Genotyping by target sequencing (GBTS)-based genetic mapping uncovers synergistic interactions for stripe rust resistance in wheat cultivar Flanders.

YrFLA.1, YrFLA.2 and YrFLA.3, identified in wheat cultivar Flanders, collaboratively boost the level of adult plant resistance to stripe rust. Bread wheat cultivar Flanders has maintained an adequate level of adult plant resistance (APR) to stripe rust in China for more than 30 years despite exposure to a changing and variable pathogen population. To identify genomic segments conferring stripe rust resistance, an F recombinant inbred line (RILs) population from a cross of Avocet S and Flanders was analyzed genetically. The population and parents were evaluated in multiple environments and genotyped using the GenoBaitsWheatSNP16K array. Three stable QTL detected on chromosome arms 1BL, 3BL and 7BL were designated QYrfla.nwafu-1BL.7 (YrFLA.1, in a hot-spot region), QYrfla.nwafu-3BL.2 (YrFLA.2, possibly novel) and QYrfla.nwafu-7BL.6 (YrFLA.3, in a hot-spot region), respectively. YrFLA.3 was more effective than YrFLA.1 and YrFLA.2 in all environments, but synergistic interaction between all three loci led to significant enhancement of resistance. Under rust-free conditions there was almost no difference in thousand grain weight, but results from the rust nursery indicated a 21.81-28.76% reduction in the RILs lacking the QTL compared to the RILs with one or more QTL. On the other side, a panel of 679 current Chinese cultivars and breeding lines based on the GenoBaits assay was used to characterize the haplotype variation and the distribution of these loci. The haplotypes with the YrFLA.1, YrFLA.2 and YrFLA.3 regions have frequencies of 65.83, 18.99 and 43.44%, respectively, reducing disease severities of 17.57-37.54%. These findings indicate that effective gene pyramiding strategy is crucial for developing high yielding and durable resistance cultivars.