.

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.

Project description:Salinity is a complex trait that affects growth and productivity in many crops, including rice. Mutation induction, a useful tool to generate salt tolerant plants, enables the analysis of plants with similar genetic background, facilitating the understanding of the salt tolerance mechanisms. In this work, we generated three salt tolerant mutant lines by irradiation of a salt-sensitive cultivar plants and screened M2 plants at seedling stage in the presence of high salinity. These three lines, SaT20, SaS62, and SaT58, showed different responses to salinity, but exhibited similar phenotype to wild type plants, except SaT20 that displayed shorter height when grown in the absence of salt. Under salt conditions, all three mutants and the parental line showed similar reduction in yield, although relevant differences in other physiological parameters, such as Na+ accumulation in healthy leaves of SaT20, were registered. Microarray analyses of gene expression profiles in roots revealed the occurrence of common and specific responses in the mutants. The three mutants showed up-regulation of responsive genes, the activation of oxido-reduction process and the inhibition of ion transport. The participation of jasmonate in the plant response to salt was evident by down-regulation of a gene coding for a jasmonate O-methyltransferase. Genes dealing with lipid transport and metabolism were, in general, up-regulated except in SaS62, that also exhibited down-regulation of genes involved in ion transport and Ca2+ signal transduction. The two most tolerant varieties, SaS62 and SaT20, displayed lower levels of transcripts involved in K+ uptake. The physiological study and the description of the expression analysis evidenced that the three lines showed different responses to salt: SaT20 showed a high Na+ content in leaves, SaS62 presented an inhibition of lipid metabolism and ion transport and SaT58 differs in both features in the response to salinity. The analysis of these salt tolerant mutants illustrates the complexity of this trait evidencing the breadth of the plant responses to salinity including simultaneous cooperation of alternative or complementary mechanisms.

Dataset Information

Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'.

Publications

Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'.

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