A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Tolerance evaluation and genetic relationship analysis among some economically important chestnut cultivars in Türkiye using drought-associated SSR and EST-SSR markers

The aim of this study was to evaluate drought tolerance and genetic relationships among some important chestnut cultivars for Türkiye by using drought-related genomic simple sequence repeat (SSR) markers and genic expressed sequence tag-simple sequence repeat (EST-SSR) markers. Using five SSR markers, the average number of alleles (avNa), mean heterozygosity (Havp) and polymorphism information content (PIC) were determined to be 9.22, 0.395 and 0.375, respectively. In addition, using eight EST-SSR markers, the values of avNa, Havp and PIC were determined to be 7.75, 0.309 and 0.262, respectively. All microsatellite markers used in this study showed 100% polymorphism among chestnut cultivars. In UPGMA dendrograms obtained with both SSR and EST-SSR markers, the Erfelek and Hacıömer chestnut cultivars were determined to be the most similar cultivars. Some assessments are discussed regarding drought tolerance for specific alleles obtained from the EST-SSR markers GOT045, GOT021, GOT004, FIR094 and VIT033 in chestnut cultivars. Some preliminary results regarding drought tolerance in chestnut cultivars were obtained in our study with the help of these markers. Our study also characterized the genetic relationships among chestnut cultivars of great importance using drought-related character-specific markers.

Applying molecular and genetic methods to trees and their fungal communities

Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.

QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane

Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03481-7.

Development of genome-specific SSR markers for the identification of introgressed segments of Sinapis alba in the Brassica juncea background

Sinapis alba L. (white mustard) is recognized for carrying host resistance against several biotic stresses including, Alternaria brassicae, which is responsible for blight disease in cultivated Brassica. However, another cultivated Brassica has a dearth for genetic resistance for these stresses due to its narrow genetic base. Therefore, we performed introgression of the genomic regions of S. alba into backcross progenies of B. juncea + S. alba somatic hybrids. These advanced generations with S. alba chromosomal segments are named B. juncea-S. alba introgression lines (ILs). In the present study, we developed the S. alba genome-specific microsatellites from the draft genome to track the S. alba genome introgressions and responsible regions for resistance to A. brassicae. For developing these SSR markers, the unique contigs of S. alba draft genome were identified through BLASTN with B. juncea, B. rapa, B. nigra, and B. oleracea reference genome assemblies, including mitochondrial and chloroplast genomes, and further used for marker development. Out of 403,423 contigs, we have identified 65,343 non-hit contigs of S. alba that yielded a total of 1231 genome-specific microsatellites, out of which 1107 were expected to produce a single allele upon amplification. Out of the total SSRs, 234 primer pairs were randomly picked from whole-genome and validated between B. juncea and S. alba genomes for their specificity. In the validation experiment, these markers gave a single amplicon into S. alba, while they did not amplify in B. juncea genome. Of these, 59 microsatellites were used to track S. alba introgressions in 80 BC2F3 lines. To the best of our knowledge, this is the first time that these two genetic resources are developed in the form of B. juncea-S. alba ILs and S. alba-specific markers. Therefore, both the resources unlock a new avenue of Brassica breeding for biotic and abiotic stresses along with quality traits.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03402-0.

Asymmetric character displacement in mixed oak stands

Ecological character displacement (ECD) refers to a pattern of increased divergence at sites where species ranges overlap caused by competition for resources. Although ECD is believed to be common, there are few in-depth studies that clearly establish its existence, especially in plants. Thus, we have compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks: Quercus dentata and Quercus aliena. In contrast to previous studies, we define sympatry and allopatry at a local scale, thereby comparing populations that can or cannot directly interact. Using genetic markers, we found greater genetic divergence between the two oak species growing in mixed stands and inferred that long-term gene flow has predominantly occurred asymmetrically from the cold-tolerant species (Q. dentata) to the warm-demanding later colonizing species (Q. aliena). Analysis of leaf traits revealed greater divergence in mixed than in pure oak stands. This was mostly due to the later colonizing species being characterized by more resource-conservative traits in the presence of the other species. Controlling for relevant environmental differences did not alter these conclusions. These results suggest that asymmetric trait divergence can take place where species coexist, possibly due to the imbalance in demographic history of species resulting in asymmetric inter-specific selection pressures.

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

Gene flow between cultivated and wild gene pools is common in the contact zone between agricultural lands and natural habitats and can be used to study the development of adaptations and selection of novel varieties. This is likely the case in the northern Adriatic region, where centuries-old cultivated orchards of sweet chestnut (Castanea sativa Mill.) are planted within the natural distribution area of the species. Thus, we investigated the population structure of several orchards of sweet chestnuts. Furthermore, the genetic background of three toponymous clonal varieties was explored. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this research, and both grafted and non-grafted individuals were included in this study. Five closely related clones were identified, which represent a singular, polyclonal marron variety, found in all three cultivation areas. Furthermore, many hybrids, a result of breeding between cultivated and wild chestnuts, have been found. Analyzed semi-wild orchards defined by a diverse genetic structure, represent a hotspot for further selection and could result in creation of locally adapted, high-yielding varieties.

