Identification and field validation of QTLs for soybean red crown rot resistance from wild soybean accessions

Four QTLs for resistance to soybean crown rot were identified in wild soybean accessions. Soybean red crown rot (RCR), a soil-borne disease caused by the fungus Calonectria ilicicola, result in can to annual yield losses of up to 30%. In this study, we identified quantitative trait loci (QTLs) associated with RCR resistance in three wild soybean accessions, 'Gs-7,' 'Gs-9,' and 'Gs-27.' QTL analysis was performed using four populations of recombinant inbred lines (RILs) derived from crosses between these wild soybean accessions and two susceptible soybean cultivars 'Enrei' (populations En7, En9, and En27, respectively) and 'Williams 82' (W9). Genetic linkage maps were constructed using 145-256 simple sequence repeat (SSR) markers for each population, and the RILs were evaluated for RCR resistance under greenhouse conditions. Four QTLs were detected across four regions: qRci1 (En9) (W9) on chromosome 8; qRci2 (En9) (En7) (W9) on chromosome 13; qRci3 (W9) on chromosome 18; qRci4 (En7) (En27) on chromosome 3. Further mapping using residual heterozygous lines localized qRci1 to a 2.52 Mb region between BARCSOYSSR_08_0371 and BARCSOYSSR_08_0507, containing 76 candidate genes. Mapping and QTL-seq analysis suggested that qRci2 is located in a 0.90 Mb region downstream of BARCSOYSSR_13_1504, containing 33 candidate genes. Three QTLs-qRci1, qRci2 and qRci4-were backcrossed into 'Enrei,' an elite Japanese cultivar, resulting in reduced disease severity in both greenhouse and field trials. No epistatic interactions were observed and pyramiding qRci2 and qRci4 conferred greater resistance than single QTLs in BC₁F₄ lines. These QTLs represent valuable genetic resources for enhancing RCR resistance in soybean breeding programs.