Assessing the Genetic Diversity in Crops with Molecular Markers: Theory and Experimental Results with CIMMYT Wheat and Maize Elite Germplasm and Genetic Resources

A proper choice of a dissimilarity measure is important in surveys investigating genetic relationships among germplasm with molecular marker data. The objective of our study was to examine 10 dissimilarity coefficients widely used in germplasm surveys, with special focus on applications in plant breeding and seed banks. In particular, we (i) investigated the genetical and mathematical properties of these coefficients, (ii) examined consequences of these properties for different areas of application in plant breeding and seed banks, and (iii) determined relationships between these 10 coefficients. The genetical and mathematical concepts of the coefficients were described in detail. A Procrustes analysis of a published data set consisting of seven CIMMYT maize populations demonstrated close affinity between Euclidean, Rogers’, modified Rogers’, and Cavalli-Sforza and Edwards’ dissimilarity on one hand and Nei’s standard and Reynolds dissimilarity on the other hand. Our investigations show that genetical and mathematical properties of dissimilarity measures are of crucial importance when choosing a genetic dissimilarity coefficient for analyzing molecular marker data. The presented results assist experimenters to extract the maximum amount of information from genetic data and, thus, facilitate the interpretation of findings from molecular marker studies on a theoretically sound basis. Q UANTIFYING the degree of dissimilarity among genera, species, subspecies, populations, and elite breeding materials is of primary concern in population genetics and plant breeding. Before 1970, measures of genetic dissimilarity between taxonomic units relied on pedigree analysis and morphological, physiological or cytological markers, as well as biometric analyses of quantitative and qualitative traits, heterosis or the segregation variance in crosses (Melchinger, 1999). During the following two decades, isozymes have successfully been employed in numerous taxonomic and evolutionary studies (Hamrick and Godt, 1997) but their use in other applications was hampered by the small number of polymorphic markers available. Molecular markers, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and single nucleotide polymorphisms (SNPs) have meanwhile replaced isozymes and are heavily used for (i) detection of relationships among different germplasm in seed banks and breeding programs (c.f., Brummer, 1999), (ii) prediction of heterosis (c.f., Melchinger, 1999), (iii) search for promising heterotic groups for hybrid breeding (c.f., Reif et al., 2003), (iv) identification of duplicates in seed banks (c.f., Treuren et al., 2001), (v) assessment of the level of genetic diversity present in germplasm pools and its flux over time (c.f., Dubreuil and Charcosset, 1998; Labate et al., 2003), and (vi) identification of essentially derived varieties in plant Corresponding author: Albrecht E. Melchinger, Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany. Email: [email protected]. Received January 28, 2004. variety protection (c.f., Smith et al., 1991; Lombard et al., 2000). In these various applications, a proper choice of a similarity s or dissimilarity coefficient d = 1 − s (following the terminology of Gower, 1985) is important and depends on factors such as (i) the properties of the marker system employed, (ii) the genealogy of the germplasm, (iii) the operational taxonomic unit (OTU) under consideration (e.g., lines, populations), (iv) the objectives of the study, and (v) necessary preconditions for subsequent multivariate analyses. In a recent review, Mohammadi and Prasanna (2003) discussed the use of six coefficients d for the analysis of dichotomous molecular marker data, but ignored coefficients based on allele frequencies, which are especially suitable for codominant marker data. Several authors (Goodman, 1972; Gower, 1985; Gower and Legendre, 1986) investigated the mathematical properties and relationships among various coefficients d. However, those coefficients were disregarded, which are based on specific genetic models and, therefore, suitable for studies with seed bank or plant breeding materials. In order to successfully conduct molecular marker surveys with plant breeding and seed bank materials, a thorough knowledge of genetical and mathematical properties of coefficients d is of crucial importance. Therefore, the objective of our study was to examine 10 coefficients d widely used in germplasm surveys, with special focus on applications in plant breeding and seed banks. In particular, we (i) investigated the genetical and mathematical properties of these coefficients, (ii) examined consequences of these properties for different areas of application in plant breeding and seed banks, and (iii) determined relationships between these 10 coefficients. Reif et al. 2004. Crop Science. In press 12 Table 1 Dissimilarity coefficients d for allelic informative marker data. pi j and qi j are allele frequencies of the jth allele at the ith locus in the two operational taxonomic units under consideration, ni is the number of alleles at the ith locus, and m refers to the number of loci.