Measuring the representativeness of a germplasm collection

Abstract

Many germplasm collections aim to preserve most of the genetic diversity present in a population so that the population could be regenerated, which provides genetic resources to ensure food security. This paper proposes a way to measure how well a germplasm collection achieve this goal. In the most common scenario, one has little information regarding the number and statistical distribution of alleles at every locus, and it is thus very difficult to measure the representativeness of the accession. Here, we show how to use samples of allelic diversity at a sample of loci to estimate the representativeness of an accession based on the coverage of a sample with point and interval estimates. Our approach avoids making unrealistic assumptions regarding the number of loci, the bounds for the number of alleles or their frequency distributions. Depending on the sampling scheme of a collection, we differentiate between absolute or relative coverage. Here, we demonstrate this methodology using data from the germplasm collection at the Leibniz Institute of Plant Genetics and Crop Plant Research.