Data and code from: Comparison of in-field and laboratory-based phenotyping methods for evaluation of aflatoxin accumulation in maize inbred lines

Authors: Jeffers, Dan; SMITH, J. SPENCER - Former ARS Employee; WOMACK, ERIKA - Mississippi State University; Read, Quentin; Windham, Gary

Submitted to: Ag Data Commons
Publication Type: Database / Dataset
Publication Acceptance Date: 4/26/2024
Publication Date: 4/26/2024
Citation: Jeffers, D., Smith, J., Womack, E.D., Read, Q.D., Windham, G.L. 2024. Data and code from: Comparison of in-field and laboratory-based phenotyping methods for evaluation of aflatoxin accumulation in maize inbred lines. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/25289518.v1.
DOI: https://doi.org/10.15482/USDA.ADC/25289518.v1

Interpretive Summary: This is a dataset to be archived on Ag Data Commons to accompany a manuscript appearing in the journal Plant Science, which contains all data and statistical software code needed to reproduce the analyses, figures, and tables appearing in the manuscript. There is a critical need to quickly and reliably identify corn genotypes that are resistant to accumulating aflatoxin in their kernels. We compared three methods of determining how resistant different corn genotypes are to aflatoxin accumulation: a field-based assay (side-needle inoculation) and two different lab-based assays (wounding and non-wounding kernel screening assays; KSA). In this data object, we present the statistical models that are fit to the data, procedures for comparing model fit of different variants of the model, and model predictions. This includes how reliably each assay identifies resistant and susceptible check varieties, and how well correlated the assay methods are with one another. Statistical analyses are done using R software, including Bayesian models fit with Stan software.

Technical Abstract: Breeding for resistance to pre-harvest aflatoxin accumulation in maize (Zea mays) has been complicated by difficulties in field phenotyping evaluations. The kernel screening assay (KSA), a post-harvest laboratory assay, has been proposed as a pre-screening tool capable of replacing or complementing field evaluations in early stages of breeding. In the present study, a set of 16 inbred lines was screened over two years for degree of susceptibility to pre-harvest aflatoxin accumulation using the field-based side-needle inoculation method and the laboratory-based KSA. The side-needle inoculation was conducted seven days post-silk and the KSA was performed on mature kernels with and without wounding the kernel prior to inoculation. Pairwise correlations between genotype aflatoxin concentration means from the wounding and non-wounding KSA treatments was 0.80, while the field-based side-needle and the KSA wounding and non-wounding were 0.55 and 0.33, respectively. Intraclass correlation coefficients from mixed models in the field-based side-needle method partitioned most of the variation to genotype while both KSA methods partitioned most of the variation to year, indicating more consistent identification of genotype differences for the field-based method. Statistical evidence for differences was observed between all resistant and susceptible checks in the field evaluation but not in the KSA evaluations. Mp313E, a resistant check, was susceptible in the KSA evaluations. Also, some highly susceptible lines in field evaluations had a resistant reaction in the KSA evaluations. Difference in developmental stage of the kernel at the time of inoculation may contribute to disparities in the results obtained.