Pinpointing Rcs3 for frogeye leaf spot resistance and tracing its origin in soybean breeding

Abstract

Frogeye leaf spot is a yield-reducing disease of soybean caused by the pathogen Cercospora sojina. Rcs3 has provided durable resistance to all known races of C. sojina since its discovery in the cultivar Davis during the 1980s. Using a recombinant inbred line population derived from a cross between Davis and the susceptible cultivar Forrest, Rcs3 was fine-mapped to a 1.15 Mb interval on chromosome 16. This single locus was confirmed by tracing Rcs3 in resistant and susceptible progeny derived from Davis, as well as three near-isogenic lines. Haplotype analysis in the ancestors of Davis indicated that Davis has the same haplotype at the Rcs3 locus as susceptible cultivars in its paternal lineage. On the basis of these results, it is hypothesized that the resistance allele in Davis resulted from a mutation of a susceptibility allele. Tightly linked SNP markers at the Rcs3 locus identified in this research can be used for effective marker-assisted selection.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01397-x.

Keywords: Disease resistance gene; Frogeye leaf spot (Cercospora sojina); Marker-assisted selection; Quantitative trait locus; Soybean (Glycine max).

Fig. 1

Genomic position of the Rcs3 locus fine-mapped in a recombinant inbred line population (N = 182). a Mapping position of Rcs3. Logarithm of the odds (LOD) scores from composite interval mapping places Rcs3 between the markers GSM859 and GSM791 on chromosome 16; dashed lines indicate the LOD threshold determined using 1000 permutations and α = 0.01; b linkage map used to fine-map the Rcs3 locus; c physical positions of the markers on chromosome 16 in the Williams82.a2 genome; the blue shaded area on the genetic and physical maps indicate the regions where marker LOD scores exceeded the significance threshold

Fig. 2

Genotypes and phenotypes of the ancestors of Davis. a Pedigree of Davis; an R or S below each name stands for resistance or susceptibility, respectively, to a bulk of five virulent C. sojina isolates. Cultivars in blue boxes carry the Davis haplotype at the Rcs3 locus, and cultivars in red boxes do not have the Davis haplotype. Gray boxes indicate the ancestor did not have SoySNP50K haplotype data or seed available for phenotyping. Dashed arrows show the inheritance of the Rcs3 locus. b The reactions of Davis, Ralsoy, and Arksoy to a bulk of five C. sojina isolates. c Genotype comparison between Davis and its ancestors using SoySNP50K; Davis has the same haplotype allele at the Rcs3 locus as Ralsoy, which is a selection from Arksoy

Fig. 3

Genotypes and phenotypes of Davis’s descendants that have crossovers in the Rcs3 region. a Pedigrees of Young, Cook, Hagood, and Dillon. An R or S below each name stands for resistance or susceptibility, respectively, to a bulk of five virulent C. sojina isolates. Cultivars in blue boxes carry all or part of the Davis haplotype at the Rcs3 locus, and cultivars in red boxes do not have the Davis haplotype. Dashed arrows show the inheritance of the Rcs3 locus. b The reactions of Young, Cook, Hagood, and Dillon to a bulk of five C. sojina isolates. (c) Genotype comparisons between Davis’s descendants that have a crossover at the Rcs3 locus using SoySNP50K. In the top panel Young carries the Davis haplotype across the Rcs3 locus. In the middle panel Cook carries the Davis haplotype downstream from the SNP at 32,539,894 bp. In the bottom panel Hagood carries the Davis haplotype upstream and Dillon carries the Davis haplotype downstream from the SNP at 34,214,614 bp. The scale bar on the bottom indicates the position of each SNP on chromosome 16 in the Williams82.a2 reference genome. The blue-shaded area shows the Rcs3 region flanked by the SNPs at 32,539,894 and 34,214,614

Fig. 4

Introgression of the Rcs3 resistance allele in three near-isogenic lines (NILs): Gordon-Rcs3, Thomas-Rcs3, and Wright-Rcs3. The Davis haplotype is shown at the top with the haplotypes of each of the recurrent parents under each NIL. The scale bar on the bottom indicates the position of each SNP on chromosome 16 in the Williams82.a2 reference genome. The blue-shaded area shows the Rcs3 locus based on the introgression regions of Thomas-Rcs3 at 32,539,894 and Wright-Rcs3 at 35,848,689

Fig. 5

Haplotypes of Davis, Ralsoy, and Arksoy on chromosome 16 segment harboring the Rcs3 QTL. SNPs targeted by flanking markers designed to differentiate the Davis from Ralsoy/Arksoy are indicated above the haplotypes, and physical positions are labeled below