Empirical assessment of allozyme and RAPD variation in Pinus sylvestris (L.) using haploid tissue analysis

Abstract

We analysed 20 allozyme and 22 putative random amplified polymorphic DNA (RAPD) loci in two populations of Pinus sylvestris (L.) from northern Sweden. Genotypes for individual allozyme and RAPD loci were inferred from segregation patterns in haploid macrogametophytes. Therefore, it was possible to distinguish between homo-and heterozygotes carrying a RAPD fragment and to estimate directly the frequencies of RAPD fragments. The percentage of polymorphic loci and the expected and observed heterozygosity were lower for allozymes than for RAPDs. Average fixation indices for both types of markers were negative indicating a heterozygote excess over panmictic expectations. The apportionment of genetic variation within and among the investigated populations was similar for allozymes and RAPDs and showed that most of the variation resided within populations. RAPD genotypes inferred from haploid material were subsequently converted to diploid phenotypes and used to estimate indirectly the frequencies of RAPD fragments. Gene diversity measurements derived from indirectly estimated RAPD frequencies were distinctly lower than those based on directly estimated RAPD frequencies. This result was caused by the absence of the null homozygote at many loci which appeared as monomorphic in the diploid data set. Population differentiation coefficients based on the indirectly estimated RAPD frequencies were not concordant with those based on directly estimated RAPD frequencies. Our present results indicate that when complete genotype information can be obtained, RAPD analysis provides genetic information similar to that revealed by analysis of allozyme variation. On the other hand, our results are concordant with theoretical results suggesting that analysis of RAPD variation in diploid material can produce unreliable estimates of population-genetic parameters.

The genetic structure of endangered populations in the Cranberry Fritillary, Boloria aquilonaris (Lepidoptera, Nymphalidae): RAPDs vs allozymes

“…This is consistent with the majority of previous studies comparing these two population genetic markers (Table 2), though there are exceptions to this trend (Liu andFurnier, 1993, LeCorre et al, 1997;Ross et al, 1999). Mostly, this difference is explained by the inherently higher rate of detectable mutations and weaker degree of selective constraint at RAPD compared to allozyme loci since RAPDs can detect variation in both coding and noncoding regions (Szmidt et al, 1996;Aagaard et al, 1998;Waycott, 1998;Sun et al, 1999;Wu et al, 1999;Oiki et al, 2001).…”

Identification of the Male Parents of Half-sib Progeny from Japanese Black Pine (Pinus thunbergii Parl.) Clonal Seed Orchard using RAPD Markers.

“…Use of RAPD markers for the parentage analysis has been limited (Welsh et al 1991, Scott et al 1992, Akerman et al 1995, because of their dominant character. However, the limitation of the dominant nature of RAPD markers can be alleviated by the segregation analysis of haploid megagametophytes (Lu et al 1995, Szmidt et al 1996. We were able to identify the male parents of most seedlings from the diagnostic progeny, by comparing the genotype of orchard clones inferred by analyzing Fig.…”

Evolutionary forces influencing variation among populations of Pinus sylvestris

“…No geographic trends could be revealed for the ribosomal DNA variation (Karvonen and Savolainen 1993). Szmidt et al (1996) reported no RAPD variation between two Swedish Pinus sylvestris populations from latitudes 64° and 67°, respectively. Owing to the high variability in some of the DNA markers as well as their presumed neutrality they are excellent tools for studies on gene flow.…”