García Gil, María Rosario - Forest Tree Genetics and Breeding

@article{gauchan_annulohypoxylon_2021,
	title = {Annulohypoxylon sp. strain {MUS1}, an endophytic fungus isolated from {Taxus} wallichiana {Zucc}., produces taxol and other bioactive metabolites},
	volume = {11},
	issn = {2190-572X, 2190-5738},
	url = {http://link.springer.com/10.1007/s13205-021-02693-z},
	doi = {10/gkcr8j},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {3 Biotech},
	author = {Gauchan, Dhurva Prasad and Vélëz, Heriberto and Acharya, Ashesh and Östman, Johnny R. and Lundén, Karl and Elfstrand, Malin and García-Gil, M. Rosario},
	month = mar,
	year = {2021},
	pages = {152},
}

@article{chen_leveraging_2021,
	title = {Leveraging breeding programs and genomic data in {Norway} spruce ({Picea} abies {L}. {Karst}) for {GWAS} analysis},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02392-1},
	doi = {10.1186/s13059-021-02392-1},
	abstract = {Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Genome Biology},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Li, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and García-Gil, Maria Rosario and Lascoux, Martin and Wu, Harry X.},
	month = jun,
	year = {2021},
	keywords = {Budburst stage, Frost damage, Genome-wide association study, MAP3K gene, Norway spruce, Wood quality},
	pages = {179},
}

Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

@article{ahlinder_life_2021,
	title = {Life stage-specific inbreeding depression in long-lived {Pinaceae} species depends on population connectivity},
	volume = {11},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-021-88128-4},
	doi = {10.1038/s41598-021-88128-4},
	abstract = {Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Scientific Reports},
	author = {Ahlinder, Jon and Giles, Barbara E. and García-Gil, M. Rosario},
	month = apr,
	year = {2021},
	pages = {8834},
}

Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.

@article{ranade_molecular_2021,
	title = {Molecular signatures of local adaptation to light in {Norway} spruce},
	volume = {253},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-020-03517-9},
	doi = {10/gjd69n},
	abstract = {Abstract
            
              Main conclusion
              Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light.
            
            
              Abstract
              The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.},
	language = {en},
	number = {2},
	urldate = {2021-06-03},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = feb,
	year = {2021},
	pages = {53},
}

Abstract Main conclusion Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. Abstract The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

@article{zhou_effect_2020,
	title = {Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of {Norway} spruce},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6737-3},
	doi = {10.1186/s12864-020-6737-3},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce (
                Picea abies
                (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments.
              
            
            
              Results
              GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30\% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95\% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12.
            
            
              Conclusions
              This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90\% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Zhou, Linghua and Chen, Zhiqiang and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {323},
}

Abstract Background Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce ( Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. Results GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12. Conclusions This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.

@article{gauchan_evaluation_2020,
	title = {Evaluation of antimicrobial, antioxidant and cytotoxic properties of bioactive compounds produced from endophytic fungi of {Himalayan} yew ({Taxus} wallichiana) in {Nepal}},
	volume = {9},
	issn = {2046-1402},
	url = {https://f1000research.com/articles/9-379/v2},
	doi = {10.12688/f1000research.23250.2},
	abstract = {Background:
              Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study,
              Taxus wallichiana,
              which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties.
            
            
              Methods:
              The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts.
            
            
              Results:
              Out of 16 different
              Taxus
              trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera:
              Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella
              and
              Daldinia
              . The ethyl acetate extracts isolated from three endophytic fungi:
              Alternaria alternata
              ,
              Cladosporium cladosporioides
              and
              Alternaria brassicae
              showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC
              50
              concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of
              C. cladosporioides
              and
              A. brassicae
              also showed promising antimicrobial activity against
              Escherichia coli
              ,
              Staphylococcus aureus
              and
              Bacillus subtilis
              with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC
              50
              of 104.2 and 125.9µg/ml, respectively.
            
            
              Conclusions:
              The crude fungal extracts obtained from endophytes:
              A. alternata
              ,
              C. cladosporioides
              and
              A. brassicae
              upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.},
	language = {en},
	urldate = {2021-06-07},
	journal = {F1000Research},
	author = {Gauchan, Dhurva Prasad and Kandel, Pratistha and Tuladhar, Astha and Acharya, Ashesh and Kadel, Upendra and Baral, Aayush and Shahi, Arjan Bir and García-Gil, María Rosario},
	month = oct,
	year = {2020},
	pages = {379},
}

Background: Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study, Taxus wallichiana, which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties. Methods: The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts. Results: Out of 16 different Taxus trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera: Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella and Daldinia . The ethyl acetate extracts isolated from three endophytic fungi: Alternaria alternata , Cladosporium cladosporioides and Alternaria brassicae showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC 50 concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of C. cladosporioides and A. brassicae also showed promising antimicrobial activity against Escherichia coli , Staphylococcus aureus and Bacillus subtilis with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC 50 of 104.2 and 125.9µg/ml, respectively. Conclusions: The crude fungal extracts obtained from endophytes: A. alternata , C. cladosporioides and A. brassicae upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.

