Identification of quantitative trait loci for seedling stage salinity tolerance using NSIC RC222 x Jumbo Jet BC1F2 Population

Salt tolerance is a quantitative trait controlled by multiple genes (QTL) acting together, making it difficult to understand the mechanisms underlying them. The complexity of these traits therefore become a problem in conventional breeding and has been one of the reasons for the breeders' increased interest in molecular breeding methods. The use of modern molecular genetic techniques and powerful statistical methods can provide insights on the genetic basis of such complex traits. By applying the procedure of QTL analysis in a particular population, the genetic control of quantitative traits can be dissected into its component parts. In this study, 184 BC1F2-JJ29-P1 lines derived from the cross between a salt-sensitive high yielding variety (NSIC Rc222) and a local landrace (Jumbo Jet) that shows high salinity tolerance at reproductive stage were grown under normal condition. Leaf samples were collected from the lines and their parents for DNA extraction and infinium SNP chip was used for SNP genotyping. Their genotype was used to correlate with the morphological and physiological traits of the 184 BC1F3-JJ29-P1 lines evaluated at seedling stage under salinized condition with an electrical conductivity (EC) of 12 dS/m. Exactly 194 markers were used to construct the genetic linkage map using inclusive composite interval mapping (ICIM) software version 4.1. The linkage map has a total length of 397.45 cM with an average interval size of 2.05 cM. Only one QTL (qSES1.2) that is associated with salinity evaluation score was identified with an LOD of 3.08 explaining 7.83% of the phenotypic variation under salt stress. It is recommended that fine-mapping of the identified QTL be conducted to help identify closely linked markers for use in marker-assisted backcrossing.