Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.)
Understanding the dynamics and mechanisms of local adaptation in natural populations provides the basis for predicting responses to environmental changes, including those associated to global climate change. European beech (Fagus sylvatica L.) is one of the most economically and ecologically importa...
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Elsevier
2025-09-01
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| Series: | Trees, Forests and People |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666719325002079 |
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| author | Cesare Garosi Cristina Vettori Lorenzo Arcidiaco Marko Bajc Hojka Kraigher Marjana Westergren Davide Travaglini Rok Damjanić Kristina Sever Andrej Breznikar Andreja Gregoric Miran Lanšćak Mladen Ivankovic Sanja Bogunović Donatella Paffetti |
| author_facet | Cesare Garosi Cristina Vettori Lorenzo Arcidiaco Marko Bajc Hojka Kraigher Marjana Westergren Davide Travaglini Rok Damjanić Kristina Sever Andrej Breznikar Andreja Gregoric Miran Lanšćak Mladen Ivankovic Sanja Bogunović Donatella Paffetti |
| author_sort | Cesare Garosi |
| collection | DOAJ |
| description | Understanding the dynamics and mechanisms of local adaptation in natural populations provides the basis for predicting responses to environmental changes, including those associated to global climate change. European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe. Nevertheless, little is known about its genomic adaptive diversity and adaptive potential. Genetic differentiation in beech sites associated with environmental adaptation was assessed by genotyping 1384 single nucleotide polymorphisms (SNPs) in candidate genes. The study included 153 beech individuals from 12 populations located in Italy, Slovenia, and Croatia, with diverse bio-geoclimatic conditions. PCA-based and the Fst-based method of differentiation (PCAdapt and LEA) and two different Environmental Association Analysis approaches (Latent Factor Mixed Model and Samβada) were used to identify loci with significant correlations with bioclimatic indicators. The results obtained in this study allowed us to identify signature of regional and local environment adaptation. Specific patterns of local adaptation were observed for each studied population. We identified allelic variants associated with the response to precipitation fluctuations and drought periods during the growing season. Particularly interesting is the observation of differences in the presence and effect of allelic variants among different sites, likely due to adaptation to the local environment and the different silvicultural history of each observed population. |
| format | Article |
| id | doaj-art-e09fa6e29ae64510839387eda57c4e2c |
| institution | Kabale University |
| issn | 2666-7193 |
| language | English |
| publishDate | 2025-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Trees, Forests and People |
| spelling | doaj-art-e09fa6e29ae64510839387eda57c4e2c2025-08-23T04:49:17ZengElsevierTrees, Forests and People2666-71932025-09-012110098110.1016/j.tfp.2025.100981Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.)Cesare Garosi0Cristina Vettori1Lorenzo Arcidiaco2Marko Bajc3Hojka Kraigher4Marjana Westergren5Davide Travaglini6Rok Damjanić7Kristina Sever8Andrej Breznikar9Andreja Gregoric10Miran Lanšćak11Mladen Ivankovic12Sanja Bogunović13Donatella Paffetti14Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144 Florence, ItalyDepartment of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy; National Research Council of Italy (CNR), Institute of Bioscience and Bioresources (IBBR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; Corresponding author.Institute of Bioeconomy, National Research Council of Italy (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, ItalySlovenian Forest Institute, Večna pot 2, 1000 Ljubljana, SloveniaSlovenian Forest Institute, Večna pot 2, 1000 Ljubljana, SloveniaSlovenian Forest Institute, Večna pot 2, 1000 Ljubljana, SloveniaDepartment of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144 Florence, ItalySlovenia Forest Service, Večna pot 2, 1000 Ljubljana, SloveniaSlovenia Forest Service, Večna pot 2, 1000 Ljubljana, SloveniaSlovenia Forest Service, Večna pot 2, 1000 Ljubljana, SloveniaSlovenia Forest Service, Večna pot 2, 1000 Ljubljana, SloveniaCroatian Forest Research Institute, Cvjetno naselje 41, 10450 Jastrebarsko, CroatiaCroatian Forest Research Institute, Cvjetno naselje 41, 10450 Jastrebarsko, CroatiaCroatian Forest Research Institute, Cvjetno naselje 41, 10450 Jastrebarsko, CroatiaDepartment of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144 Florence, ItalyUnderstanding the dynamics and mechanisms of local adaptation in natural populations provides the basis for predicting responses to environmental changes, including those associated to global climate change. European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe. Nevertheless, little is known about its genomic adaptive diversity and adaptive potential. Genetic differentiation in beech sites associated with environmental adaptation was assessed by genotyping 1384 single nucleotide polymorphisms (SNPs) in candidate genes. The study included 153 beech individuals from 12 populations located in Italy, Slovenia, and Croatia, with diverse bio-geoclimatic conditions. PCA-based and the Fst-based method of differentiation (PCAdapt and LEA) and two different Environmental Association Analysis approaches (Latent Factor Mixed Model and Samβada) were used to identify loci with significant correlations with bioclimatic indicators. The results obtained in this study allowed us to identify signature of regional and local environment adaptation. Specific patterns of local adaptation were observed for each studied population. We identified allelic variants associated with the response to precipitation fluctuations and drought periods during the growing season. Particularly interesting is the observation of differences in the presence and effect of allelic variants among different sites, likely due to adaptation to the local environment and the different silvicultural history of each observed population.http://www.sciencedirect.com/science/article/pii/S2666719325002079SNPSBioclimatic indicators associationClimate changeFagus sylvaticaLocal adaptationEnvironmental Association analyses |
| spellingShingle | Cesare Garosi Cristina Vettori Lorenzo Arcidiaco Marko Bajc Hojka Kraigher Marjana Westergren Davide Travaglini Rok Damjanić Kristina Sever Andrej Breznikar Andreja Gregoric Miran Lanšćak Mladen Ivankovic Sanja Bogunović Donatella Paffetti Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.) Trees, Forests and People SNPS Bioclimatic indicators association Climate change Fagus sylvatica Local adaptation Environmental Association analyses |
| title | Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.) |
| title_full | Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.) |
| title_fullStr | Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.) |
| title_full_unstemmed | Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.) |
| title_short | Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.) |
| title_sort | genome wide snp association analysis reveals the genomic signature of local adaptation in natural populations of european beech fagus sylvatica l |
| topic | SNPS Bioclimatic indicators association Climate change Fagus sylvatica Local adaptation Environmental Association analyses |
| url | http://www.sciencedirect.com/science/article/pii/S2666719325002079 |
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