FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry

Abstract

Optimal strategies for genetic improvement in crops depend on accurate assessments of the genetic architecture of traits. The overall objective of the present study was to determine the genetic architecture of anthracnose fruit rot (AFR) resistance caused by the fungus Colletotrichum acutatum in the University of Florida strawberry (Fragaria × ananassa) breeding germplasm. In 2016-2017, 33 full-sib families resulting from crosses between parents with varying levels of AFR resistance were tested. In 2017-2018, six full-sib families resulting from putative heterozygous resistant parents and homozygous susceptible parents were tested. Additionally, a validation population consisting of 77 advanced selections and ten cultivars was tested in the second season. Inoculation was performed using a mixture of three local isolates of the C. acutatum species complex. Phenotypes were scored weekly, and genotyping was performed using the IStraw35 Affymetrix Axiom^® SNP array. A pedigree-based QTL analysis was performed using FlexQTL™ software. A major resistance locus, which we name FaRCa1, was detected in both seasons with a peak located at 55-56 cM on LG 6B and explaining at least 50% of the phenotypic variation across trials and seasons. The resistant allele exhibited partial dominance in all trials. The FaRCa1 locus is distinct from the previously discovered Rca2 locus, which mapped to LG 7B. While Rca2 is effective against European isolates from pathogenicity group 2, FaRCa1 appears to confer resistance to isolates of pathogenicity group 1.

Fig. 1

Frequency distributions of disease incidence for AFR caused by C. acutatum for a discovery population, 2016–2017; b discovery population, 2017–2018; and c validation population, 2017–2018

Fig. 2

Graphical outputs from GWAS using 38,506 SNPs for discovery populations in 2016–2017 (a) and 2017–2018 (b) and a validation population in 2017–2018 (c) with SNP physical positions anchored to the Fragaria vesca spp. bracteata genome assembly

Fig. 3

a Traces of the QTL models across 28 LGs. Each dot represents an iteration, and continuous dots that form a line confirm the presence of a QTL. b Posterior probability of the QTL position. When the Bayes factor (BF) is greater than 25, the evidence of presence of a QTL is considered decisive

Fig. 4

Single-marker analysis in two discovery populations and a validation population for 11 SNP markers located in the FaRCa1 region. Six of the 19 SNP markers analyzed were highly monomorphic and thus not informative and two could not be confidently ordered on the linkage group

Fig. 5

Box plots showing disease incidence by marker genotype for IStraw35 SNP probe AX-89838986

Fig. 6

Schematic of LG 6 subgenomes based on a genetic map, showing the location of FaRCa1 approximately 10 cM from FaRCg1 on LG 6B