Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)

Henry O Awika,Kranthi K Mandadi,Renesh Bedre,Carlos A Avila,Thiago G Marconi

doi:10.1038/s41438-019-0214-7

Henry O Awika, Kranthi K Mandadi + Show 3 more

Open Access

https://doi.org/10.1038/s41438-019-0214-7

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Journal: Horticulture Research	Publication Date: Dec 1, 2019
Citations: 6	License type: open-access

Affiliation: Texas College, Texas A&M University

Abstract

Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.

Highlights

Genetic association studies can be used to determine whether a genetic variant is associated with a particular trait
For the associated loci, the mean minor allele frequency (MAF) were significantly higher in the white rust (WR)-DSR distribution tail containing the most susceptible accessions compared to the WR disease severity ratings (WR-DSRs) distribution tail containing the most resistant accessions (Fig. 3; Table 3), suggesting that these may be among the alleles most commonly associated with WR in this study
A limitation of the outlined basic allelic association methods is the possible occurrence of false positives that may be an artefact of the population structure[8]

Summary

Introduction

Genetic association studies can be used to determine whether a genetic variant is associated with a particular trait. If an association is present, a particular allele, genotype, or haplotype will be seen more often than is expected by chance in individuals or groups carrying the corresponding trait[1]. An individual carrying one or two copies of a particular allele is more likely to present the associated trait, such as susceptibility to a disease. One possibility is to perform a GWA to target minor alleles implicated as risk factors in susceptibility to the disease[7]. Determining the distribution of such alleles in diseased plants might illuminate the underpinnings of minor alleles important for WR susceptibility in spinach

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