A Genome Wide Association Study (GWAS) Identifies SNPs Associated with Resistance to Tobacco Rattle Virus (TRV) and Potato Mop-Top Virus (PMTV) in a Tetraploid Mapping Population of Potato

• Published in: American journal of potato research 2024-02, Vol.101 (1), p.1-16
• Main Authors: Anglin, Noelle L., Yellarreddygari, Shashi K. R., Gudmestad, Neil C., Sathuvalli, Vidyasagar, Brown, Charles R., Feldman, Max, De Jong, Walter S., Douches, David S., Novy, Richard G., Coombs, Joseph J.
• Format: Article
• Language: English
• Subjects: Agriculture; Biomedical and Life Sciences; Castles; Chemical control; Chromosome 9; Chromosomes; Control methods; Core analysis; Disease resistance; Gene mapping; Genome-wide association studies; Genomes; Genotypes; Harvesting; Life Sciences; Mapping; Marker-assisted selection; Necrosis; Pest resistance; Phenotypes; Plant breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant Pathology; Plant Sciences; Plant virus diseases; Plant viruses; Polygenic inheritance; Polymerase chain reaction; Potatoes; Quantitative trait loci; Single-nucleotide polymorphism; Tobacco; Tubers; Vegetables; Viruses
• ISSN: 1099-209X; 1874-9380
• DOI: 10.1007/s12230-023-09933-3

Potato mop top virus (PMTV) and Tobacco rattle virus (TRV) are significant soil borne pathogens of potato vectored by powdery scab and stubby-root nematodes, respectively. These viruses adversely impact tuber quality with infected tubers displaying brown streaks in the flesh and/or necrotic arcs on the surface contributing to the rejection of tubers in commercial settings. Currently, limited agricultural control methods for PMTV are available to farmers outside of planting resistant genotypes and avoiding fields with its vector; however, for TRV chemical control of the nematode vector is an option. Field screening for susceptibility to PMTV and TRV identified ‘Castle Russet’ to be resistant to both PMTV and TRV. In order to localize virus resistance genes for the development of marker assisted selection, a tetraploid mapping population (A15001) was developed by hybridizing ‘Castle Russet’ x A06084-1TE (susceptible to both viruses) and its progeny were subsequently trialed for two years in fields known to be infested with PMTV and TRV (two separate disease trial sites) near Larimore, ND. The population was phenotyped for PMTV and TRV incidence and severity of necrotic tubers at two time points post-harvest (approximately 19 days after harvest and 89 days after storage) with several genotypes in the population showing little or no virus induced necrosis over the years of evaluation, making them useful as parents in hybridizations by the potato breeding community. Tubers produced from the population were further assayed for PMTV and TRV infection by testing tuber core samples with a quantitative polymerase chain reaction (qPCR) assay. The A15001 population and the parents, 241 individuals, were genotyped with the Illumina Infinium SolCAP V2 12K Potato SNP Array yielding 6,704 quality-filtered, informative SNP markers. A genome wide association study (GWAS) analysis revealed SNP markers on multiple chromosomes (1, 2, 3, 5, and 11) that were significantly associated with PMTV incidence and negative qPCR suggesting polygenic inheritance. Conversely, GWAS revealed a significant QTL on chromosome 9 associated with all TRV phenotypes indicative of a major gene contributing to TRV resistance. These data can guide the development of molecular markers to select genotypes resistant to PMTV and TRV in potato breeding programs.