A dense linkage map of hybrid cottonwood (Populus fremontii × P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree

Heterozygous Trees Rebound the Fastest after Felling by Beavers to Positively Affect Arthropod Community Diversity

Although genetic diversity within stands of trees is known to have community-level consequences, whether such effects are present at an even finer genetic scale is unknown. We examined the hypothesis that genetic variability (heterozygosity) within an individual plant would affect its dependent community, which adds a new dimension to the importance of genetic diversity. Our study contrasted foliar arthropod community diversity and microsatellite marker-derived measures of genetic diversity of cottonwood (Populus fremontii) trees that had been felled by beavers (Castor canadensis) and were resprouting, relative to adjacent standing, unfelled trees. Three patterns emerged: 1. Productivity (specific leaf area), phytochemical defenses (salicortin), and arthropod community richness, abundance, and diversity were positively correlated with the heterozygosity of individual felled trees, but not with that of unfelled trees; 2. These relationships were not explained by population substructure, genetic relatedness of the trees, or hybridization; 3. The underlying mechanism appears to be that beaver herbivory stimulates increased productivity (i.e., 2× increase from the most homozygous to the most heterozygous tree) that is the greatest in more heterozygous trees. Salicortin defenses in twigs were also expressed at higher concentrations in more heterozygous trees (i.e., 3× increase from the most homozygous to the most heterozygous tree), which suggests that this compound may dissuade further herbivory by beavers, as has been found for other mammalian herbivores. We suggest that high stress to trees as a consequence of felling reveals a heterozygosity–productivity linkage, which in turn is attractive to arthropods. Although experiments are required to demonstrate causality, these results link the genetic diversity of individual trees to community diversity, supporting the hypothesis that interactions among foundation species (beavers and trees) have community-level effects, and underscores the importance of genetic diversity for biodiversity, conservation, and restoration.

High-Quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus

With the advances in high-throughput sequencing technologies and the development of new software for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F₁ hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female P. deltoides map contained 4018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male P. simonii map showed similar characteristics, consisting of 2097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of P. simonii to chromosomes. The 2 parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.

Identification of recombination events in outbred species with next-generation sequencing data

BACKGROUND

Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps.

RESULTS

We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F₁ hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO .

CONCLUSIONS

The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.

Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH‐salicortin (R² = .52) that colocated with a QTL for salicortin on chr12. Using the V3.0 Populus genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD‐type acyltransferase that has been potentially linked to PopulusSPGs. Our results complement other recent studies in Populus with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full‐sib mapping population to identify QTL intervals and gene lists associated with SPGs.

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population

The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid) and Populus nigra (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.

Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.

Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies

Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker-assisted breeding. Recent advances in high-throughput sequencing have enabled strategies that integrate linkage-linkage disequilibrium (LD) mapping in Populus. We used an integrated method of quantitative trait locus (QTL) dissection with a high-resolution linkage map and multi-gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals). Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) ≥ 2.5), and explained 2.7-18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi-gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P ≤ 0.0001; FDR ≤ 0.10) that exhibited reproducible associations with additive/dominant effects, and further determined 11 top-ranked genes tightly linked to the QTLs. Epistasis analysis uncovered a uniquely interconnected gene-gene network for each trait. This study opens up opportunities to uncover the causal networks of interacting genes in plants using an integrated linkage-LD mapping approach.

High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.

Genetic Map Construction and Detection of Genetic Loci Underlying Segregation Distortion in an Intraspecific Cross of Populus deltoides

Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies.

Climate relicts and their associated communities as natural ecology and evolution laboratories

Climate relicts, marginal populations that have become isolated via climate-driven range shifts, preserve ecological and evolutionary histories that can span millennia. Studies point to climate relicts as 'natural laboratories' for investigating how long-term environmental change impacts species and populations. However, we propose that such research should be expanded to reveal how climate change affects 'interacting' species in ways that reshape community composition and evolution. Biotic interactions and their community and ecosystem effects are often genetically based and driven by associations with foundation species. We discuss evolution in climate relicts within the context of the emerging fields of community and ecosystem genetics, exploring the idea that foundation relicts are also natural community and ecosystem laboratories and windows to future landscapes.

