Skip to main content
ARS Home » Plains Area » Fort Collins, Colorado » Center for Agricultural Resources Research » Agricultural Genetic Resources Preservation Research » Research » Publications at this Location » Publication #390901

Research Project: Efficient and Effective Preservation and Management of Plant and Microbial Genetic Resource Collections

Location: Agricultural Genetic Resources Preservation Research

Title: Development of an SNP assay for marker-assisted selection of soil-borne Rhizoctonia solani AG-2-2-IIIB resistance in sugar beet

item RAVI, SAMATHMIKA - University Of Padua
item HASSANI, MAHDI - Agricultural Research, Education And Extension Organization (AREEO)
item HEIDARI, BAHRAM - Shiraz University
item DEB, SAPTARATHI - University Of Padua
item ORSINI, ELENA - Strube Research Gmbh & Co Kg
item LI, JINQUAN - Strube Research Gmbh & Co Kg
item Richards, Christopher
item PANELLA, LEE - US Department Of Agriculture (USDA)
item SRINIVASAN, SUBHASHINI - Institute Of Bioinformatics And Applied Biotechnology (IBAB)
item CAMPAGNA, GIOVANNI - Cooperative Beet Producers
item CONCHERI, GIUSEPPE - University Of Padua
item SQUARTINI, ANDREA - University Of Padua
item STEVANATO, PIERGIORGIO - University Of Padua

Submitted to: Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/27/2021
Publication Date: 12/29/2021
Citation: Ravi, S., Hassani, M., Heidari, B., Deb, S., Orsini, E., Li, J., Richards, C.M., Panella, L., Srinivasan, S., Campagna, G., Concheri, G., Squartini, A., Stevanato, P. 2021. Development of an SNP assay for marker-assisted selection of soil-borne Rhizoctonia solani AG-2-2-IIIB resistance in sugar beet. Biology. 11(1). Article e49.

Interpretive Summary: Sustainable breeding of sugar beet against Rhizoctonia solani relies on the continuous identification of resistance genes to allow their integration into new and modern cultivars. Better control of the disease may thus be achieved by a combination of tolerant or resistant cultivars selected based on molecular markers such as SNPs. The utility of one such marker, RsBv1 (Chromosome 6, 9,000,093 bp, C/T), located in an ADP-ribosylation factor and associated with Rhizoctonia resistance resulting from validation of three geographically diverse plant materials is reported.

Technical 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.