Improved Estimation and Graphical Representation of the Reliability Measures of the SNP Marker Method for Crop Variety Identification

Molecular marker identification is a technique used to ensure fairness when submitting innovative crop varieties. Based on data from a collaborative experiment, our study appraised the reliability of the SNP molecular marker method applied simultaneously to China’s five major crops (wheat, rice, maize, cotton, and soybean) and proposed improved methods to (1) estimate detection uncertainty statistics and (2) graphically represent the detection results. We found that the detection method was quite reliable, as the average trueness rates for wheat, rice, cotton, soybean, and maize were 99.5%, 99.2%, 98.1%, 97.2%, and 96.2%, respectively, in sequence. The laboratory effect, genotype effect, and the effect of the interaction between the laboratory and the genotype all reached highly significant levels in the detection results, but their significance differed between crops. The proposed multi-genotype method confirmed the overestimation of the uncertainty statistics by up to 13% through the single-genotype method currently recommended in ISO 5725. The proposed Lab plus Lab by Genotype interaction (LLG) biplot provides a simple, intuitive, and efficient way to present, in two distinct and complementary biplot views, the trueness–precision of the detection results and the accuracy of the laboratories involved, respectively.