@article{baison_genetic_2020,
	title = {Genetic control of tracheid properties in {Norway} spruce wood},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-72586-3},
	doi = {10.1038/s41598-020-72586-3},
	abstract = {Abstract
            
              Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (
              Picea abies
              (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are:
              Picea abies BIG GRAIN 2
              (
              PabBG2)
              with a predicted function in auxin transport and sensitivity, and
              MA\_373300g0010
              encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Baison, J. and Zhou, Linghua and Forsberg, Nils and Mörling, Tommy and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry X. and Mellerowicz, Ewa J. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {18089},
}

Abstract Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce ( Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 ( PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

@article{gil-munoz_transcriptomic_2020,
	title = {Transcriptomic {Analysis} {Reveals} {Salt} {Tolerance} {Mechanisms} {Present} in {Date}-{Plum} {Persimmon} {Rootstock} ({Diospyros} lotus {L}.)},
	volume = {10},
	issn = {2073-4395},
	url = {https://www.mdpi.com/2073-4395/10/11/1703},
	doi = {10/gjd6kb},
	abstract = {Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Agronomy},
	author = {Gil-Muñoz, Francisco and Delhomme, Nicolas and Quiñones, Ana and Naval, Maria del Mar and Badenes, Maria Luisa and García-Gil, M. Rosario},
	month = nov,
	year = {2020},
	pages = {1703},
}

Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt–tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.

@article{calleja-rodriguez_analysis_2019,
	title = {Analysis of phenotypic- and {Estimated} {Breeding} {Values} ({EBV}) to dissect the genetic architecture of complex traits in a {Scots} pine three-generation pedigree design},
	volume = {462},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S002251931830554X},
	doi = {10.1016/j.jtbi.2018.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Journal of Theoretical Biology},
	author = {Calleja-Rodriguez, Ainhoa and Li, Zitong and Hallingbäck, Henrik R. and Sillanpää, Mikko J. and Wu, Harry X. and Abrahamsson, Sara and García-Gil, Maria Rosario},
	month = feb,
	year = {2019},
	pages = {283--292},
}

@article{zhou_genetic_2019,
	title = {Genetic analysis of wood quality traits in {Norway} spruce open-pollinated progenies and their parent plus trees at clonal archives and the evaluation of phenotypic selection of plus trees},
	volume = {49},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0117},
	doi = {10/gjcjw5},
	abstract = {A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h
              2
              ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h
              2
              estimate, selection of the best clones from clonal archives would be an effective alternative.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Zhou, Linghua and Chen, Zhiqiang and Lundqvist, Sven-Olof and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {810--818},
}

A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h 2 ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h 2 estimate, selection of the best clones from clonal archives would be an effective alternative.

@article{baison_genomewide_2019,
	title = {Genome‐wide association study identified novel candidate loci affecting wood formation in {Norway} spruce},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14429},
	doi = {10/gjcj3d},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Baison, John and Vidalis, Amaryllis and Zhou, Linghua and Chen, Zhi‐Qiang and Li, Zitong and Sillanpää, Mikko J. and Bernhardsson, Carolina and Scofield, Douglas and Forsberg, Nils and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry and Ingvarsson, Pär K. and Lundqvist, Sven‐Olof and Niittylä, Totte and García‐Gil, M Rosario},
	month = oct,
	year = {2019},
	pages = {83--100},
}

@article{ranade_global_2019,
	title = {Global gene expression analysis in etiolated and de-etiolated seedlings in conifers},
	volume = {14},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0219272},
	doi = {10/gjcsvr},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, M. Rosario},
	editor = {Zhang, Jin-Song},
	month = jul,
	year = {2019},
	pages = {e0219272},
}

@article{ranade_transcriptome_2019,
	title = {Transcriptome analysis of shade avoidance and shade tolerance in conifers},
	volume = {250},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-019-03160-z},
	doi = {10/gjcr99},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {299--318},
}

@article{chen_accuracy_2018,
	title = {Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in {Norway} spruce},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5256-y},
	doi = {10/ghk9pc},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Baison, John and Pan, Jin and Karlsson, Bo and Andersson, Bengt and Westin, Johan and García-Gil, María Rosario and Wu, Harry X.},
	month = dec,
	year = {2018},
	pages = {946},
}

