Evolution and applications of pine microsatellites

Abstract

<div lang="en" class="abs"><p class="abs_header">Abstract</p><p>The evolution of microsatellites was studied within and between the pine species. Sequences showed that microsatellites do not necessarily mutate in a stepwise fashion and that size homoplasy is common due to flanking sequence and repeat area changes within and between the species. Thus, some assumptions of statistical methods based on changes in repeat numbers may not hold.</p><p>Sequences from cross-species amplifications revealed evidence of duplications of microsatellite loci in pines. On two independent occasions, the repeat area of the microsatellite had undergone a rapid expansion during the last 10–25 million of years.</p><p>Microsatellite markers were used together with other molecular markers (allozymes, RFLPs, RAPDs, rDNA RFLPs) and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (<em>Pinus sylvestris</em>) in Finland. All molecular markers showed high level of within population variation, while differentiation among populations was low (F_ST = 0.02). Of the total variation in bud set, 36.4 % was found among the populations which experience a steep climatic gradient. Thus, the markers applied were poor predictors of population differentiation of the quantitative trait studied</p><p>The distribution of genetic variation was studied in five natural populations of radiata pine (<em>Pinus radiata</em>), species which has gone through bottlenecks in the past. Null allele frequencies were estimated and used in later analyses. Microsatellites showed high level of variability within populations (H_e = 0.68–0.77). Allele length distributions and average number of alleles per locus showed some traces of bottlenecks. Instead, comparison of observed genetic diversities and expected diversities suggested post-bottleneck expansion of populations. Genetic differentiation (F_ST and R_ST) among populations was over 10%, reflecting situation in the isolated radiata pine populations.</p><p>Using microsatellites and a newly developed Bayesian method, individual inbreeding coefficients were estimated in five populations of radiata pine. Most individuals were outbred while some were selfed. Presumably, in ancestral radiata pine populations the recessive deleterious alleles have been eliminated after bottlenecks and the mating system has changed as a consequence.</p></div>