BackgroundSalinity is one of the many abiotic stresses limiting rice production worldwide. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated to salinity tolerance. However, due to large confidence interval for the position of QTLs, utility of reported QTLs and the associated markers has been limited in rice breeding programs. The main objective of this study is to construct a high-density rice genetic map for identification QTLs and candidate genes for salinity tolerance at seedling stage.ResultsWe evaluated a population of 187 recombinant inbred lines (RILs) developed from a cross between Bengal and Pokkali for nine traits related to salinity tolerance. A total of 9303 SNP markers generated by genotyping-by-sequencing (GBS) were mapped to 2817 recombination points. The genetic map had a total map length of 1650 cM with an average resolution of 0.59 cM between markers. For nine traits, a total of 85 additive QTLs were identified, of which, 16 were large-effect QTLs and the rest were small-effect QTLs. The average interval size of QTL was about 132 kilo base pairs (Kb). Eleven of the 85 additive QTLs validated 14 reported QTLs for shoot potassium concentration, sodium-potassium ratio, salt injury score, plant height, and shoot dry weight. Epistatic QTL mapping identified several pairs of QTLs that significantly contributed to the variation of traits. The QTL for high shoot K+ concentration was mapped near the qSKC1 region. However, candidate genes within the QTL interval were a CC-NBS-LRR protein, three uncharacterized genes, and transposable elements. Additionally, many QTLs flanked small chromosomal intervals containing few candidate genes. Annotation of the genes located within QTL intervals indicated that ion transporters, osmotic regulators, transcription factors, and protein kinases may play essential role in various salt tolerance mechanisms.ConclusionThe saturation of SNP markers in our linkage map increased the resolution of QTL mapping. Our study offers new insights on salinity tolerance and presents useful candidate genes that will help in marker-assisted gene pyramiding to develop salt tolerant rice varieties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0125-2) contains supplementary material, which is available to authorized users.

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.

Rice tungro disease (RTD) is a serious constraint to rice production in South and Southeast Asia. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Rice cv. Utri Merah is resistant to RTSV. To identify the gene or genes involved in RTSV resistance, the association of genotypic and phenotypic variations for RTSV resistance was examined in backcross populations derived from Utri Merah and rice germplasm with known RTSV resistance. Genetic analysis revealed that resistance to RTSV in Utri Merah was controlled by a single recessive gene (tsv1) mapped within an approximately 200-kb region between 22.05 and 22.25 Mb of chromosome 7. A gene for putative translation initiation factor 4G (eIF4G(tsv1)) was found in the tsv1 region. Comparison of eIF4G(tsv1) gene sequences among susceptible and resistant plants suggested the association of RTSV resistance with one of the single nucleotide polymorphism (SNP) sites found in exon 9 of the gene. Examination of the SNP site in the eIF4G(tsv1) gene among various rice plants resistant and susceptible to RTSV corroborated the association of SNP or deletions in codons for Val(1060-1061) of the predicted eIF4G(tsv1) with RTSV resistance in rice.

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.

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