@article{lundqvist_age_2018,
	title = {Age and weather effects on between and within ring variations of number, width and coarseness of tracheids and radial growth of young {Norway} spruce},
	volume = {137},
	issn = {1612-4669, 1612-4677},
	url = {http://link.springer.com/10.1007/s10342-018-1136-x},
	doi = {10.1007/s10342-018-1136-x},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Lundqvist, Sven-Olof and Seifert, Stefan and Grahn, Thomas and Olsson, Lars and García-Gil, Maria Rosario and Karlsson, Bo and Seifert, Thomas},
	month = oct,
	year = {2018},
	pages = {719--743},
}

@article{hayatgheibi_genetic_2018,
	title = {Genetic control of transition from juvenile to mature wood with respect to microfibril angle in {Norway} spruce ( \textit{{Picea} abies} ) and lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {48},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0140},
	doi = {10.1139/cjfr-2018-0140},
	abstract = {Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h
              2
              ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h
              2
              were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Forsberg, Nils Erik Gustaf and Lundqvist, Sven-Olof and Mörling, Tommy and Mellerowicz, Ewa J. and Karlsson, Bo and Wu, Harry X. and García-Gil, M. Rosario},
	month = nov,
	year = {2018},
	pages = {1358--1365},
}

Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h 2 ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h 2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.

@article{razzak_differential_2017,
	title = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light: {Scots} pine response to light intensity and shade},
	volume = {40},
	issn = {01407791},
	shorttitle = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light},
	url = {http://doi.wiley.com/10.1111/pce.12921},
	doi = {10.1111/pce.12921},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Razzak, Abdur and Ranade, Sonali Sachin and Strand, Åsa and García-Gil, M. R.},
	month = aug,
	year = {2017},
	pages = {1332--1340},
}

@article{ranade_application_2016,
	title = {Application of monochromatic blue light during germination and hypocotyl development improves outplanted {Scots} pine ({Pinus} sylvestris {L}.) trees performance},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S037811271500657X},
	doi = {10.1016/j.foreco.2015.11.034},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Ranade, Sonali Sachin and García Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {368--374},
}

@article{ranade_non-functional_2016,
	title = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch}): insights from in silico analysis of nuclear and organellar genomes},
	volume = {291},
	issn = {1617-4615, 1617-4623},
	shorttitle = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch})},
	url = {http://link.springer.com/10.1007/s00438-015-1159-7},
	doi = {10.1007/s00438-015-1159-7},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Molecular Genetics and Genomics},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Rosselló, Josep A.},
	month = apr,
	year = {2016},
	pages = {935--941},
}

@article{bernhardsson_present_2016,
	title = {Present genetic structure is congruent with the common origin of distant {Scots} pine populations in its {Romanian} distribution},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112715006052},
	doi = {10.1016/j.foreco.2015.10.047},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Bernhardsson, C. and Floran, V. and Ganea, S.L. and García-Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {131--143},
}

@article{ranade_fungal_2015,
	title = {Fungal {Infection} {Increases} the {Rate} of {Somatic} {Mutation} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {106},
	issn = {1465-7333 (Electronic) 0022-1503 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25890976},
	doi = {10.1093/jhered/esv017},
	abstract = {Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {J Hered},
	author = {Ranade, S. S. and Ganea, L. S. and Razzak, A. M. and Garcia Gil, M. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/04/22},
	keywords = {*Mutation Rate, Basidiomycota/*pathogenicity, DNA, Plant/genetics, Genetic Markers, Genetics, Population, Genome, Plant, Genomic Instability, Genotype, Host-Pathogen Interactions/*genetics, Microsatellite Repeats, Mutation, Pinus sylvestris/*genetics/microbiology, Plant Diseases/genetics/*microbiology, Scots pine, Sequence Analysis, DNA, Somatic mutation., Sweden, abiotic stress, microsatellite, simple sequence repeats},
	pages = {386--94},
}

Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).

@article{li_functional_2014,
	title = {Functional {Multi}-{Locus} {QTL} {Mapping} of {Temporal} {Trends} in {Scots} {Pine} {Wood} {Traits}},
	volume = {4},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/4/12/2365/6025852},
	doi = {10/f3p5gx},
	abstract = {Abstract
            Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Li, Zitong and Hallingbäck, Henrik R and Abrahamsson, Sara and Fries, Anders and Gull, Bengt Andersson and Sillanpää, Mikko J and García-Gil, M Rosario},
	month = dec,
	year = {2014},
	pages = {2365--2379},
}

Abstract Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.

