QTL mapping and marker-assisted backcrossing for developing salinity tolerant rice (Oryza sativa L.)

The present study was carried out to identify quantitative trait loci (QTL) controlling salinity tolerance in rice using molecular markers and to transfer Saltol, a major QTL associated with salinity tolerance, to a mega variety to enhance salt stress tolerance. A population of 177 F2 plants from the cross of Kalarata, the salt tolerant parent and Azucena, the salt sensitive. was phenotyped for salt tolerance in a nutrient solution with salt stress of 12 dS/m using NaCl. A genetic linkage map was constructed with 100 SSRs and InDel markers which covers 1,405 cm with an average distance of 14.05 cm between loci. A total of 27 QTLs were identified using Composite Interval Mapping with 17 traits studied. The short arm of chromosome 1 had the highest density of detected QTLs responsible for salinity tolerance and seedling vigor, which coincide with the Saltol locus; emphasizing the importance of this locus for candidate gene discovery and for use in rice breeding. Introgression of Saltol QTL from the donor parent, FL478. into the recipient parent IR64 was completed through marker assisted backcrossing (MABC). The markers selected for foreground selection that were closely linked to Saltol locus showed high accuracy in tracing its inheritance. The use of flanking and background markers considerably enhanced the recovery rate of the recurrent parent genome within three backcross generations, which could have saved from 2-3 backcross compared with conventional schemes, to achieve the same results. Effectiveness of MABC was confirmed by evaluating the performance of five IR64. Saltol lines using saline culture solution at EC of 12 dS/m. Based on selected physiological and growth parameters, the new Saltol introgression lines were similar to their recurrent parent IR64. The results of this study confirmed the enormous benefits of the applications of molecular markers in plant breeding to enhance tolerance of abiotic stresses.