Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers

Thomas, Barb R.; Macdonald, S. Ellen; Hicks, Matt; Adams, Denise; Hodgetts, Ross B.

doi:10.1007/s001220051136

Cited by 86 publications

(67 citation statements)

References 38 publications

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“…The mean number of alleles, observed and expected heterozygosities for SSR loci (A=11-36; H o =0.549-0.718; H e =0.877-0.944; see Electronic supplementary materials, Appendix 1) were also relatively higher than those estimated with the same type and number of markers in conifers with wide geographical distributions, such as Larix occidentalis (A=5.5, H o =0.521, H e =0.580; Khasa et al 2006), Pinus strobus (A=9.6, H o =0.522, H e =0.607; Rajora et al 2000;Marquardt and Epperson 2004), Pinus contorta (A=21.0, H e =0.425; Thomas et al 1999), Picea glauca (A=16.4, H o =0.649, H e =0.851; Rajora et al 2005), and also P. menziesii (A=7.5, H e =0.673; Amarasinghe and Carlson 2002) studied earlier. The difference can be explained by the fact that the SSR loci in our study were preselected as the most polymorphic.…”

Section: Discussionmentioning

confidence: 78%

Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Krutovsky

Clair

Saich

et al. 2009

Tree Genetics & Genomes

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Characterizing population structure using neutral markers is an important first step in association genetic studies in order to avoid false associations between phenotypes and genotypes that may arise from nonselective demographic factors. Population structure was studied in a wide sample of ∼1,300 coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] trees from Washington and Oregon. This sample is being used for association mapping between cold hardiness and phenology phenotypes and single-nucleotide polymorphisms in adaptive-trait candidate genes. All trees were genotyped for 25 allozyme and six simple sequence repeat (SSR) markers using individual megagametophytes. Population structure analysis was done separately for allozyme and SSR markers, as well as for both datasets combined.

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Section: Discussionmentioning

confidence: 78%

Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Krutovsky

Clair

Saich

et al. 2009

Tree Genetics & Genomes

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“…Neither the mode of seed harvest nor selective effects prior to or after the establishment of plantations caused noticeable losses of diversity at the observed nuclear gene markers or chloroplast haplotypes (see below). No significant impact of the regeneration method (natural regeneration versus plantation) on levels of genetic diversity at nSSRs was also reported by Thomas et al (1999) for P. contorta.…”

Section: Genetic Variation Within Populationsmentioning

confidence: 84%

“…The assessment of genetic variation within populations at nSSRs often revealed higher (e.g. P. pinaster: Mariette et al, 2001; P. contorta: Thomas et al, 1999;P. canariensis: Navascus and Emerson, 2007) or comparable (e.g.…”

Section: Genetic Variation Within Populationsmentioning

confidence: 99%

Genetic similarity of natural populations and plantations of Pinus roxburghii Sarg. in Nepal

