Interactive Epistatic QTLs Mapping for Morpho-Physiological Traits Influencing the Salinity Tolerance at Seedling Stage in Rice

Salinity limits rice establishment and productivity, particularly during early growth. This study investigated pairwise epistatic quantitative trait loci (QTLs) associated with seven morpho-physiological responses to salt stress at the seedling stage in rice. A mapping population comprising 234 F₂ individuals derived from MTU 1061 (salt-tolerant) × MTU 1121 (salt-susceptible) was genotyped using 104 polymorphic simple sequence repeat (SSR) markers. Their F₂:₃ progenies and the parental cultivars were evaluated in a hydroponic screening system with salinity increased from an electrical conductivity of 6 to 12 dS m⁻¹. Salt injury score, shoot sodium and potassium concentrations, shoot Na⁺/K⁺ ratio, shoot length, root length and shoot dry weight were recorded. A linkage map covering 12 rice chromosomes spanned 2,956.12 cM. Interval mapping for epistatic interactions (IM-EPI) identified 257 QTL pairs across these seven traits: 32 for salt injury score, 21 for shoot Na⁺ concentration, 15 for shoot K⁺ concentration, 52 for the shoot Na⁺/K⁺ ratio, 60 for shoot length, 72 for root length and 5 for shoot dry weight. The distribution of interactions across traits suggests that pairwise genetic effects contribute to variation in seedling responses to salinity. The mapped regions provide a basis for further examination of the genetic architecture of seedling-stage salt tolerance, although their utility for marker-assisted selection requires validation.