QTL mapping for salinity tolerance using an elite rice (Oryza sativa) breeding population

QTL mapping for salinity tolerance using an elite rice (Oryza sativa) breeding population

A recombinant inbred line (RIL) population was previously developed with two high yielding rice varieties, At354, a salt tolerant parent and Bg352, a salt susceptible parent aiming at identifying salinity tolerant QTLs together with varietal development. In this study we used 100 F5 RILs of At354 x Bg352 to characterize the population and map genes for salt tolerance. Nine morpho-physiological parameters related to salinity tolerance were assessed under hydroponics supplemented with 100 mM NaCl concentration (12 dS/m). Frequency distributions of these 9 morpho-physiological traits, standard evaluation score, salinity survival index, shoot length, root length, shoot dry weight, root dry weight, shoot Na+ concentration, shoot K+ concentration and shoot Na+/K+ ratio indicated the broad spectrum of genetic variability in the RIL population under salinity stress while correlation coefficients also were significant with each other. Broad sense heritability also proved that the population was suitable for the gene mapping for salinity tolerance. Composite Interval mapping revealed 6 QTLs distributed in chromosome 1 and 4 namely, qSSI1, qSL1, qSNK1, qSL4, qSNK4 and qSSI4, explaining 10.8%, 10%, 8.9%, 15%, 11% and 16% of the phenotypic variations respectively. In all QTLs At354 allele contributed in favour of salinity tolerance. However, closer flanking markers could not be detected due to the low rate of polymorphism in SSR markers which generated low density molecular map. Therefore, further studies incorporating high throughput marker technologies would be necessary for detecting QTLs with narrow marker intervals.

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