New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage

Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems. Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace ‘Hasawi’ as a donor parent to generate three F2 offspring (consisting each of 500 individuals) with three African cultivars (‘NERICA-L-19’, ‘Sahel 108’ and ‘BG90-2’) used as recipient parents (RP). The F2s and F2:3s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F2-derived offspring, e.g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP’s grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. ‘Hasawi’ contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.