Strategies to Identify Adaptive Genes in Hybridizing Trees like Oaks and Poplars

Ecologically divergent, hybridizing species such as oaks and poplars provide models to identify genomic regions under selection and adaptive alleles that are transferred between species in hybrid zones. Oaks show patterns of genomic divergence characteristic for early stages of speciation with gene flow, in which large genomic regions are homogenized by interspecific gene flow interspersed by smaller regions (outlier regions) with high interspecific differentiation as result of divergent selection. These outlier regions can be identified using genome scans in hybrid zones and anchored to the Quercus robur genome sequence which will become available in the near future. Combined outlier and association genetic approaches can assess the role of individual genes in outlier genomic regions in adaptive trait variation. In contrast, hybridizing poplar species show a pattern of genomic divergence with large genomic regions of high interspecific differentiation punctuated by smaller regions of low differentiation as the result of interspecific gene flow. Genome scans in multiple hybrid zones of interfertile poplar species and in populations outside the area of sympatry will allow for the identification of genes that are exchanged between species by interspecific gene flow using the Populus trichocarpa genome sequence as a reference. Again association genetic approaches can be used for the characterization of variation in these introgressed genes with adaptive trait variation. In the present paper, the application of genomic approaches to identify genes for adaptive species divergence and reproductive isolation, and introgressed genes between species is discussed

Experimental evidence for selection against hybrids between two interfertile red oak species

Reproductive isolation between related oak species within one taxonomic section is incomplete. Even though pre- and post-zygotic isolation mechanisms have been described for interfertile oak species, natural hybridization is common in contact zones between related oaks. The apparent restriction of inter-specific hybrids between ecologically divergent species to intermediate environments in contact zones suggests postzygotic isolation via environmental selection against hybrids in parental environments. Overrepresentation of hybrids in seeds as compared to adult trees provides additional indirect evidence for selection against hybrids. Here, we used genetic assignment analyses in progeny obtained from a sympatric stand of Quercus rubra and Quercus ellipsoidalis, two interfertile species with different adaptations to drought, to characterize the number of hybrids and “pure” species in the non-germinated acorns and in seedlings. The occurrence of 43.6 % F1 hybrids and introgressive forms among the non-germinated acorns and their very low frequency in the seedlings (9.3 %) is to our knowledge the first direct evidence for early selection against hybrids in oaks possibly as result of genetic incompatibilities. Additionally, we found a signature of positive selection on EST-SSR PIE200 in Q. rubra which needs further confirmation. These results contribute to our understanding of reproductive isolation and divergence between interfertile oak species with different ecological adaptations

Analysis of environment-marker associations in American chestnut

American chestnut (Castanea dentata Borkh.) was a dominant tree species in its native range in eastern North America until the accidentally introduced fungus Cryphonectria parasitica (Murr.) Barr, that causes chestnut blight, led to a collapse of the species. Different approaches (e.g., genetic engineering or conventional breeding) are being used to fight against chestnut blight and to reintroduce the species with resistant planting stock. Because of large climatic differences within the distribution area of American chestnut, successful reintroduction of the species requires knowledge and consideration of local adaptation to the prevailing environmental conditions. Previous studies revealed clear patterns of genetic diversity along the northeast-southwest axis of the Appalachian Mountains, but less is known about the distribution of potentially adaptive genetic variation within the distribution area of this species. In this study, we investigated neutral and potentially adaptive genetic variation in nine American chestnut populations collected from sites with different environmental conditions. In total, 272 individuals were genotyped with 24 microsatellite (i.e., simple sequence repeat (SSR)) markers (seven genomic SSRs and 17 EST-SSRs). An FST-outlier analysis revealed five outlier loci. The same loci, as well as five additional ones, were significantly associated with environmental variables of the population sites in an environmental association analysis. Four of these loci are of particular interest, since they were significant in both methods, and they were associated with environmental variation, but not with geographic variation. Hence, these loci might be involved in (temperature-related) adaptive processes in American chestnut. This work aims to help understanding the genetic basis of adaptation in C. dentata, and therefore the selection of suitable provenances for further breeding efforts

