Tolerance of wheat to vegetative stage soil waterlogging is conditioned by both constitutive and adaptive QTL

Soil waterlogging is a primary constraint to crop yield both globally and in the United States, yet little is known about the genetic control of waterlogging tolerance in wheat. The objective of this study was to characterize genetic variation for key adaptive traits influencing waterlogging tolerance at the vegetative stage and to identify associated quantitative trait loci (QTL). Traits measured included shoot and root biomass, root length, tiller number, seedling height, stem elongation, and chlorophyll content. Waterlogging reduced traits means by 8–58 % in the greenhouse and by 22–32 % in the field, with the largest reduction observed for root length. Both root biomass and root length showed significant genotype by treatment interaction indicating an adaptive growth response in waterlogged versus non-waterlogged soils and a possible mechanism of tolerance. A positive correlation was observed between chlorophyll content and shoot biomass, and between root and shoot biomass under waterlogging, which may make indirect selection possible. QTL analysis identified 48 individual QTL that clustered into 10 genomic regions consistently detected in both the greenhouse and field experiments. While most clusters were constitutively expressed, regions on chromosomes 1B and 6D were found to be adaptive to conditions of soil waterlogging, with no QTL detected in the non-waterlogged controls. A QTL region on chromosome 1D specific for chlorophyll content was significant across environments and repeated measurements, explaining up to 24 % of the phenotypic variation. This study provides the first reported QTL for waterlogging tolerance in wheat identified under both field and greenhouse conditions. The QTL can be targeted by breeders for future genetic improvement.