@article{abrahamsson_maternal_2013,
	title = {Maternal heterozygosity and progeny fitness association in an inbred {Scots} pine population},
	volume = {141},
	issn = {0016-6707, 1573-6857},
	url = {http://link.springer.com/10.1007/s10709-013-9704-y},
	doi = {10/f2242n},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Genetica},
	author = {Abrahamsson, S. and Ahlinder, J. and Waldmann, P. and García-Gil, M. R.},
	month = mar,
	year = {2013},
	pages = {41--50},
}

@article{ranade_pinus_2013,
	title = {Pinus taeda {cDNA} {Microarray} as a {Tool} for {Candidate} {Gene} {Identification} for {Local} {Red}/{Far}-{Red} {Light} {Adaptive} {Response} in {Pinus} sylvestris},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	url = {http://www.scirp.org/Journal/Paperabs.aspx?paperid=28683},
	doi = {10/gjcmm4},
	abstract = {Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.},
	language = {en},
	number = {3},
	urldate = {2021-06-21},
	journal = {American Journal of Plant Sciences},
	author = {Ranade, Sonali S. and Abrahamsson, Sara and Niemi, Juha and García-Gil, María Rosario},
	month = mar,
	year = {2013},
	note = {Number: 3
Publisher: Scientific Research Publishing},
	pages = {479--493},
}

Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{floran_organelle_2011,
	title = {Organelle {Genetic} {Diversity} and {Phylogeography} of {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {39},
	doi = {10/gg32mz},
	abstract = {The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Floran, Valentina and Sestras, Radu and Garcia Gil, Rosario},
	month = may,
	year = {2011},
	pages = {317--322},
}

The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.

@article{garcia-gil_evolutionary_2008,
	title = {Evolutionary {Aspects} of {Functional} and {Pseudogene} {Members} of the {Phytochrome} {Gene} {Family} in {Scots} {Pine}},
	volume = {67},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-008-9135-z},
	doi = {10/dmzkqj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Journal of Molecular Evolution},
	author = {García-Gil, Maria Rosario},
	month = aug,
	year = {2008},
	pages = {222--232},
}

@article{pyhajarvi_demographic_2007,
	title = {Demographic {History} {Has} {Influenced} {Nucleotide} {Diversity} in {European} \textit{{Pinus} sylvestris} {Populations}},
	volume = {177},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/177/3/1713/6064487},
	doi = {10/cmrqmt},
	abstract = {Abstract
            To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Pyhäjärvi, Tanja and García-Gil, M Rosario and Knürr, Timo and Mikkonen, Merja and Wachowiak, Witold and Savolainen, Outi},
	month = nov,
	year = {2007},
	pages = {1713--1724},
}

Abstract To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.

@article{notivol_genetic_2007,
	title = {Genetic variation of growth rhythm traits in the limits of a latitudinal cline in {Scots} pine},
	volume = {37},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/X06-243},
	doi = {10/bjtx48},
	abstract = {Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q
              ST
              = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14\% ± 8\%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Notivol, E. and García-Gil, M. R. and Alía, R. and Savolainen, O.},
	month = mar,
	year = {2007},
	pages = {540--551},
}

Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q ST = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14% ± 8%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.

@article{waldmann_comparing_2005,
	title = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits: an application to {Pinus} sylvestris},
	volume = {94},
	copyright = {2005 The Genetics Society},
	issn = {1365-2540},
	shorttitle = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits},
	url = {https://www.nature.com/articles/6800672},
	doi = {10.1038/sj.hdy.6800672},
	abstract = {Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.},
	language = {en},
	number = {6},
	urldate = {2021-06-11},
	journal = {Heredity},
	author = {Waldmann, P. and García-Gil, M. R. and Sillanpää, M. J.},
	month = jun,
	year = {2005},
	note = {Number: 6
Publisher: Nature Publishing Group},
	pages = {623--629},
}

Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.

@article{savolainen_genetic_2004,
	title = {Genetic variation in cessation of growth and frost hardiness and consequences for adaptation of {Pinus} sylvestris to climatic changes},
	volume = {197},
	issn = {0378-1127},
	doi = {10/dvn6cp},
	abstract = {Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.},
	language = {English},
	number = {1-3},
	journal = {Forest Ecology and Management},
	author = {Savolainen, O. and Bokma, F. and Garcia-Gil, R. and Komulainen, P. and Repo, T.},
	month = aug,
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000223382700007},
	keywords = {abies l karst, adaptation, boreal forests, climate change, cold-hardiness, contorta, f-st, frost hardiness, nucleotide diversity, pollen migration, populations, responses, scots pine, timing of growth, traits},
	pages = {79--89},
}

Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.

@article{komulainen_comparing_2003,
	title = {Comparing {EST}-based genetic maps between {Pinus} sylvestris and {Pinus} taeda},
	volume = {107},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-003-1312-2},
	doi = {10/fvc7mz},
	abstract = {A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40\% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Theoretical and Applied Genetics},
	author = {Komulainen, P. and Brown, G. R. and Mikkonen, M. and Karhu, A. and García-Gil, M. R. and O'Malley, D. and Lee, B. and Neale, D. B. and Savolainen, O.},
	month = aug,
	year = {2003},
	pages = {667--678},
}

A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.