Analysis of Environment-Marker Associations in American Chestnut

American chestnut (Castanea dentata Borkh.) was a dominant tree species in its native range in eastern North America until the accidentally introduced fungus Cryphonectria parasitica (Murr.) Barr, that causes chestnut blight, led to a collapse of the species. Different approaches (e.g., genetic engineering or conventional breeding) are being used to fight against chestnut blight and to reintroduce the species with resistant planting stock. Because of large climatic differences within the distribution area of American chestnut, successful reintroduction of the species requires knowledge and consideration of local adaptation to the prevailing environmental conditions. Previous studies revealed clear patterns of genetic diversity along the northeast-southwest axis of the Appalachian Mountains, but less is known about the distribution of potentially adaptive genetic variation within the distribution area of this species. In this study, we investigated neutral and potentially adaptive genetic variation in nine American chestnut populations collected from sites with different environmental conditions. In total, 272 individuals were genotyped with 24 microsatellite (i.e., simple sequence repeat (SSR)) markers (seven genomic SSRs and 17 EST-SSRs). An FST-outlier analysis revealed five outlier loci. The same loci, as well as five additional ones, were significantly associated with environmental variables of the population sites in an environmental association analysis. Four of these loci are of particular interest, since they were significant in both methods, and they were associated with environmental variation, but not with geographic variation. Hence, these loci might be involved in (temperature-related) adaptive processes in American chestnut. This work aims to help understanding the genetic basis of adaptation in C. dentata, and therefore the selection of suitable provenances for further breeding efforts

Patterns of contemporary hybridization inferred from paternity analysis in a four-oak-species forest

<p>Abstract</p> <p>Background</p> <p>Few studies address the issue of hybridization in a more than two-species context. The species-rich <it>Quercus </it>complex is one of the systems which can offer such an opportunity. To investigate the contemporary pattern of hybridization we sampled and genotyped 320 offspring from a natural mixed forest comprising four species of the European white oak complex: <it>Quercus robur</it>, <it>Q. petraea</it>, <it>Q. pubescens</it>, and <it>Q. frainetto</it>.</p> <p>Results</p> <p>A total of 165 offspring were assigned unambiguously to one of the pollen donors within the study plot. The minimum amount of effective pollen originating from outside the plot varied markedly among the seed parents, ranging from 0.18 to 0.87. The majority of the successful matings (64.1%) occurred between conspecific individuals indicating the existence of reproductive barriers between oak species. However, the isolation was not complete since we found strong evidence for both first-generation (8.4%) and later-generation hybrids (27.5%). Only two out of eight seed parents, belonging to <it>Q. petraea </it>and <it>Q. robur</it>, showed a high propensity to hybridize with <it>Q. pubescens </it>and <it>Q. petraea</it>, respectively. Significant structure of the effective pollen pools (<it>Φ</it>_{<it>pt </it>}= 0.069, P = 0.01) was detected in our sample. However, no support was found for the isolation by distance hypothesis. The proportion of hybrids was much higher (79%) in the seed generation when compared to the adult tree generation.</p> <p>Conclusion</p> <p>First-generation hybrids were observed only between three out of six possible species combinations. Hybrids between one pair of species preferred to mate with one of their parental species. The observation of first and later-generation hybrids in higher frequency in acorns than in adults might be explained by selection against hybrid genotypes, the history of this uneven-aged forest or past introgression between species.</p

Analysis of Environment-Marker Associations in American Chestnut

American chestnut (Castanea dentata Borkh.) was a dominant tree species in its native range in eastern North America until the accidentally introduced fungus Cryphonectria parasitica (Murr.) Barr, that causes chestnut blight, led to a collapse of the species. Different approaches (e.g., genetic engineering or conventional breeding) are being used to fight against chestnut blight and to reintroduce the species with resistant planting stock. Because of large climatic differences within the distribution area of American chestnut, successful reintroduction of the species requires knowledge and consideration of local adaptation to the prevailing environmental conditions. Previous studies revealed clear patterns of genetic diversity along the northeast-southwest axis of the Appalachian Mountains, but less is known about the distribution of potentially adaptive genetic variation within the distribution area of this species. In this study, we investigated neutral and potentially adaptive genetic variation in nine American chestnut populations collected from sites with different environmental conditions. In total, 272 individuals were genotyped with 24 microsatellite (i.e., simple sequence repeat (SSR)) markers (seven genomic SSRs and 17 EST-SSRs). An FST-outlier analysis revealed five outlier loci. The same loci, as well as five additional ones, were significantly associated with environmental variables of the population sites in an environmental association analysis. Four of these loci are of particular interest, since they were significant in both methods, and they were associated with environmental variation, but not with geographic variation. Hence, these loci might be involved in (temperature-related) adaptive processes in American chestnut. This work aims to help understanding the genetic basis of adaptation in C. dentata, and therefore the selection of suitable provenances for further breeding efforts

Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community

<p>Abstract</p> <p>Background</p> <p>Analysis of interspecific gene flow is crucial for the understanding of speciation processes and maintenance of species integrity. Oaks (genus <it>Quercus</it>, <it>Fagaceae</it>) are among the model species for the study of hybridization. Natural co-occurrence of four closely related oak species is a very rare case in the temperate forests of Europe. We used both morphological characters and genetic markers to characterize hybridization in a natural community situated in west-central Romania and which consists of <it>Quercus robur</it>, <it>Q. petraea</it>, <it>Q. pubescen</it>s, and <it>Q. frainetto</it>, respectively.</p> <p>Results</p> <p>On the basis of pubescence and leaf morphological characters ~94% of the sampled individuals were assigned to pure species. Only 16 (~6%) individual trees exhibited intermediate morphologies or a combination of characters of different species. Four chloroplast DNA haplotypes were identified in the study area. The distribution of haplotypes within the white oak complex showed substantial differences among species. However, the most common haplotypes were present in all four species. Furthermore, based on a set of 7 isozyme and 6 microsatellite markers and using a Bayesian admixture analysis without any a priori information on morphology we found that four genetic clusters best fit the data. There was a very good correspondence of each species with one of the inferred genetic clusters. The estimated introgression level varied markedly between pairs of species ranging from 1.7% between <it>Q. robur </it>and <it>Q. frainetto </it>to 16.2% between <it>Q. pubescens </it>and <it>Q. frainetto</it>. Only nine individuals (3.4%) appeared to be first-generation hybrids.</p> <p>Conclusion</p> <p>Our data indicate that natural hybridization has occurred at relatively low rates. The different levels of gene flow among species might be explained by differences in flowering time and spatial position within the stand. In addition, a partial congruence between phenotypically and genetically intermediate individuals was found, suggesting that intermediate appearance does not necessarily mean hybridization. However, it appears that natural hybridization did not seriously affect the species identity in this area of sympatry.</p

Leaf morphological and genetic variation between Quercus rubra and Quercus ellipsoidalis: comparison of sympatric and parapatric populations

Species boundaries in oaks are often not clear-cut, which is potentially a result of interspecific hybridization with trait introgression and phenotypic plasticity. Quercus rubra L. and Quercus ellipsoidalis E.J. Hill are two interfertile partially sympatric red oak species (section Lobatae) with different adaptations to drought. Quercus ellipsoidalis is the most drought tolerant of the North American red oak species and is characterized by deep tap roots, a shrubby growth and by deeply dissected leaves. Genetic differentiation between species is low for most molecular markers. However, one genic microsatellite in a CONSTANS-like (COL) gene, FIR013, was previously identified as outlier locus under strong divergent selection between species. In this study, we analyzed leaf morphometric traits in neighboring (parapatric) Q. rubra/Q. ellipsoidalis populations and in one sympatric population from the same region along an environmental gradient. Using multivariate statistics of leaf traits both species showed distinct bimodal frequency distributions for the first canonical discriminant function with some overlap in the phenotypic extremes, especially in the sympatric population. Leaf dissection traits showed strong and consistent differentiation between species in sympatric and parapatric populations, while differentiation for leaf size was lower in the sympatric population under more similar environmental conditions. Leaf phenotypes in F1 hybrids and introgressive forms suggested maternal effects and introgression of leaf traits between species. The association of outlier gene copy number at FIR013 with species-discriminating leaf traits in Quercus rubra can be a reflection of population differences since outlier gene copy number and population membership show significant collinearity. Similar environmental selection pressures on outlier alleles and leaf shape could also have resulted in this association. In future studies, segregating full-sib families could be used to test whether outlier alleles and associated genomic regions are indeed associated with leaf traits or other species-discriminating characters

An Early Reference to DNA Barcode for the Anacardiaceae Family

Anacardiaceae is well-known for its edible fruits and economically important species in Indonesia. Approximately 3% of Indonesia's endangered and vulnerable species belong to this family. Fast and accurate species identification is crucial to support the conservation efforts for this family, such as employing DNA sequences. Species identification using DNA sequences, known as DNA barcoding, has been widely used in many applied fields. So far, the application of DNA barcoding for Anacardiaceae plant species is limited to several genera only, such as Mangifera and Spondias. This research aimed to enrich the DNA barcode references of Anacardiaceae and to evaluate the most suitable and effective genetic marker as DNA barcodes to identify species of 35 samples representing sixteen species of the Anacardiaceae family using chloroplast markers matK and rbcL as barcode regions. When comparing the morphological identification with the molecular assignments, the barcode accuracy was 62.50% (matK), 60.61% (rbcL), and 73.33% (matK+rbcL) at the genus level. All the markers failed to show a barcoding gap, even though the t-test showed that the intraspecific and interspecific genetic distances were significantly different for matK and rbcL+matK. Among others, Gluta walichii (Hook.f.) Ding Hou and Melanochyla caesia Jack were the only species successfully resolved by all markers. Nevertheless, new DNA barcodes of six Anacardiaceae species were made available by this study, enriching the genetic references of tropical flora diversity