Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover

Abstract

Key message High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding. Abstract Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.

Multi-location trials and population-based genotyping reveal high diversity and adaptation to breeding environments in a large collection of red clover

“…The overall high plant density in SRB after Y1 (Figure 9) is likely caused by the late sowing (autumn compared to spring for other trials) and the mild winter following sowing. In the Swiss trial, which experienced high southern anthracnose disease pressure, average plant densities after Y1 were highest for local, American and Eastern European accessions (62%, 57% and 59%, respectively) and lowest for Northern European accessions (21%), which is in agreement with the level of southern anthracnose resistance observed for these accessions in artificial inoculation experiments (Frey et al, 2022). The low plant density after Y1 resulted in non-satisfactory data quality in the second year for many accessions.…”

“…Although studies on genetic diversity can substantially assist breeding decisions, knowledge about phenotypic diversity is key to efficiently exploit red clover germplasm for cultivar development. While some studies have investigated the variability and inheritance of specific traits such as disease resistance (Frey et al, 2022), seed yield (Herrmann et al, 2005) or flowering time (Jones et al, 2020), only a few studies have investigated phenotypic diversity of several traits within a region or country and even fewer have studied diversity across regions. A study by Zanotto et al (2021) that was conducted with 48 ecotypes and six cultivars from Norway, Sweden, and Finland found large variation in winter survival and yield between the accessions.…”

Multi-location trials and population-based genotyping reveal high diversity and adaptation to breeding environments in a large collection of red clover

“…Genotyping of the 395 accessions and SNP calling was conducted as described in Frey et al (2022). In brief, plants from all accessions were grown in the greenhouse in 96-compartment trays.…”

“…SNP calling and calculations of allele frequencies were done as described in Keep et al (2020). A detailed description of the parameters used for this study are given in the supplementary methods of Frey et al (2022). SNPs were only retained if allele frequencies of at least 10 accessions were between 0.05 and 0.95 and if mean allele frequencies across all accessions were between 0.05 and 0.95.…”

“…Although studies on genetic diversity can substantially assist breeding decisions, knowledge about phenotypic diversity is key to efficiently exploit red clover germplasm for cultivar development. While some studies have investigated the variability and inheritance of specific traits such as disease resistance (Frey et al, 2022), seed yield (Herrmann et al, 2005) or flowering time (Jones et al, 2020), only a few studies have investigated phenotypic diversity of several traits within a region or country and even fewer have studied diversity across regions. A study by Zanotto et al (2021) that was conducted with 48 ecotypes and six cultivars from Norway, Sweden, and Finland found large variation in winter survival and yield between red clover accessions.…”