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United States Department of Agriculture

Agricultural Research Service


Location: Hard Winter Wheat Genetics Research

Title: In the eye of the beholder: The effect of rater variability and different rating scales on QTL mapping

item Poland, Jesse
item Nelson, Rebecca

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2010
Publication Date: 2/1/2011
Publication URL: http://doi:10.1094/PHYTO-03-10-0087
Citation: Poland, J.A., Nelson, R. 2011. In the eye of the beholder: The effect of rater variability and different rating scales on QTL mapping. Phytopathology. 101:290-298.

Interpretive Summary: Breeding for disease resistance has been a long-standing and important objective for plant breeders. Reflecting this, many studies have been conducted to find molecular markers that are linked to genes conferring disease resistance in order to assist breeding efforts through marker assisted selection. These previous studies have been almost exclusively conducted using visual assessment of disease severity on the population of interest. Visual assessment of disease severity raises questions over the variability of ratings among different raters and how this affects the results and interpretations of these studies. In the present study, 22 individuals rated the same maize population for resistance to northern leaf blight, an important disease throughout the world. We then examined the impact of rater variability and different rating scales on the results of genetically mapping disease resistance genes. We found that despite considerable variability among raters, the genetic location of identified disease resistance genes was largely consistent. However, the estimated strength of that resistance was variable among raters. We concluded that differences between raters are real and may affect results in some cases.

Technical Abstract: The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. While previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate and/or a 0-9 ordinal rating scale. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as three-fold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, as this was highly variable and rater-dependent.

Last Modified: 06/25/2017
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