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers

Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.

Genetic Structure of Natural Northern Range-Margin Mainland, Peninsular, and Island Populations of Northern Red Oak (Quercus rubra L.)

Plant populations at the leading edge of the species’ native range often exhibit genetic structure as a result of genetic drift and adaptation to harsh environmental conditions. Hence, they are likely to harbour rare genetic adaptations to local environmental conditions and therefore are of particular interest to understand climate adaptation. We examined genetic structure of nine northern marginal mainland, peninsular and isolated island natural populations of northern red oak (Quercus rubraL.), a valuable long-lived North American hardwood tree species, covering a wide climatic range, using 17 nuclear microsatellites. We found pronounced genetic differentiation of a disjunct isolated island population from all mainland and peninsular populations. Furthermore, we observed remarkably strong fine-scale spatial genetic structure (SGS) in all investigated populations. Such high SGS values are uncommon and were previously solely observed in extreme range-edge marginal oak populations in one other study. We found a significant correlation between major climate parameters and SGS formation in northern range-edge red oak populations, with more pronounced SGS in colder and drier regions. Most likely, the harsh environment in leading edge populations influences the density of reproducing trees within the populations and therefore leads to restricted overlapping of seed shadows when compared to more central populations. Accordingly, SGS was negatively correlated with effective population size and increased with latitude of the population locations. The significant positive association between genetic distances and precipitation differences between populations may be indicative of isolation by adaptation in the observed range-edge populations. However, this association was not confirmed by a multiple regression analysis including geographic distances and precipitation distances, simultaneously. Our study provides new insights in the genetic structure of long-lived tree species at their leading distribution edge.

Population and Landscape Genetics Provide Insights Into Species Conservation of Two Evergreen Oaks in Qinghai-Tibet Plateau and Adjacent Regions

The combination of population and landscape genetics can facilitate the understanding of conservation strategy under the changing climate. Here, we focused on the two most diverse and ecologically important evergreen oaks: Quercus aquifolioides and Quercus spinosa in Qinghai-Tibetan Plateau (QTP), which is considered as world's biodiversity hotspot. We genotyped 1,657 individuals of 106 populations at 15 nuclear microsatellite loci throughout the species distribution range. Spatial patterns of genetic diversity were identified by mapping the allelic richness (AR) and locally common alleles (LCA) according to the circular neighborhood methodology. Migration routes from QTP were detected by historical gene flow estimation. The response pattern of genetic variation to environmental gradient was assessed by the genotype-environment association (GEA) analysis. The overall genetic structure showed a high level of intra-species genetic divergence of a strong west-east pattern. The West-to-East migration route indicated the complex demographic history of two oak species. We found evidence of isolation by the environment in Q. aqu-East and Q. spi-West lineage but not in Q. aqu-West and Q. spi-East lineage. Furthermore, priority for conservation should be given to populations that retain higher spatial genetic diversity or isolated at the edge of the distribution range. Our findings indicate that knowledge of spatial diversity and migration route can provide valuable information for the conservation of existing populations. This study provides an important guide for species conservation for two oak species by the integration of population and landscape genetic methods.

Physiological, Biochemical and Transcriptomic Analysis of the Aerial Parts (Leaf-Blade and Petiole) of Asarum sieboldii Responding to Drought Stress

Asarum sieboldii Miq. is a leading economic crop and a traditional medicinal herb in China. Leaf-blade and petiole are the only aerial tissues of A. sieboldii during the vegetative growth, playing a vital role in the accumulation and transportation of biomass energy. They also act as critical indicators of drought in agricultural management, especially for crops having underground stems. During drought, variations in the morphology and gene expression of the leaves and petioles are used to control agricultural irrigation and production. Besides, such stress can also alter the differential gene expression in these tissues. However, little is known about the drought-tolerant character of the aerial parts of A. sieboldii. In this study, we examined the physiological, biochemical and transcriptomic responses to the drought stress in the leaf blades and petioles of A. sieboldii. The molecular mechanism, involving in drought stress response, was elucidated by constructing the cDNA libraries and performing transcriptomic sequencing. Under drought stress, a total of 2912 and 2887 unigenes were differentially expressed in the leaf blade and petiole, respectively. The detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in drought tolerance. In response to drought, the leaf blade and petiole displayed a general physiological character, a higher SOD and POD activity, a higher MDA content and lower chlorophyll content. Three unigenes encoding POD were up-regulated, which can improve POD activity. Essential oil in petiole was extracted. The relative contents of methyleugenol and safrole in essential oil were increased from 0.01% to 0.05%, and 3.89% to 16.97%, respectively, while myristicin slightly reduced from 24.87% to 21.52%. Additionally, an IGS unigene, involved in eugenol biobiosynthesis, was found up-regulated under drought stress, which was predicated to be responsible for the accumulation of methyleugenol and safrole. Simple sequence repeats (SSRs) were characterized in of A. sieboldii, and a total of 5466 SSRs were identified. Among them, mono-nucleotides were the most abundant repeat units, accounting for 44.09% followed by tri-, tetra-, penta and hexa-nucleotide repeats. Overall, the present work provides a valuable resource for the population genetics studies of A. sieboldii. Besides, it provides much genomic information for the functional dissection of the drought-resistance in A. sieboldii, which will be useful to understand the bio-regulatory mechanisms linked with drought-tolerance to enhance its yield.

