Measuring the representativeness of a germplasm collection
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.
KeywordsCoverage Allele conservation Seed accession
The author would like to thank Dr. Marion Roder, who kindly shared the data set used in Huang et al. (2002) paper.
Carlos Hernandez-Suarez developed the methodology, performed the simulations, wrote the manuscript.
Compliance with ethical standards
Conflict of interest
The author declares no conflict of interest.
- Brown AHD (1995) The core collection at the crossroads. In: Hodgkin T, Brown AHD, van Hintum TJL, Morales EAV (eds) Core collections of plant genetic resources. Wiley, Chichester, pp 3–19Google Scholar
- Darwin C (1866) On the origin of species by means of natural selection: or the preservation of favoured races in the struggle for life. John Murray, LondonGoogle Scholar
- Esty W (1985) Estimation of the number of classes in a population and the coverage of a sample. Math Sci 10:41–50Google Scholar
- van Hintum TJ, Brown AHD, Spillane C, Hodkin T (2000) Core collections of plant genetic resources (IPGRI Technical Bulletin No. 3., Rome, Italy, 2000)Google Scholar