Comparison of DUS testing and SNP fingerprinting for variety identification in cucumber

Variety identification plays an important role in protecting the intellectual property of varieties, ensuring seed quality, and encouraging breeding innovation. Currently, morphological evaluation in the field, such as distinctness, uniformity, and stability (DUS) testing, and DNA fingerprinting in the laboratory using molecular markers are two dominant methods used for variety identification. Few studies have compared the results of these approaches, and the relationship between the two methods is obscure. In this study, 134 dominant cucumber varieties were evaluated using 50 DUS testing traits and genotyped by 40 single nucleotide polymorphisms (SNPs). The 40 SNPs were developed in our previous study and are well suited for variety identification. In the DUS testing, significant positive or negative correlations among 50 DUS traits were observed, and 20 core traits, including 15 fruit traits, were further selected to increase field inspection efficiency. This suggested that fruit shape plays an important role in variety identification. The ratio of fruit length/diameter was the most important trait, explaining 9.2% of the phenotypic variation. In the DNA fingerprinting test, the 40 SNPs were highly polymorphic and could distinguish all of the 134 cucumber varieties, and 14 core SNPs were selected to improve the identification rate. Interestingly, the population structure analysis of 134 cucumber varieties by phenotypic data in the DUS test was in accordance with the genotypic data from the DNA fingerprinting, indicating that all varieties could be divided into the same four subgroups: European type, North China type, South China type, and hybrids of the North China and South China types. Moreover, linear correlativity of distinguishment for each pair of varieties was observed between the DUS test and the DNA fingerprinting. These results indicated that these two methods have good application in future research, especially for the scaled-up analysis of hundreds of varieties.