Characterizing the Leaf Transcriptome of Chrysanthemum rhombifolium (Ling et C. Shih), a Drought Resistant, Endemic Plant From China

Chrysanthemum rhombifolium (Ling et C. Shih), an endemic plant that is extremely well-adapted to harsh environments. However, little is known about its molecular biology of the plant's resistant traits against stress, or even its molecular biology of overall plant. To investigate the molecular biology of C. rhombifolium and mechanism of stress adaptation, we performed transcriptome sequencing of its leaves using an Illumina platform. A total of 130,891 unigenes were obtained, and 97,496 (~74.5%) unigenes were annotated in the public protein database. The similarity search indicated that 40,878 and 74,084 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Of these, 56,213 and 42,005 unigenes were assigned to the Gene Ontology (GO) database and Cluster of Orthologous Groups (COG), respectively, and 38,918 unigenes were mapped into five main categories, including 18 KEGG pathways. Metabolism was the largest category (23,128, 59.4%) among the main KEGG categories, suggesting active metabolic processes in C. rhombifolium. About 2,459 unigenes were annotated to have a role in defense mechanism or stress tolerance. Transcriptome analysis of C. rhombifolium revealed the presence of 12,925 microsatellites in 10,524 unigenes and mono, trip, and dinucleotides having higher polymorphism rates. The phylogenetic analysis based on GME gene among related species confirmed the reliability of the transcriptomic data. This work is the first genetic study of C. rhombifolium as a new plant resource of stress-tolerant genes. This large number of transcriptome sequences enabled us to comprehensively understand the basic genetics of C. rhombifolium and discover novel genes that will be helpful in the molecular improvement of chrysanthemums.

A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.)

Studies of genetic variation underlying traits related to drought tolerance in forest trees are of great importance for understanding their adaptive potential under a climate change scenario. In this study, using a candidate gene approach, associations between SNPs and drought related traits were assessed in saplings of European beech (Fagus sylvatica L.) representing trees growing along steep precipitation gradients. The saplings were subjected to experimentally controlled drought treatments. Response of the saplings was assessed by the evaluation of stem diameter growth (SDG) and the chlorophyll fluorescence parameters FV/FM, PIabs, and PItot. The evaluation showed that saplings from xeric sites were less affected by the drought treatment. Five SNPs (7.14%) in three candidate genes were significantly associated with the evaluated traits; saplings with particular genotypes at these SNPs showed better performance under the drought treatment. The SNPs were located in the cytosolic class I small heat-shock protein, CTR/DRE binding transcription factor, and isocitrate dehydrogenase genes and explained 5.8-13.4% of the phenotypic variance. These findings provide insight into the genetic basis of traits related to drought tolerance in European beech and could support the development of forest conservation management strategies under future climatic conditions.

Fast sequence-based microsatellite genotyping development workflow

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana

Liquidambar formosana (Hamamelidaceae) is a relatively fast-growing deciduous tree of high ornamental value that is indigenous to China. However, few molecular markers are available for the species or its close relatives; this has hindered genomic and genetic studies. Here, we develop a series of transferable expressed sequence tag-simple sequence repeats (EST-SSRs) for genomic analysis of L. formosana. We downloaded the sequence of the L. formosana transcriptome from the National Center of Biotechnology Information Database and identified SSR loci in the Unigene library. We found 3284 EST-SSRs by mining 34,491 assembled unigenes. We synthesized 100 random primer pairs for validation of eight L. formosana individuals; of the 100 pairs, 32 were polymorphic. We successfully transferred 12 EST-SSR markers across three related Liquidambar species; the markers exhibited excellent cross-species transferability and will facilitate genetic studies and breeding of Liquidambar. A total of 72 clones of three Liquidambar species were uniquely divided into three main clusters; principal coordinate analysis (PCoA) supported this division. Additionally, a set of 20 SSR markers that did not exhibit nonspecific amplification were used to genotype more than 53 L. formosana trees. The mean number of alleles (Na) was 5.75 and the average polymorphism information content (PIC) was 0.578, which was higher than that of the natural L. formosana population (0.390). In other words, the genetic diversity of the plus L. formosana population increased, but excellent phenotypic features were maintained. The primers will be valuable for genomic mapping, germplasm characterization, gene tagging, and further genetic studies. Analyses of genetic diversity in L. formosana will provide a basis for efficient application of genetic materials and rational management of L. formosana breeding programs.

Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution

Contents Summary 669 I. Model clades for the study and integration of ecology and evolution 670 II. Oaks: an important model clade 671 III. Insights from the history of the American oaks for understanding community assembly and ecosystem dominance 673 IV. Bridging the gap between micro- and macroevolutionary processes relevant to ecology 679 V. How do we reconcile evidence for adaptive evolution with niche conservatism and long-term stasis? 682 VI. High plasticity and within-population genetic variation contribute to population persistence 683 VII. Emerging technologies for tracking functional change 685 VIII. Conclusions 685 Acknowledgements 686 References 686 SUMMARY: Ecologists and evolutionary biologists are concerned with explaining the diversity and composition of the natural world and are aware of the inextricable linkages between ecological and evolutionary processes that maintain the Earth's life support systems. Yet examination of these linkages remains challenging due to the contrasting nature of focal systems and research approaches. Model clades provide a critical means to integrate ecology and evolution, as illustrated by the oaks (genus Quercus), an important model clade, given their ecological dominance, remarkable diversity, and growing phylogenetic, genomic, and ecological data resources. Studies of the clade reveal that their history of sympatric parallel adaptive radiation continues to influence community assembly today, highlighting questions on the nature and extent of coexistence mechanisms. Flexible phenology and hydraulic traits, despite evolutionary stasis, may have enabled adaptation to a wide range of environments within and across species, contributing to their high abundance and diversity. The oaks offer fundamental insights at the intersection of ecology and evolution on the role of diversification in community assembly processes, on the importance of flexibility in key functional traits in adapting to new environments, on factors contributing to persistence of long-lived organisms, and on evolutionary legacies that influence ecosystem function.

Genetic Variation of European Beech Populations and Their Progeny from Northeast Germany to Southwest Switzerland

Climate change can adversely affect the growth of European beech (Fagus sylvatica L.) across its entire distribution range. Therefore, knowledge of the adaptive potential of this species to changing climatic conditions is of foremost importance. Genetic diversity is the basis for adaptation to environmental stress, and the regeneration phase of forests is a key stage affecting genetic diversity. Nevertheless, little is known about the effect of climate change on the genetic diversity of adult trees compared to their progeny. Here, we present genetic diversity data for 24 beech populations ranging from northeast Germany to southwest Switzerland. Potentially adaptive genetic variation was studied using single nucleotide polymorphism (SNP) markers in candidate genes that are possibly involved in adaptive trait variation. In addition, more than 2000 adult trees and 3000 of their seedlings were genotyped with simple sequence repeat (SSR) markers to determine selectively neutral genetic diversity and differentiation among populations. All populations showed high SSR and SNP variation, and no differences in genetic diversity were found between adult trees and their offspring. The genetic differentiation between adults and seedlings within the same stands was also insignificant or very low. Therefore, we can conclude tentatively that the transfer of genetic variation among tree generations, currently, is not much affected by climate change, at least in the studied beech populations.

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite-associated DNA sequencing (RAD-seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.

Species Boundaries Between Three Sympatric Oak Species: Quercus aliena, Q. dentata, and Q. variabilis at the Northern Edge of Their Distribution in China

Oaks are important timber trees with wide distributions in China, but few genetic studies have been conducted on a fine scale. In this study, we seek to investigate the genetic diversity and differentiation of three sympatric oak species (Quercus aliena Blume, Quercus dentata Thunb. ex Murray, and Quercus variabilis Blume) in their northern distribution in China using 17 bi-parentally inherited nSSRs markers and five maternally inherited chloroplast DNA (cpDNA) fragments. Both the cpDNA and the nSSRs show a high level of genetic differentiation between different oak sections. The chloroplast haplotypes are clustered into two lineages. Clear species boundaries are detected between Q. variabilis and either Q. aliena or Q. dentata. The sharing of chloroplast haplotype H1 between Q. aliena and Q. dentata suggests very recent speciation and incomplete lineage sorting or introgression of H1 from one species to another. The nSSRs data indicate a complete fixation of variation within sites for all three oak species, and that extensive gene flow occurs within species whereas only limited gene flow is detected between Q. aliena and Q. dentata and nearly no gene flow can be detected between Q. aliena and Q. variabilis and between Q. dentata and Q. variabilis. Prezygotic isolation may have contributed to the species boundaries of these three sympatric oak species.

First interspecific genetic linkage map for Castanea sativa x Castanea crenata revealed QTLs for resistance to Phytophthora cinnamomi

