Identification and Validation of the Genomic Regions for Waterlogging Tolerance at Germination Stage in Wheat

Waterlogging occurs when field soil is saturated with water induced by extensive rainfall or improper irrigation, which is a severe abiotic stress influencing wheat plant growth and yield production. At the germination stage, waterlogging usually induces rot of seeds and reduced germination rate and seedling survival. Development of tolerant wheat varieties is the most efficient approach to improve seed germination and mitigate the damages caused by waterlogging. In this study, we screened 432 wheat accessions at germination stage by waterlogging treatment, and identified 27 tolerant accessions with a germination rate of over 80% after treatment. To identify quantitative trait loci (QTL) for waterlogging tolerance, two segregation populations were developed by crossing waterlogging-tolerant cultivars Shannong 135 and Huaimai 18 with sensitive cultivars Siyang 936 and CD1840, respectively. Three QTL qWlg5A, qWlg7B and qWlg2D for waterlogging tolerance were detected on chromosomes 5A, 7B and 2D through bulked segregation analysis genotyped by wheat 55K SNP array. Two, one, and two kompetitive allele specific PCR (KASP) assays linked with qWlg5A, qWlg7B and qWlg2D were developed and validated in the two populations, respectively. The identified waterlogging tolerant germplasm lines, the QTL for waterlogging tolerance and the high-throughput KASP markers, were highly valuable in improving waterlogging tolerance in wheat-marker-assisted breeding.