Quantitative Trait Loci Mapping for Vigour and Survival Traits of Barley Seedlings after Germinating under Salinity Stress

Seed germination and seedling establishment are the most critical stages in the barley (Hordeum vulgare ssp. vulgare L.) life cycle that contribute substantially to grain yield. These two phases are exposed to several forms of environmental stresses such as salinity due to high level of salt accumulation in the soil rhizosphere where seed germination takes place and seedlings emerge from. Previously, we have reported genotypic variability and independent QTLs associated with salinity tolerance at seedling and germination stages. However, genotypic studies on revival of a seedling germinating under salinity stress are yet to close the lack of information between germination and seedling stages. Here, we attempt to close the genetic gap by targeting early seedling survival traits in barley after germination under salinity (NaCl) stress and the various seedling vigour indices. Seedling vigour parameters formed the basis for Quantitative trait locus (QTL) linkage mapping in 103 Doubled Haploid (DH) lines of CM72/Gairdner population, and validated the phenotypic response using a selected diverse panel of 85 barley germplasm. The results indicate that 150 mM NaCl stress significantly reduced all the recorded phenotypic traits compared to 75, 90 and 120 mM NaCl. In both DH population and diversity panel barley germplasm, the highest percentage reduction was recorded in shoot length (65.6% and 50.3%) followed by seedling vigour index length (56.5% and 41.0%), while root length (28.6% and 15.8%) and root dry weight (29.3% and 28.0%) were least reduced when control was compared to150 mM NaCl stress treatment. Six QTLs containing 13 significant markers were detected in the DH population, 3 on chromosomes 1H, 8 on 3H and 2 on 4H with LOD values ranging from 3 to 8 associated with seedling survival traits under salinity stress. Three QTLs one on 1H and two on 3H with closely linked significant markers (Bmac0032, bPb-9418 and bPb-4741), (bPb-4576 and bPb-9624) and (bPb-3623, bPb-5666 and bPb-6383) for 1H and two on 3H respectively formed the regions with high possibility of candidate genes. A QTL on 3H flanked with markers bPb-4576 and bPb-9624 that were detected in more than one salinity survival trait and were closely linked to each other will form a basis for detailed studies leading to gene functional analysis, genetic transformation and marker assisted selection (MAS).