This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na + /K + homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for markerassisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress.

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New salt-tolerant landraces were identified that are genetically and physiologically distinct from known donors. These landraces can be used to develop better salt-tolerant varieties and could provide new sources of quantitative trait loci/alleles for salt tolerance for use in molecular breeding. The diversity observed within this set and in other donors suggests multiple mechanisms that can be combined for higher salt tolerance.

Background Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F 2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. Results Out of the 231 F 2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na + concentration, K + concentration, Na + -K + ratio and survival; chromosome 3 for Na + concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na + concentration, survival, Na + -K + ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. Conclusions Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol , will facilitate breeding varieties that are highly tolerant of salt stress. Electronic supplementary material The online version of this article (10.1186/s12284-019-0319-5) contains supplementary material, which is available to authorized users.

Salt sensitivity in rice plants is associated with the accumulated amount of Na+ and Cl– in shoots and, more significantly, in photosynthetic tissues. Therefore, salt removal ability at the leaf sheath level is an important mechanism of salt tolerance. In the present study we attempted to determine whether rice leaf sheaths excluded Cl– as well as Na+, and to identify the tissues that were involved in the removal ability of both ions. In two rice genotypes, salt-tolerant FL478 and -sensitive IR29, leaf sheaths excluded Na+ and Cl– under NaCl treatment as estimated using their sheath:blade ratios. The sheath:blade ratio of Na+ but not of Cl–, was increased by NaCl treatment. Under NaCl treatment, Na+ concentration was higher in the basal leaf sheath, whereas Cl– concentration was higher in the middle and tip parts. At the tissue level, fundamental parenchyma cells of leaf sheaths retained the highest amounts of Na and Cl when treated with high amount of NaCl. These results imply that the leaf sheath potentially functions to remove excess Na+ and Cl– from xylem vessels in different locations along the axis, with the fundamental parenchyma cells of leaf sheaths being involved in over-accumulation of both Na+ and Cl–.