Mapping QTLs Related to Salt Tolerance in Rice at the Young Seedling Stage using 384-plex Single Nucleotide Polymorphism SNP, Marker Sets

Abstract

Salinity is one of the most serious factors limiting the productivity of rice crops, with adverse effects on germination, plant vigor and crop yield. A population of 300 F 5:6 recombinant inbred lines (RILs), which was derived from a cross between IR29 (indica sensitive to salinity) and Hasawi (Saudi cultivar showing salt tolerance), was evaluated at a young seedling stage under hydroponic conditions at an EC of 12 dsm -1 . Such RIL population when fixed can be repeatedly used for investigating QTLs of various phenotypes under different environments. Transgressive segregation was noted for all traits in the RILs; In all 31 RILs (10% of the 300 RILs) had tolerance level similar or better than Hasawi as determined by their standard evaluation system (SES) score of 4 or less, performance under both saline and non-saline conditions for plant height, root length, shoot dry weight and shoot fresh weight; suggesting these RILs can be rated as tolerant to salinity and are been advanced in our breeding program Quantitative trait loci (QTL) related to salt tolerance were detected using 142 F 5 RILs and single nucleotide polymorphisms (SNPs) chip composed of 384 SNP markers for indica x indica background. There were seven significant QTL related to 4 different traits associated to salt tolerance at young seedling stage. They were mapped on chromosomes 1, 2 and 6. The QTL qDW1.1, qDW2.1, qDW2.2 and qDW6.1 co-segregated with shoot dry weight and accounted between 10.6 and 42.3% of its phenotypic variation, while qPH1.1 and qPH1.2 were associated with plant height (explaining between 12.7 and 13.8% of its phenotypic variation), and qF2.1 co-segregated with shoot fresh weight (10.6% of trait variation) was accounted by SNP marker (id2007526). These QTLs had positive additive effects confirming that Hasawi alleles contributed to enhance traits related to salt tolerance at young seedling stage. The SNP markers associated with the QTLs identified in this study could be useful for further marker-aided breeding aiming at developing new rice cultivars for saline-prone agro-ecosystems