Abstract
Salinity is one of the most widespread abiotic stresses in rice growing areas of the world. Salinity tolerance in rice varies for different growth stages. Rice is relatively tolerant during germination, becomes very sensitive during the early seedling stage, gains tolerance during active tillering, becomes sensitive during reproductive stage and then relatively more tolerant at maturity. Thus, the seedling and reproductive stages are the most vulnerable to salt stress and plant experience greater damage from salt stress mostly at these stages. Very poor correlation exists between tolerance at the seedling stage and during reproduction, suggesting that tolerance at these two stages is regulated by a different set of genes. The reproductive stage is most crucial as it ultimately determines grain yield. This study was conducted to reveal the important mechanisms associated with salinity tolerance during reproductive development and identify underlying quantitative trait loci (QTLs) or genes using contrasting rice genotypes viz. Cheriviruppu and Pusa Basmati1. Cheriviruppu is an indica rice variety highly salt tolerant at seedling and reproductive stage is from Kerala coast of India. Pusa Basmati1 is an aromatic premium quality aromatic-indica rice variety sensitive to salinity at reproductive stage. These two varieties were crossed to develop F₂ mapping population that was used to identify the QTLs using co-dominant molecular markers like microsatellite/ simple sequence repeat (SSR). Each F₂ plant was phenotyped for agronomical (plant height, tiller no., panicle no., panicle length, grain weight, grain yield and biomass) cytological (pollen fertility) and physiological characters (Na⁺, K⁺ and Na⁺-K⁺ ratio in flag leaf). For the parental polymorphism survey, 510 microsatellite and Insertion/ Deletion (InDel) markers were used out of which 131 (25.7%) were found polymorphic between the two parents were used to construct linkage map of 1458.5 cM with a mean inter-marker distance of 11.1 cM. Sixteen QTLs with significant threshold of P < 0.001 (corresponding to an interval mapping LOD > 3.0 or a composite interval mapping LOD > 3.0) were detected. The LOD value of these QTLs ranged from 3.2-22.3 with phenotypic variation explained by those QTLs range from 4-47%. Genome-wide analysis using Map Manager QTX for all pairs of marker loci was performed and identified 29 significant epistatic (digenic) interactions which are falling into three groups: 2 interactions between QTLs, 15 interactions between complementary loci and 12 interactions between QTLs and background loci. The graphical genotyping analysis verified the position of detected QTLs for salt tolerance in this population. Results infers that Na⁺ concentration (mmol g⁻¹ dwt), Na⁺-K⁺ ratio and pollen fertility are the most important mechanisms controlling the salt tolerance at reproductive stage. This is the first report on identification of novel genomic loci for reproductive-stage salt tolerance related traits in rice. The present study reports the construction of the first genetic map for this population at reproductive-stage salt tolerance in rice and demonstrates its utility for molecular mapping of QTLs controlling salinity tolerance related traits which will be useful in marker assisted selection in future.