Evaluation of the use of high-density SNP genotyping to implement UPOV Model 2 for DUS testing in barley

• Published in: Theoretical and applied genetics 2013-04, Vol.126 (4), p.901-911
• Main Authors: Jones, Huw, Norris, Carol, Smith, David, Cockram, James, Lee, David, O’Sullivan, Donal M, Mackay, Ian
• Format: Article
• Language: English
• Subjects: Agriculture; Barley; Biochemistry; Biomedical and Life Sciences; Biotechnology; Calibration; Cluster Analysis; Corn; Genetic aspects; Genetic Association Studies - methods; genetic markers; Genetic Markers - genetics; Genetic screening; Genotype; genotyping; Genotyping Techniques - methods; Hordeum - genetics; Hordeum vulgare; Life Sciences; Methods; Morphology; Multivariate Analysis; new variety; Oilseeds; Original Paper; Phenotype; Physiological aspects; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Polymorphism, Single Nucleotide - genetics; Rape plants; Registration; single nucleotide polymorphism; Single nucleotide polymorphisms; Species Specificity; spring barley; United Kingdom
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-012-2024-2

Developments in high-throughput genotyping provide an opportunity to explore the application of marker technology in distinctness, uniformity and stability (DUS) testing of new varieties. We have used a large set of molecular markers to assess the feasibility of a UPOV Model 2 approach: “Calibration of threshold levels for molecular characteristics against the minimum distance in traditional characteristics”. We have examined 431 winter and spring barley varieties, with data from UK DUS trials comprising 28 characteristics, together with genotype data from 3072 SNP markers. Inter varietal distances were calculated and we found higher correlations between molecular and morphological distances than have been previously reported. When varieties were grouped by kinship, phenotypic and genotypic distances of these groups correlated well. We estimated the minimum marker numbers required and showed there was a ceiling after which the correlations do not improve. To investigate the possibility of breaking through this ceiling, we attempted genomic prediction of phenotypes from genotypes and higher correlations were achieved. We tested distinctness decisions made using either morphological or genotypic distances and found poor correspondence between each method.