Abstract
Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide polymorphism (SNP) marker linked to Rhizoctonia resistance using restriction site-associated DNA (RAD) sequencing of two geographically discrete sets of plant materials with different degrees of resistance/susceptibility to enable a wider selection of superior genotypes. The variant calling pipeline utilized SAMtools for variant calling and the resulting raw SNPs from RAD sequencing (15,988 and 22,439 SNPs) were able to explain 13.40% and 25.45% of the phenotypic variation in the two sets of material from different sources of origin, respectively. An association analysis was carried out independently on both the datasets and mutually occurring significant SNPs were filtered depending on their contribution to the phenotype using principal component analysis (PCA) biplots. To provide a ready-to-use marker for the breeding community, a systematic molecular validation of significant SNPs distributed across the genome was undertaken to combine high-resolution melting, Sanger sequencing, and rhAmp SNP genotyping. We report that RsBv1 located on Chromosome 6 (9,000,093 bp) is significantly associated with Rhizoctonia resistance (p < 0.01) and able to explain 10% of the phenotypic disease variance. The related SNP assay is thus ready for marker-assisted selection in sugar beet breeding for Rhizoctonia resistance.
Highlights
Sugar beet cultivation, contributing to ~20% of the world’s sugar production, is distressed by different pathogens
We report the discovery and validation of useful single-nucleotide polymorphism (SNP) associated with Rhizoctonia resistance tested in several international sugar beet germplasm
The plant material provided by the Sugar Beet Seed Institute (SBSI), Iran, comprised
Summary
Sugar beet cultivation, contributing to ~20% of the world’s sugar production, is distressed by different pathogens. One such fungal pathogen is the soil-borne fungus, Rhizoctonia solani which is recurrent and perennial in all sugar beet production areas and causes the typical root and crown rot. Symptoms can range from localized brown to black lesions on the root surface to complete rotting of the root. Symptoms are characterized by sudden wilting of the leaves and black lesions on the petioles attaching to the crown area. The extent of the damage it causes and the yield losses vary in sugar beet farms and are considerable and dramatic [1,2,3,4]. The loss in terms of recoverable white sugar is estimated at 50–60% and sometimes results in complete crop failure too [1,2,3]
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