Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type

Genetic diversity of crop plants resulting from breeding and selection is preserved in gene banks. Utilization of such materials for further crop improvement depends on knowledge of agronomic performance and useful traits, which is usually obtained by phenotypic evaluation. Associations between DNA markers and agronomic characters in collections of crop plants would (i) allow assessment of the genetic potential of specific genotypes prior to phenotypic evaluation, (ii) identify superior trait alleles in germplasm collections, (iii) facilitate high resolution QTL mapping and (iv) validate candidate genes responsible for quantitative agronomic characters. The feasibility of association mapping was tested in a gene bank collection of 600 potato cultivars bred between 1850 and 1990 in different countries. The cultivars were genotyped with five DNA markers linked to previously mapped QTL for resistance to late blight and plant maturity. Specific DNA fragments were tested for association with these quantitative characters based on passport evaluation data. Highly significant association with QTL for resistance to late blight and plant maturity was detected with PCR markers specific for R1, a major gene for resistance to late blight, and anonymous PCR markers flanking the R1 locus at 0.2 Centimorgan genetic distance. The marker alleles associated with increased resistance and later plant maturity were traced to an introgression from the wild species S. demissum. These DNA markers are the first marker that are diagnostic for quantitative agronomic characters in a large collection of cultivars.