The Japanese chestnut (Castanea crenata) carries resistance to Phytophthora cinnamomi, the destructive and widespread oomycete causing ink disease. The European chestnut (Castanea sativa), carrying little to no disease resistance, is currently threatened by the presence of the oomycete pathogen in forests, orchards and nurseries. Determining the genetic basis of P. cinnamomi resistance, for further selection of molecular markers and candidate genes, is a prominent issue for implementation of marker assisted selection in the breeding programs for resistance. In this study, the first interspecific genetic linkage map of C. sativa x C. crenata allowed the detection of QTLs for P. cinnamomi resistance. The genetic map was constructed using two independent, control-cross mapping populations. Chestnut populations were genotyped using 452 microsatellite and single nucleotide polymorphism molecular markers derived from the available chestnut transcriptomes. The consensus genetic map spans 498,9 cM and contains 217 markers mapped with an average interval of 2.3 cM. For QTL analyses, the progression rate of P. cinnamomi lesions in excised shoots inoculated was used as the phenotypic metric. Using non-parametric and composite interval mapping approaches, two QTLs were identified for ink disease resistance, distributed in two linkage groups: E and K. The presence of QTLs located in linkage group E regarding P. cinnamomi resistance is consistent with a previous preliminary study developed in American x Chinese chestnut populations, suggesting the presence of common P. cinnamomi defense mechanisms across species. Results presented here extend the genomic resources of Castanea genus providing potential tools to assist the ongoing and future chestnut breeding programs.

De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech

Despite the ecological and economic importance of European beech (Fagus sylvatica L.) genomic resources of this species are still limited. This hampers an understanding of the molecular basis of adaptation to stress. Since beech will most likely be threatened by the consequences of climate change, an understanding of adaptive processes to climate change-related drought stress is of major importance. Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. In a drought stress trial with beech saplings, 50 samples were taken for RNA extraction at five points in time during a soil desiccation experiment. De novo transcriptome assembly and analysis of differential gene expression revealed 44,335 contigs, and 662 differentially expressed genes between the stress and normally watered control group. Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species.

Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

BACKGROUND

Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence repeats in expressed sequence tags) molecular primers can be designed, which will greatly facilitate further investigations of the population genetics and demographic histories of DT plants.

METHODS

In the present study, we used the platform Illumina HiSeq™2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information, the EST-SSR markers were developed, and the functional annotation of ESTs containing polymorphic SSRs were obtained through BLASTX.

RESULTS

A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to the known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to Gene Ontology (GO) classifications and Cluster of Orthologous Groups (COG), respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with stable, highly polymorphic loci were selected for polymorphism screening. There was a total of 65 alleles, with 2-6 alleles at each locus. Primarily due to the unique biological characteristics of plants, the HE (0-0.196), HO (0.082-0.14) and PIC (0-0.155) per locus were very low. The functional annotation distribution centered on ESTs containing di- and tri-nucleotide SSRs, and the ESTs containing primers BC2, BC4 and BC12 were annotated to vegetative dehydration/desiccation pathways.

DISCUSSION

This work is the first genetic study of B. clarkeana as a new plant resource of DT genes. A substantial number of transcriptome sequences were generated in this study. These sequences are valuable resources for gene annotation and discovery as well as molecular marker development. These sequences could also provide a valuable basis for future molecular studies of B. clarkeana.

High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra

Background

Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The statistical inference of linear order must be as accurate as possible for the correct ordering of sequence scaffolds and contigs to chromosomal locations. Accurate maps also facilitate the discovery of chromosome segments containing allelic variants conferring resistance to the biotic and abiotic stresses that threaten forest trees worldwide. We used ddRADseq for genetic mapping in the tree Quercus rubra, with an approach optimized to produce a high-quality map. Our study design also enabled us to model the results we would have obtained with less depth of coverage.

Results

Our sequencing design produced a high sequencing depth in the parents (248×) and a moderate sequencing depth (15×) in the progeny. The digital normalization method of generating a de novo reference and the SAMtools SNP variant caller yielded the most SNP calls (78,725). The major drivers of map inflation were multiple SNPs located within the same sequence (77% of SNPs called). The highest quality map was generated with a low level of missing data (5%) and a genome-wide threshold of 0.025 for deviation from Mendelian expectation. The final map included 849 SNP markers (1.8% of the 78,725 SNPs called). Downsampling the individual FASTQ files to model lower depth of coverage revealed that sequencing the progeny using 96 samples per lane would have yielded too few SNP markers to generate a map, even if we had sequenced the parents at depth 248×.

Conclusions

The ddRADseq technology produced enough high-quality SNP markers to make a moderately dense, high-quality map. The success of this project was due to high depth of coverage of the parents, moderate depth of coverage of the progeny, a good framework map, an optimized bioinformatics pipeline, and rigorous premapping filters. The ddRADseq approach is useful for the construction of high-quality genetic maps in organisms lacking a reference genome if the parents and progeny are sequenced at sufficient depth. Technical improvements in reduced representation sequencing (RRS) approaches are needed to reduce the amount of missing data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3765-8) contains supplementary material, which is available to authorized users.

De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.

Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding

Red clover (Trifolium pratense) is an important forage plant worldwide. This study was directed to broadening current knowledge of red clover's coding regions and enhancing its utilization in practice by specific reanalysis of previously published assembly. A total of 42,996 genes were characterized using Illumina paired-end sequencing after manual revision of Blast2GO annotation. Genes were classified into metabolic and biosynthetic pathways in response to biological processes, with 7,517 genes being assigned to specific pathways. Moreover, 17,727 enzymatic nodes in all pathways were described. We identified 6,749 potential microsatellite loci in red clover coding sequences, and we characterized 4,005 potential simple sequence repeat (SSR) markers as generating polymerase chain reaction products preferentially within 100-350 bp. Marker density of 1 SSR marker per 12.39 kbp was achieved. Aligning reads against predicted coding sequences resulted in the identification of 343,027 single nucleotide polymorphism (SNP) markers, providing marker density of one SNP marker per 144.6 bp. Altogether, 95 SSRs in coding sequences were analyzed for 50 red clover varieties and a collection of 22 highly polymorphic SSRs with pooled polymorphism information content >0.9 was generated, thus obtaining primer pairs for application to diversity studies in T. pratense. A set of 8,623 genome-wide distributed SNPs was developed and used for polymorphism evaluation in individual plants. The polymorphic information content ranged from 0 to 0.375. Temperature switch PCR was successfully used in single-marker SNP genotyping for targeted coding sequences and for heterozygosity or homozygosity confirmation in validated five loci. Predicted large sets of SSRs and SNPs throughout the genome are key to rapidly implementing genome-based breeding approaches, for identifying genes underlying key traits, and for genome-wide association studies. Detailed knowledge of genetic relationships among breeding material can also be useful for breeders in planning crosses or for plant variety protection. Single-marker assays are useful for diagnostic applications.

Moderate Genetic Diversity and Genetic Differentiation in the Relict Tree Liquidambar formosana Hance Revealed by Genic Simple Sequence Repeat Markers

Chinese sweetgum (Liquidambar formosana) is a relatively fast-growing ecological pioneer species. It is widely used for multiple purposes. To assess the genetic diversity and genetic differentiation of the species, genic SSR markers were mined from transcriptome data for subsequent analysis of the genetic diversity and population structure of natural populations. A total of 10645 potential genic SSR loci were identified in 80482 unigenes. The average frequency was one SSR per 5.12 kb, and the dinucleotide unit was the most abundant motif. A total of 67 alleles were found, with a mean of 6.091 alleles per locus and a mean polymorphism information content of 0.390. Moreover, the species exhibited a relatively moderate level of genetic diversity (He = 0.399), with the highest was found in population XY (He = 0.469). At the regional level, the southwestern region displayed the highest genetic diversity (He = 0.435) and the largest number of private alleles (n = 5), which indicated that the Southwestern region may be the diversity hot spot of L. formosana. The AMOVA results showed that variation within populations (94.02%) was significantly higher than among populations (5.98%), which was in agreement with the coefficient of genetic differentiation (Fst = 0.076). According to the UPGMA analysis and principal coordinate analysis and confirmed by the assignment test, 25 populations could be divided into three groups, and there were different degrees of introgression among populations. No correlation was found between genetic distance and geographic distance (P > 0.05). These results provided further evidence that geographic isolation was not the primary factor leading to the moderate genetic differentiation of L. formosana. As most of the genetic diversity of L. formosana exists among individuals within a population, individual plant selection would be an effective way to use natural variation in genetic improvement programs. This would be helpful to not only protect the genetic resources but also attain effective management and exploit genetic resources.

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

Background

Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce.

Results

RNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis (SNPs and INDELs) was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database (National Center for Biotechnology Information), against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated.

Conclusions

This work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2631-4) contains supplementary material, which is available to authorized users.

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks

Background

Reference transcriptomes provide valuable resources for understanding evolution within and among species. We de novo assembled and annotated a reference transcriptome for Quercus lobata and Q. garryana and identified single-nucleotide polymorphisms (SNPs) to provide resources for forest genomicists studying this ecologically and economically important genus. We further performed preliminary analyses of genes important in interspecific divergent (positive) selection that might explain ecological differences among species, estimating rates of nonsynonymous to synonymous substitutions (d_N/d_S) and Fay and Wu’s H. Functional classes of genes were tested for unusually high d_N/d_S or low H consistent with divergent positive selection.

Results

Our draft transcriptome is among the most complete for oaks, including 83,644 contigs (23,329 ≥ 1 kbp), 14,898 complete and 13,778 partial gene models, and functional annotations for 9,431 Arabidopsis orthologs and 19,365 contigs with Pfam hits. We identified 1.7 million possible sequence variants including 1.1 million high-quality diallelic SNPs — among the largest sets identified in any tree. 11 of 18 functional categories with significantly elevated d_N/d_S are involved in disease response, including 50+ genes with d_N/d_S > 1. Other high-d_N/d_S genes are involved in biotic response, flowering and growth, or regulatory processes. In contrast, median d_N/d_S was low (0.22), suggesting that purifying selection influences most genes. No functional categories have unusually low H.

Conclusions

These results offer preliminary support for the hypothesis that divergent selection at pathogen resistance are important factors in species divergence in these hybridizing California oaks. Our transcriptome provides a solid foundation for future studies of gene expression, natural selection, and speciation in Quercus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1761-4) contains supplementary material, which is available to authorized users.

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

BACKGROUND

Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection.

RESULTS

The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment.

