Abstract
Salt stress is one of the major abiotic constraints across rice producing areas worldwide. Rice is highly sensitive to salt stress at seedling and reproductive stages, and tolerance at seedling stage is particularly important for better crop establishment in coastal areas. This study was undertaken to identify quantitative trait loci (QTLs) associated with salinity tolerance at seedling stage; confirm the significance of one major QTL other than Saltol and introgress Saltol into BRRI dhan29 through marker-assisted backcrossing (MABC) to enhance its salt tolerance. A mapping population of 250 F2 individuals and their corresponding F3 families, derived from a cross between a Bangladeshi salt tolerant landrace Chikiram Patnai (Indica) and the salt sensitive variety Azucena (Japonica) was used to map QTLs for salt tolerance at seedling stage. F23 families were evaluated for 15 traits potentially associated with salinity tolerance at seedling stage. Phenotyping was performed in hydroponics with salt stress of EC 12 dS m1. A framework linkage map was constructed with 111 SSR/InDel markers spanning the 12 chromosomes, with a total length of 2081.0 cM, and an average distance of 18.8 CM between the markers. A total of 37 QTLs were identified by single marker analysis (SMA), interval mapping (IM) and composite interval mapping (CIM) with an LOD≥ 3.0. Five major QTLs were detected for shoot Na" (qNal.1) and K* (qK1.1) concentrations, shoot Na*-K ratio (qNaK1.1), root K (qR-K1.1) concentration and root Na*-K* ratio (qR-NaK1.1) on the short arm of chromosome 1 with LOD values in the range of 4.2-12.9 and phenotypic variance of 7.5-21.2%. These QTLs are in the same locus as the Saltol QTL identified before. The major QTLs, qSES1.1, qRL1.1, qRDW11.1, qR- Na6.1 and qR-NaK8.1 on chromosomes 1, 11, 6 and 8 are novel in this study and can be further exploited for fine mapping, gene discovery and for subsequent use in breeding by pyramiding them with other QTLs for salinity tolerance or for tolerance of other abiotic stresses. Furthermore, a novel QTL was mapped to a smaller segment on the long arm of chromosome 1 in a BC3F4 near isogenic lines (NILS) developed from the cross of FL478/IR29. Twenty-three single nucleotide polymorphisms (SNPs) and six SSR/InDels were used to generate a genetic linkage map in the target region (119.8- 166.1 CM), with an average interval of 1.6 cM between markers, and the total length of 46.3 CM. The QTL region was narrowed down from 33.0 cM to 5.6 CM, and the QTL was found to be linked to the SNP marker id1023967 and flanked between id1023967 and id1024972. In addition, QTLs for root biomass, shoot Na* and K* concentrations, shoot Na*-K* ratio and root Na* concentration were also identified in this region. These QTLs could further be validated and fine-mapped for use in breeding to develop varieties that are highly tolerant of salt stress at seedling stage. The Saltol QTL from FL478 was successfully introgressed into BRRI dhan29, a popular variety for irrigated ecosystem in Bangladesh, through MABC. Homozygous BC3F3 individuals were selected, three of them within 2.3 Mb (11.0-13.3 Mb) and seven within 1.2 Mb (11.0-12.2 Mb) introgression segment containing the Saltol locus, and were 98.9% and 99.3% similar to BRRI dhan29, respectively. Background recovery and the Saltol introgression were further confirmed using a 384-plex GoldenGate SNP assay, which showed 97.3% to 99.3% of the recurrent parent genome recovery. All the introgressed lines did not show any undesirable traits. Three BR29-Saltol lines viz. IR98066-86-B, IR98066-102-B and IR98066- 146-B were ultimately selected for further evaluation for release as new salt tolerant varieties or for use in breeding to develop varieties suitable for salt affected areas.