Comparison of Genetic Structure Assessed by Amplified Fragment Length Polymorphism and Retrotransposon-based Sequence-specific Amplification Polymorphism for Portuguese Populations of Pinus pinea L.

Abstract

In order to assess genetic diversity within and among populations of Pinus pinea L. (stone pine), seven Portuguese populations originating from three Provenance Regions were selected and genotyped using two marker systems. We compared the genetic variation of these populations using retrotransposon-based sequence-specific amplification polymorphism (SSAP) and amplified fragment length polymorphism (AFLP). In total, 105 trees were screened with three primer enzyme combinations (PEC), producing 232 SSAP and 132 AFLP loci. Where SSAP yielded approximately twice-the number of polymorphic fragments compared to AFLP. Differentiation was slightly higher for SSAP, than for AFLP (F ST = 0.105 for SSAP and 0.074 for AFLP), and both significantly different from zero, P < 0.01. The levels of average genetic diversity within-population found with the two types of marker were not significantly different between SSAPs and AFLPs (26.6 % and 22.8 %, respectively). The populations that displayed the highest and lowest genetic diversity scores were the same for both markers, and only two populations had significantly different H e estimates. The neighbor-joining tree based on the Nei's genetic distance displayed some geographic pattern. With the AFLP markers the populations grouped according to the provenance regions where they were sampled, resulting in one well supported cluster with the Southern populations, but with SSAP the pattern was not so coherent. In this study SSAP generated more polymorphic fragments and higher estimates of genetic diversity than AFPL did, due, probably, to the higher mutation rate of retrotransposition relative to base mutation. Nevertheless, congruence was found between estimates obtained with both markers, which is very interesting, for, in general, SSAP markers have lower costs compared to AFLPs, and they might be an interesting alternative marker system, when higher resolution is requested.

Growth of Stone pine (Pinus pinea L.) European provenances in central Chile

“…Nasri et al (2005) studied fatty acids of seeds in French and Turkish provenances, and the low genetic diversity detected was attributed to the homogeneity of the reproductive material due to the human-induced species propagation. Likewise, Evaristo et al (2008) indicated a lack of differentiation between provenances in relation with growth.…”

Stone Pine (Pinus pinea L.) High-Added-Value Genetics: An Overview

“…It was found that retrotransposons are excellent markers for taxonomic analysis, going as far as elucidating evolutionary relationships between plant species [86]. Stone pine retrotransposons provide taxonomic identifications more closely aligned with morphological data than other genome fragment analysis [25]. This fact illustrates the importance of these sequences for the validation of taxonomic identification.…”

“…There was a 9-year period where no works were published on P. pinea's genome, revealing a lack of interest in this particular subject. Retrotransposon markers were used by Evaristo et al (2008) [25] to generate taxonomic data that are more consistent with morphological criteria than amplified fragment length polymorphism (AFLP)-based markers for P. pinea. Retrotransposon markers were more effective in determining population-specific genomic diversity than previous approaches based on polymorphic regions.…”

Recommendations for increasing yield of the edible Pinus pinea L. pine nuts

“…Similarly, average PY value (3.9%) is also within the range of historical values reported for Italy (3.6% [40,44] and Spain (2.7-4.4% [45]). However, the average PY value is higher than values reported for Europe after the arrival of L. occidentalis, which caused a drastic decrease in Spain (1.1-2.1% [31,45]) and Portugal (1.7% [46]; 3.0% [44]). In Chile, a trend towards PY decrease was also reported [23,47].…”