CONCLUSION

In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.

De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers

Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp). The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO) database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%), suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.

A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the 'species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory.

De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

Background

Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants.

Results

Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10^-5. In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members.

Conclusions

Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

Electronic supplementary material

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Intra-specific variations in expression of stress-related genes in beech progenies are stronger than drought-induced responses

Rapidly decreasing water availability as a consequence of climate change is likely to endanger the range of long-lived tree species. A pressing question is, therefore, whether adaptation to drought exists in important temperate tree species like European beech (Fagus sylvatica L.), a wide-spread, dominant forest tree in Central Europe. Here, five beech stands were selected along a precipitation gradient from moist to dry conditions. Neutral genetic markers revealed strong variation within and little differentiation between the populations. Natural regeneration from these stands was transferred to a common garden and used to investigate the expression of genes for abscisic acid (ABA)-related drought signaling [9-cis-epoxy-dioxygenase (NCED), protein phosphatase 2C (PP2C), early responsive to dehydration (ERD)] and stress protection [ascorbate peroxidase (APX), superoxide dismutase (SOD), aldehyde dehydrogenase (ALDH), glutamine amidotransferase (GAT)] that are involved in drought acclimation. We hypothesized that progenies from dry sites exhibit constitutively higher expression levels of ABA- and stress-related genes and are less drought responsive than progenies from moist sites. Transcript levels and stress responses (leaf area loss, membrane integrity) of well-irrigated and drought-stressed plants were measured during the early, mid- and late growing season. Principal component (PC) analysis ordered the beech progenies according to the mean annual precipitation at tree origin by the transcript levels of SOD, ALDH, GAT and ERD as major loadings along PC1. PC2 separated moist and drought treatments with PP2C levels as important loading. These results suggest that phosphatase-mediated signaling is flexibly acclimated to the current requirements, whereas stress compensatory measures exhibited genotypic variation, apparently underlying climate selection. In contrast to expectation, the drought responses were less pronounced than the progeny-related differences and the transcript levels were constitutively lower in beeches from dry than from moist sites. These results imply that beeches from dry origins may have evolved mechanisms to avoid oxidative stress.

RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development

Quercus pubescens Willd., a species distributed from Spain to southwest Asia, ranks high for drought tolerance among European oaks. Q. pubescens performs a role of outstanding significance in most Mediterranean forest ecosystems, but few mechanistic studies have been conducted to explore its response to environmental constrains, due to the lack of genomic resources. In our study, we performed a deep transcriptomic sequencing in Q. pubescens leaves, including de novo assembly, functional annotation and the identification of new molecular markers. Our results are a pre-requisite for undertaking molecular functional studies, and may give support in population and association genetic studies.

254,265,700 clean reads were generated by the Illumina HiSeq 2000 platform, with an average length of 98 bp. De novo assembly, using CLC Genomics, produced 96,006 contigs, having a mean length of 618 bp. Sequence similarity analyses against seven public databases (Uniprot, NR, RefSeq and KOGs at NCBI, Pfam, InterPro and KEGG) resulted in 83,065 transcripts annotated with gene descriptions, conserved protein domains, or gene ontology terms. These annotations and local BLAST allowed identify genes specifically associated with mechanisms of drought avoidance. Finally, 14,202 microsatellite markers and 18,425 single nucleotide polymorphisms (SNPs) were, in silico, discovered in assembled and annotated sequences. We completed a successful global analysis of the Q. pubescens leaf transcriptome using RNA-seq. The assembled and annotated sequences together with newly discovered molecular markers provide genomic information for functional genomic studies in Q. pubescens, with special emphasis to response mechanisms to severe constrain of the Mediterranean climate. Our tools enable comparative genomics studies on other Quercus species taking advantage of large intra-specific ecophysiological differences.

Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera

BACKGROUND

Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).

RESULTS

Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.

CONCLUSIONS

Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background

Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management.

Results

We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org.

Conclusions

This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

Evidence for selection on a CONSTANS-like gene between two red oak species

BACKGROUND AND AIMS

Hybridizing species such as oaks may provide a model to study the role of selection in speciation with gene flow. Discrete species' identities and different adaptations are maintained among closely related oak species despite recurrent gene flow. This is probably due to ecologically mediated selection at a few key genes or genomic regions. Neutrality tests can be applied to identify so-called outlier loci, which demonstrate locus-specific signatures of divergent selection and are candidate genes for further study.

METHODS

Thirty-six genic microsatellite markers, some with putative functions in flowering time and drought tolerance, and eight non-genic microsatellite markers were screened in two population pairs (n = 160) of the interfertile species Quercus rubra and Q. ellipsoidalis, which are characterized by contrasting adaptations to drought. Putative outliers were then tested in additional population pairs from two different geographic regions (n = 159) to support further their potential role in adaptive divergence.

KEY RESULTS

A marker located in the coding sequence of a putative CONSTANS-like (COL) gene was repeatedly identified as under strong divergent selection across all three geographically disjunct population pairs. COL genes are involved in the photoperiodic control of growth and development and are implicated in the regulation of flowering time.

