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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).

ABSTRACT: 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.

SUBMITTER: Eckert AJ

PROVIDER: S-EPMC2746152 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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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).

Eckert Andrew J AJ Wegrzyn Jill L JL Pande Barnaly B Jermstad Kathleen D KD Lee Jennifer M JM Liechty John D JD Tearse Brandon R BR Krutovsky Konstantin V KV Neale David B DB

Genetics 20090713 1

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 ge ...[more]

PMID: 19596906

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Project description:Key message Douglas-fir growth correlates with the climate, the soil moisture regime, and the soil nutrient status, reflecting a broad physiological amplitude. Even though planting this non-native tree species is suggested as a viable strategy to improve adaptiveness of European forests to a more extreme climate and to assure future productivity, the expected temperature increase may induce a decline in forest stand productivity for Douglas-fir in already warm and dry regions. ContextTree species selection is one of the most important forest management decisions to enhance forest productivity and stand stability on a given site. Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii), a non-native species from north-western America, is seen as an important additional species option for adapting Central European forests to a changing climate.AimsThis study assesses Douglas-fir forest productivity derived from site conditions. We investigate climatic and physico-chemical soil characteristics and productivity of 28 mature Douglas-fir stands growing on siliceous, as well as carbonate bedrock material in southern Germany and north-eastern Austria.MethodsThe importance of climatic and physico-chemical soil characteristics was analyzed with the machine learning method Random Forests.ResultsThe results show that Douglas-fir growth correlates with climate, soil moisture, and soil nutrient availability derived from ten climatic and physico-chemical soil parameters.ConclusionThe broad pH optimum between 4.5 and 7.2 reflects the broad physiological amplitude of Douglas-fir, and no significant differences were detectable between carbonate and siliceous bedrock. We also conclude that climate change may induce a forest stand productivity decline, because lower productivity with the highest mean summer temperature across our study range was observed at the warmest sites in Eastern Austria.Electronic supplementary materialThe online version of this article (10.1007/s13595-019-0805-3) contains supplementary material, which is available to authorized users.

Project description:BACKGROUND: Douglas-fir (Pseudotsuga menziesii) extends over a wide range of contrasting environmental conditions, reflecting substantial local adaptation. For this reason, it is an interesting model species to study plant adaptation and the effects of global climate change such as increased temperatures and significant periods of drought on individual trees and the forest landscape in general. However, genomic data and tools for studying genetic variation in natural populations to understand the genetic and physiological mechanisms of adaptation are currently missing for Douglas-fir. This study represents a first step towards characterizing the Douglas-fir transcriptome based on 454 sequencing of twelve cDNA libraries. The libraries were constructed from needle and wood tissue of coastal and interior provenances subjected to drought stress experiments. RESULTS: The 454 sequencing of twelve normalized cDNA libraries resulted in 3.6 million reads from which a set of 170,859 putative unique transcripts (PUTs) was assembled. Functional annotation by BLAST searches and Gene Ontology mapping showed that the composition of functional classes is very similar to other plant transcriptomes and demonstrated that a large fraction of the Douglas-fir transcriptome is tagged by the PUTs. Based on evolutionary conservation, we identified about 1,000 candidate genes related to drought stress. A total number of 187,653 single nucleotide polymorphisms (SNPs) were detected by three SNP detection tools. However, only 27,688 SNPs were identified by all three methods, indicating that SNP detection depends on the particular method used. The two alleles of about 60% of the 27,688 SNPs are segregating simultaneously in both coastal and interior provenances, which indicates a high proportion of ancestral shared polymorphisms or a high level of gene flow between these two ecologically and phenotypically different varieties. CONCLUSIONS: We established a catalogue of PUTs and large SNP database for Douglas-fir. Both will serve as a useful resource for the further characterization of the genome and transcriptome of Douglas-fir and for the analysis of genetic variation using genotyping or resequencing methods.

Project description:Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.

Dataset Information

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).

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).

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