et al. 2009

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Abstract• Genetic structures of five population pairs each consisting of one natural population and one neighbouring plantation of Pinus roxburghii Sarg. in Nepal were assessed using nuclear (nSSRs) and chloroplast microsatellite loci (cpSSRs).• The mean number of alleles at nSSRs loci in natural populations was 5.0 compared to 4.93 in plantations while the average observed heterozygosities were the same in both groups (H 0 = 0.50). Most of the alleles were common to all the populations, indicating that the populations correspond to a single genetic entity. Similarly forty-seven haplotypes were observed in natural populations compared to fifty haplotypes in plantations. Mean haplotype diversities of natural populations (0.953) and plantations (0.955) were very similar. Genetic diversity of Pinus roxburghii was relatively high with low or no evidence of inbreeding while genetic differentiation among all populations was very low (about 1%).• The very low differentiation among natural populations indicates efficient long-distance gene flow among populations resulting in homogeneous genetic structures at least at selectively neutral loci. Even though the harvest and production of seeds and seedlings was largely uncontrolled, genetic structures of most plantations show no signs of reduced variation, inbreeding or other negative effects compromising the adaptedness or adaptability of planted forests. • Les structures génétique de cinq paires de populations composées chacune d'une population naturelle et d'une plantation voisine de Pinus roxburghii Sarg. au Népal ont été évalués à l'aide de loci nucléaires (nSSRs) et de loci microsatellites chloroplastiques (cpSSRs). Mots• Le nombre moyen d'allèles à loci nSSRs dans les populations naturelles était de 5,0 comparé à 4,93 dans les plantations alors que la moyenne des hétérozygoties observées étaient les mêmes dans les deux groupes (H 0 = 0,50). La plupart des allèles étaient communs à toutes les populations, indiquant que les populations correspondent à une seule entité génétique. De même, quarante-sept haplotypes ont été observés dans les populations naturelles par rapport à cinquante haplotypes dans les plantations. La diversité moyenne des haplotypes des populations naturelles (0,953) et des plantations (0,955) étaient très similaires. La diversité génétique de Pinus roxburghii a été relativement importante, avec peu ou pas de preuve de consanguinité tandis que la différenciation génétique entre les populations était très faible (environ 1 %).• Le très faible différenciation entre les populations naturelles indique des flux de gènes efficaces à longue distance entre les populations issues de structures génétiques homogènes avec au moins une sélectivité neutre des loci. Même si la récolte et la production de semences et de plants ont été largement incontrôlées, les structures génétiques de la plupart des plantations ne montrent aucun signe de réduction de la variation de la consanguinité ou d'autres effets négatifs compromettant la faculté d'adaptation des forêts plant...

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“…Adopting population-based approaches, Mariette et al (2001) Correlations between diversity estimates were low, except when performed at the regional or subspecific levels rather than at the population level (Mariette et al, , 2002a). If we also consider RAPDs vs microsatellites comparisons, Sun et al (1998) reported a significantly positive correlation between diversity levels obtained with both markers within Elymus fibrosus populations, whereas in their study on Pinus contorta, Thomas et al (1999) found a positive but nonsignificant correlation (recalculated by Mariette, 2001). Concerning estimates of population differentiation, Cagigas et al (1999), on Salmo trutta, and Huang et al (2000), on Haliotis rubra, found that RAPD and microsatellites were in agreement.…”

Section: Introductionmentioning

confidence: 91%

Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers

et al. 2004

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Genetic diversity and structure of 12 populations of Eryngium alpinum L. were investigated using 63 dominant amplified fragment length polymorphism (AFLP) and seven codominant microsatellite (48 alleles) markers. Within-population diversity estimates obtained with both markers were not correlated, but the microsatellite-based fixation index F is was correlated with both AFLP diversity indices (number of polymorphic bands and Nei's expected heterozygosity). Only AFLP diversity indices increased with the size of populations, although they did not significantly differ among them (Kruskall-Wallis test). The discrepancy between AFLPs and microsatellites may be explained by a better coverage of the genome with numerous AFLPs, the higher mutation rates of microsatellites or the absence of significant difference among withinpopulation diversity estimates. Genetic differentiation was higher with AFLPs (y ¼ 0.40) than with microsatellites (y ¼ 0.23), probably due to the higher polymorphism of microsatellites. Thus, we considered global qualitative patterns rather than absolute estimates to compare the performance of both types of markers. On a large geographic scale, the Mantel test and multivariate analysis showed that genetic patterns were more congruent with the spatial arrangement of populations when inferred from microsatellites than from AFLPs, suggesting higher homoplasy of AFLP markers. On a small spatial scale, AFLPs managed to discriminate individuals from neighboring populations whereas microsatellites did not (multivariate analysis), and the percentage of individuals correctly assigned to their population of origin was higher with AFLPs than with microsatellites. However, dominant AFLPs cannot be used to study heterozygosity-related topics. Thus, distinct molecular markers should be used depending on the biological question and the geographical scale investigated.

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Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers

Cited by 86 publications

References 38 publications

Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Genetic similarity of natural populations and plantations of Pinus roxburghii Sarg. in Nepal

Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers

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