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

Authors: Anglin, Noelle; YELLARREDDYGARI, SHASHI - North Dakota State University; GUDMESTAD, NEIL - North Dakota State University; SATHUVALLI, VIDYASAGAR - Oregon State University; BROWN, CHARLES - Former ARS Employee; Feldman, Max; DE JONG, WALTER - Cornell University; DOUCHES, DAVID - Michigan State University; Novy, Richard - Rich; COOMBS, JOSEPH - Michigan State University

Submitted to: American Journal of Potato Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2023
Publication Date: 12/19/2023
Citation: Anglin, N.L., Yellarreddygari, S.K., Gudmestad, N.C., Sathuvalli, V., Brown, C., Feldman, M.J., De Jong, W.S., Douches, D.S., Novy, R.G., Coombs, J.J. 2023. 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. American Journal of Potato Research. 101:1–16. https://doi.org/10.1007/s12230-023-09933-3.
DOI: https://doi.org/10.1007/s12230-023-09933-3

Interpretive Summary: Potato mop top virus (PMTV) and Tobacco rattle virus (TRV) are significant disease problems in potato. Both are transmitted in the soil and can affect tuber quality leading to rejection of tubers in the marketplace. These viruses can cause the tubers to have brown streaks in the flesh with symptoms so similar to one another, they are difficult for even disease experts to tell which of the viruses caused the problem. Many potato plants and their tubers show no symptoms of these diseases; yet, they are positive for these viruses leading to further dissemination of the virus. Limited options are available for growers to control these disease and no cultivars have been identified that are completely immune to these viruses. Therefore, in an effort to locate resistance genes and develop laboratory tools to select for resistance, a population with a susceptible and resistant parent was grown in North Dakota in fields infested with PMTV and TRV over a period of several years. Tubers were harvested and evaluated for prevalence of symptoms associated with these viruses. Laboratory testing was carried out to determine how many samples were positive for these viruses. Genetic analyses was performed and genes associated with resistance were identified. These data can guide the development of laboratory tests to select genotypes resistant to PMTV and TRV in potato breeding programs.

Technical Abstract: Potato mop top virus (PMTV) and Tobacco rattle virus (TRV) are significant soil borne pathogens of potato vectored by Spongospora subterranea f. sp. subterranea and stubby-root nematodes, respectively. These viruses adversely impact tuber quality with infected tubers displaying brown streaks in the flesh and 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 insensitive 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 insensitive 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). The population was phenotyped for PMTV and TRV incidence and severity of necrotic tubers at two time points post-harvest 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 22K potato SNP array yielding 6,790 quality-filtered, informative SNP markers. A genome wide association study (GWAS) analysis revealed a significant QTL on chromosome 9 associated with all TRV phenotypes indicative of a major gene contributing to TRV resistance. Conversely, SNP markers were identified on five chromosomes that were significantly associated with PMTV incidence and negative qPCR frequencies suggesting polygenic inheritance. These data can guide the development of molecular markers to select genotypes insensitive to PMTV and TRV in potato breeding programs.