Accurate phenotyping reveals better QTL for waterlogging tolerance in barley

Tolerance to soil waterlogging stress is an important plant breeding objective in high rainfall or poorly drained areas across many countries in the world. Similar to other abiotic stresses, waterlogging tolerance is a complicated trait and the selection for tolerance has been a major obstacle in breeding programmes. Molecular marker-assisted selection (MAS) can be very effective. However, the success of MAS depends on the development of reliable markers which requires accurate phenotyping when searching for the markers linked to the tolerance. In this experiment, a new screening facility, with the environment closer to field conditions, has been used to screen a double haploid population produced from a cross between waterlogging tolerant and susceptible varieties. A new scoring system of plant healthiness (0 = plant died from waterlogging; 10 = not affected by waterlogging) was also used in this experiment. The results were compared with a previous glasshouse pot experiment. Some quantitative trait loci (QTL) identified from the current experiment and previous pot experiment were quite different. From this experiment, two major QTL (QWL.YeFr.4H and QWL.YeFr.2H.2, accounting 24% and 17% of phenotypic variation) and two minor QTL (QWL.YeFr.2H.1 and QWL.YeFr.3H, accounting 8% and 7% of the variation) were found. These four markers can be very effectively used to select waterlogging tolerance. By selecting all four closely linked markers, all the lines will be quite tolerant with an average score of 7.6. In contrast, if none of above markers were selected all the lines would be susceptible with an average score of 1.4.