CONCLUSIONS

The location of the polymorphism in the Quercus COL gene and given the potential role of COL genes in adaptive divergence and reproductive isolation makes this a promising candidate speciation gene. Further investigation of the phenological characteristics of both species and flowering time pathway genes is suggested in order to elucidate the importance of phenology genes for the maintenance of species integrity. Next-generation sequencing in multiple population pairs in combination with high-density genetic linkage maps could reveal the genome-wide distribution of outlier genes and their potential role in reproductive isolation between these species.

In-silico mining, type and frequency analysis of genic microsatellites of finger millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS-LRR regions of finger millet with rice

In recent years, the increased availability of the DNA sequences has given the possibility to develop and explore the expressed sequence tags (ESTs) derived SSR markers. In the present study, a total of 1956 ESTs of finger millet were used to find the microsatellite type, distribution, frequency and developed a total of 545 primer pairs from the ESTs of finger millet. Thirty-two EST sequences had more than two microsatellites and 1357 sequences did not have any SSR repeats. The most frequent type of repeats was trimeric motif, however the second place was occupied by dimeric motif followed by tetra-, hexa- and penta repeat motifs. The most common dimer repeat motif was GA and in case of trimeric SSRs, it was CGG. The EST sequences of NBS-LRR region of finger millet and rice showed higher synteny and were found on nearly same positions on the rice chromosome map. A total of eight, out of 15 EST based SSR primers were polymorphic among the selected resistant and susceptible finger millet genotypes. The primer FMBLEST5 could able to differentiate them into resistant and susceptible genotypes. The alleles specific to the resistant and susceptible genotypes were sequenced using the ABI 3130XL genetic analyzer and found similarity to NBS-LRR regions of rice and finger millet and contained the characteristic kinase-2 and kinase 3a motifs of plant R-genes belonged to NBS-LRR region. The In-silico and comparative analysis showed that the genes responsible for blast resistance can be identified, mapped and further introgressed through molecular breeding approaches for enhancing the blast resistance in finger millet.

Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers

Oil-rich seeds of Jatropha curcas are being focussed as a source of bio-diesel. However, prior to its industrial use, a lot of crop improvement efforts are required in Jatropha. Availability of a large number of EST sequences of Jatropha in public domain allow identification of candidate genes for several agronomic characters including oil content in seeds. Here, we have analysed 42,477 ESTs of Jatropha spanning 22.9 Mbp for microsatellites and fatty acid metabolism related sequences. Unigene sequences were built using CAP 3 programme resulted in 12,358 contigs and 5,730 singlets. Nearly, 8 % unigenes showed presence of microsatellites, slightly over-represented compared to their occurrence in ESTs. Most of the microsatellites were either di- or tri-nucleotide repeats, while other categories of tetra-, penta- and hexa-nucleotide repeats together constituted ~4 % of total microsatellites. Assessment of functional relevance of unigenes was carried out using Blast2GO using its default settings. The overall sequence similarity level against sequences in 'nr' database was >80 %. A total of 931 sequences that participated in any of the pathways related to fatty acid or lipid metabolism were found at GO level 6. Among these, GO terms "Fatty acid metabolic process" and "Fatty acid biosynthetic process" were most over-represented. Overall, our work has due relevance in identifying molecular markers for the candidate genes for oil content in Jatropha seeds, and will prove to be an important reference for further studies for identification of trait specific markers in Jatropha.

De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba

Background

Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus.

Results

Next generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads.

Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic.

Conclusions

This study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data.

The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will strongly contribute to genomics resources for P. alba functional analysis and genetics. Finally, it will also potentially contribute to the development of population-based genome studies in the genera.

Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database

BACKGROUND

Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html).

CONCLUSIONS

The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.

Molecular characterization and genetic structure of Quercus acutissima germplasm in China using microsatellites

Quercus acutissima is native to eastern Asia. It has a wide distribution in China and China is an important component in understanding the ecology and genetic structure of this species. Q. acutissima attained high economic value for hardwood product and can be managed as an energy tree species. To investigate the genetic variation of Q. acutissima provenances, 12 microsatellite primer pairs were used to analyze 672 trees sampled from 28 provenances of Q. acutissima in China. All of the tested microsatellite loci proved to be effective for the studied Q. acutissima provenances. The results revealed that allele numbers varied from 5 to 13 per locus, with an average of 8 alleles per locus. The mean observed heterozygosity and expected heterozygosity were 0.4927 and 0.7023, respectively. The relatedness of the provenances was studied using the arithmetic mean algorithm based on Nei's genetic distance and principal coordinates analysis. Interestingly, both approaches revealed two main groups: one consisted of the eastern Chinese provenances, and the other comprised of the western Chinese provenances. An analysis of molecular variance indicated that most genetic variation was contained within populations (84 %). The two microsatellite markers developed in this study may be employed for genetic characterization of other oak species. Considering the management or breeding programs of Q. acutissima provenances in China, we should treat each main group as a single gene resource.