ORIGINAL PAPER J. Jansen Æ H. Verbakel Æ J. Peleman Th. J. L. van Hintum A note on the measurement of genetic diversity within genebank accessions of lettuce (Lactuca sativa L.) using AFLP markers Received: 19 April 2005 / Accepted: 13 November 2005 / Published online: 3 December 2005 Ó Springer-Verlag 2005 Abstract This paper discusses a statistical approach for measuring genetic diversity within genebank accessions of a self-fertilising species. This approach is applied to lettuce (Lactuca sativa L.), using AFLP marker data on a set of 1,390 accessions, representing six different let- tuce types. Knowledge of the within-accession genetic diversity is important for decisions about the way accessions have to be maintained by genebanks. It is argued that if the within-accession diversity is small, as can be expected for a self-fertilising species like L. sativa, the best approach is to sample as many accessions as possible with only two plants per accession and estimate the within-accession diversity by the proportion of accessions of which the individuals are different. Introduction Genebanks conserve the genetic diversity of crop spe- cies, which forms the raw material of plant breeding. If possible, genetic diversity is conserved in the form of accessions: batches of seed sampled from wild popula- tions, traditional landraces, modern cultivars, genetic stock or other research material. In genebank collections of self-fertilising species the genetic diversity is largely distributed between acces- sions. The exception may be landraces of a self-fertilising species which may be composed of mixtures of pure lines. Between accessions, genetic diversity has been studied for many crop species. A survey of methods for the analysis of this form of genetic diversity is given by Mohammadi and Prasanna (2003). Depending on the species, considerable diversity can be found within accessions. If it concerns a cross-fertilising species propagated using open pollination, the within-accession diversity will generally be large. If it concerns a strictly self-fertilising species the within-accession diversity, especially of modern varieties, will be small or even absent. Within-accession diversity has great implications for both the conservation and the use of accessions. Homogeneous accessions of self-fertilising species may be considered to consist of one genotype. All plants of the accession are equal and, in principle, one plant could suffice to regenerate an accession. However, in the genebank practice, always more plants are used, e.g. in order to guarantee enough seed. If within-accession diversity is present, always a greater number of plants are required to regenerate an accession since the variants occurring in the accession must be represented in the sample that is used for regeneration. In addition, if redundancy is to be reduced in a collection, within- accession diversity can cause many complications. For example, accessions will no longer be either completely identical or entirely different, but may partly overlap (van Treuren et al. 2004). It is generally assumed that within-accession diversity occurs mainly in cross-fertil- ising species and, to a lesser extent, in wild populations and landraces of a self-fertilising species. When molecular markers came available it appeared that in modern varieties of a self-fertilising species, some residual diversity could be found. For example, van Treuren and van Hintum (2001) showed, using AFLP markers, that even accessions of modern barley varieties contain diversity, although this crop species is usually considered as completely self-fertilising. This diversity, less than 2% of the polymorphisms, can be expected to be either point mutations or remnants of the original diversity in the cross that yielded the variety. Communicated by A. E. Melchinger J. Jansen (&) Biometris, P.O. Box 100, 6700 AC Wageningen, The Netherlands E-mail: johannes.jansen@wur.nl H. Verbakel Æ J. Peleman KeyGene N.V., P.O. Box 216, 6700 AE Wageningen, The Netherlands Th. J. L. van Hintum Centre for Genetic Resources, P.O. Box 16, 6700 AA Wageningen, The Netherlands Theor Appl Genet (2006) 112: 554–561 DOI 10.1007/s00122-005-0162-5