Marker-assisted recurrent selection improves the crown rot resistance of bread wheat

Crown rot of wheat and barley is a serious disease caused by the fungus Fusarium pseudograminearum, a stubble-borne pathogen common in no-till farming systems in water-limited grain growing regions. Marker assisted recurrent selection (MARS) was used to more effectively pyramid minor genes controlling plant response to crown rot disease. Two populations comprising 475 genotypes were phenotyped for adult plant resistance and genotyped using a 9K SNP array. A genome-wide association study (GWAS) was used to estimate quantitative trait locus (QTL) effects as more than two parents were recombined in each population. A total of 23 significant and unique marker-trait associations (MTAs) were identified in both populations. A Kompetitive allele-specific PCR (KASP) assay was developed and used to genotype the progeny and parents of each recombination cycle. Following two cycles of recombination among progeny, up to 22 markers of a possible 23 were recombined. Two hundred ninety-seven double haploid-derived lines representing both cycles of recombination, the original parents, parents selected from the base population and local cultivars were evaluated for crown rot resistance in 2016 and 2017 in the field under crown rot inoculation pressure. A significant and positive response to each cycle of recurrent selection was observed. MARS was an effective breeding strategy for combining many QTLs of small effect for crown rot resistance in wheat.