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

Krutovsky, Konstantin V.; Clair, J. Bradley St.; Saich, Robert; Hipkins, Valerie D.; Neale, David B.

doi:10.1007/s11295-009-0216-y

Cited by 37 publications

(39 citation statements)

References 91 publications

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“…Population structure and historical demography: The extent of structure among populations of coastal Douglas fir observed at chloroplast and nuclear microsatellites, as well as allozymes, is low and consistent with weak effects of isolation by distance (Li and Adams 1989;Viard et al 2001;Krutovsky et al 2009). We analyzed patterns of differentiation for all 115 polymorphic candidate genes, using pairwise measures of divergence (D xy ) among the six populations, and related this measure to geographical distance using Mantel tests.…”

Section: Methodsmentioning

confidence: 71%

Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)

et al. 2009

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Forest trees exhibit remarkable adaptations to their environments. The genetic basis for phenotypic adaptation to climatic gradients has been established through a long history of common garden, provenance, and genecological studies. The identities of genes underlying these traits, however, have remained elusive and thus so have the patterns of adaptive molecular diversity in forest tree genomes. Here, we report an analysis of diversity and divergence for a set of 121 cold-hardiness candidate genes in coastal Douglas fir (Pseudotsuga menziesii var. menziesii). Application of several different tests for neutrality, including those that incorporated demographic models, revealed signatures of selection consistent with selective sweeps at three to eight loci, depending upon the severity of a bottleneck event and the method used to detect selection. Given the high levels of recombination, these candidate genes are likely to be closely linked to the target of selection if not the genes themselves. Putative homologs in Arabidopsis act primarily to stabilize the plasma membrane and protect against denaturation of proteins at freezing temperatures. These results indicate that surveys of nucleotide diversity and divergence, when framed within the context of further association mapping experiments, will come full circle with respect to their utility in the dissection of complex phenotypic traits into their genetic components.

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Section: Methodsmentioning

confidence: 71%

Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)

et al. 2009

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“…Populations of coastal Douglas fir are not differentiated strongly from one another using allozymes (Li and Adams 1989), RAPDs (Aagaard et al 1998), or chloroplast and nuclear microsatellites (Viard et al 2001;Krutovsky et al 2009). The average level of population differentiation (G ST ) was $0.02-0.07 in all studies, with Li and Adams (1989) noting weak to moderate (r , 0.30) isolation-by-distance effects in the coastal populations.…”

Section: Methodsmentioning

confidence: 99%

Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits

et al. 2009

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Adaptation to cold is one of the greatest challenges to forest trees. This process is highly synchronized with environmental cues relating to photoperiod and temperature. Here, we use a candidate gene-based approach to search for genetic associations between 384 single-nucleotide polymorphism (SNP) markers from 117 candidate genes and 21 cold-hardiness related traits. A general linear model approach, including population structure estimates as covariates, was implemented for each marker–trait pair. We discovered 30 highly significant genetic associations [false discovery rate (FDR) Q < 0.10] across 12 candidate genes and 10 of the 21 traits. We also detected a set of 7 markers that had elevated levels of differentiation between sampling sites situated across the Cascade crest in northeastern Washington. Marker effects were small (r2 < 0.05) and within the range of those published previously for forest trees. The derived SNP allele, as measured by a comparison to a recently diverged sister species, typically affected the phenotype in a way consistent with cold hardiness. The majority of markers were characterized as having largely nonadditive modes of gene action, especially underdominance in the case of cold-tolerance related phenotypes. We place these results in the context of trade-offs between the abilities to grow longer and to avoid fall cold damage, as well as putative epigenetic effects. These associations provide insight into the genetic components of complex traits in coastal Douglas fir, as well as highlight the need for landscape genetic approaches to the detection of adaptive genetic diversity.

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“…Allozyme and microsattelite markers used to study the population structure of coastal Douglas-fir have shown that there is weak differentiation between the coastal populations (KRUTOVSKY et al, 2009). Had the trials examined here been established on harsher sites in New Zealand, particularly with a lot of wind exposure or where rainfall is more limited, it is possible that the genotype x environment interaction found would have increased.…”

Section: G X E and Snc Resistancementioning

confidence: 99%

“…Had the trials examined here been established on harsher sites in New Zealand, particularly with a lot of wind exposure or where rainfall is more limited, it is possible that the genotype x environment interaction found would have increased. The evidence of low differentiation from KRUTOVSKY et al (2009) suggests that there may not be value in doing so. It would, however, be productive to integrate data from these studies in New Zealand with those from (DEAN, 2007;DEAN, 2008;DEAN, 2009) or similar studies, to determine whether similar levels of provenance x environment effects exist.…”

Section: G X E and Snc Resistancementioning

confidence: 99%

Developing breeding and deployment options for Douglas-fir in New Zealand: breeding for future forest conditions

et al. 2012

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Genetic improvement of Douglas-fir in New Zealand was initiated in 1955 with large provenance trials established in the late 1950's. These trials illustrated that material from the coast of Oregon and California grew faster than other provenances tested. Further collections were made to evaluate provenance and familylevel performance from these two areas, and in 1996 additional trials were established at four low-altitude sites across New Zealand.Genotype ϫ environment (GxE) interaction among these sites was found to be important for diameter at breast height (DBH), less important for stem straightness and malformation and not important for outerwood acoustic velocity (a surrogate for wood stiffness). Heritabilities were low to moderate for all growth traits, and very low for malformation. Heritability for needle cast due to Swiss needle cast, measured as needle retention on the one site where infection was relatively high, was moderate at 0.37, and was likely a major factor creating GxE interactions for growth among sites. The heritability of wood acoustic velocity was moderate to high at individual sites (0.26-0.74) and across sites (0.49). Individual-trait selection revealed the potential for good genetic gains to be made when selecting the top 20 families for diameter growth (an average of 10.7 %), straightness (an average of 11.5%) and acoustic velocity (an average of 7.0%).When we examined predicted genetic gains while selecting for needle retention and/or DBH, we found that selecting for needle cast at the affected site did not compromise DBH gains at that site. Selecting for genotypes with low needle cast at the affected site did, however, reduce gains for DBH estimated across all sites. In order to maximise gains across the current Douglas-fir growing estate, a division of growing sites between those known and predicted to be affected by needle cast and those not affected would seem appropriate. This is particularly relevant given recent climate modelling work suggests that Swiss needle cast will become more important in the South Island, and even more destructive in the North Island of New Zealand. We suggest addressing differences in site through the development of separate deployment populations.

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

Cited by 37 publications

References 91 publications

Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)

Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)

Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits

Developing breeding and deployment options for Douglas-fir in New Zealand: breeding for future forest conditions

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