The sex-linked region in Populus tremuloides Turesson 141 corresponds to a pericentromeric region of about two million base pairs on P. trichocarpa chromosome 19

In the dioecious genus Populus, sex determination has been located to chromosome 19. However, despite a high degree of genome collinearity, various Populus species seem to differ with regard to the location of the sex-determining region on the respective chromosome and the apparent heterogametic sex. In this study, the boundaries of the recombination-suppressed, sex-linked region of the male P. tremuloides clone Turesson 141 were localised by genetic mapping using new SNP and InDel markers. The respective region seems to be located in a pericentromeric position. The corresponding P. trichocarpa genome region spans about two million bp and comprises 65 gene loci, which were bioinformatically evaluated for their potential as candidate genes for sex determination. Three putative transcription factor genes and four genes that are potentially involved in flower development processes, e.g. meristem transition from the vegetative to the reproductive phase, were identified. Populus tremuloides sequence data of the sex-linked region is required for a final search for candidate genes.

Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis)

Despite the worldwide consumption and high economic importance of tea, the plant (Camellia sinensis) is not well studied in molecular biology. Under the few circumstances in which the plant is studied, C. sinensis flowers, which are important for reproduction and cross-breeding, receive less emphasis than investigation of its leaves or roots. Using high-throughput Illumina RNA sequencing, we analyzed a C. sinensis floral transcriptome, and 26.9 million clean reads were assembled into 75,531 unigenes averaging 402 bp. Among them, 50,792 (67.2%) unigenes were annotated with a BLAST search against the NCBI Non-Redundant (NR) database and 10,290 (16.67%) were detected that contained one or more simple sequence repeats (SSRs). From these SSR-containing sequences, 2,439 candidate SSR markers were developed and 720 were experimentally tested, validating 431 (59.9%) novel polymorphic SSR markers for C. sinensis. Then, a consensus SSR-based linkage map was constructed that covered 1,156.9 cM with 237 SSR markers distributed in 15 linkage groups. Both transcriptome information and the genetic map of C. sinensis presented here offer a valuable foundation for molecular biology investigations such as functional gene isolation, quantitative trait loci mapping, and marker-assisted selection breeding in this important species.

[Progress on whole genome sequencing in woody plants]

In recent years, the number of sequencing data of plant whole genome have been increasing rapidly and the whole genome sequencing has been also performed widely in woody plants. However, there are a set of obstacles in investigating the whole genome sequencing in woody plants, which include larger genome, complex genome structure, limitations of assembly, annotation, functional analysis, and restriction of the funds for scientific research. Therefore, to promote the efficiency of the whole genome sequencing in woody plants, the development and defect of this field should be analyzed. The three-generation sequencing technologies (i.e., Sanger sequencing, synthesis sequencing, and single molecule sequencing) were compared in our studies. The progress mainly focused on the whole genome sequencing in four woody plants (Populus, Grapevine, Papaya, and Apple), and the application of sequencing results also was analyzed. The future of whole genome sequencing research in woody plants, consisting of material selection, establishment of genetic map and physical map, selection of sequencing technology, bioinformatic analysis, and application of sequencing results, was discussed.

Disrupting mycorrhizal mutualisms: a potential mechanism by which exotic tamarisk outcompetes native cottonwoods

The disruption of mutualisms between plants and mycorrhizal fungi is a potentially powerful mechanism by which invasives can negatively impact native species, yet our understanding of this mechanism's role in exotic species invasion is still in its infancy. Here, we provide several lines of evidence indicating that invasive tamarisk (Tamarix sp.) negatively affects native cottonwoods (Populus fremontii) by disrupting their associations with arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. At a field site in the early stages of tamarisk invasion, cottonwoods with tamarisk neighbors had reduced EM colonization and altered EM fungal community composition relative to cottonwoods with native neighbors, leading to reductions in EM propagule abundance in the soil beneath tamarisk. Similarly, AM colonization of cottonwoods was reduced with a tamarisk neighbor, but there were no significant changes in AM fungal spore communities or propagule abundance. Root colonization by nonmycorrhizal fungi, including potential pathogens, was higher in cottonwoods with tamarisk neighbors. A greenhouse experiment in which AM and EM inoculation and plant neighbor were manipulated in a fully factorial design showed that cottonwoods benefited from mycorrhizas, especially EM, in terms of shoot biomass when grown with a conspecific, but shoot biomass was similar to that of nonmycorrhizal controls when cottonwoods were grown with a tamarisk neighbor. These results are partially explained by a reduction in EM but not AM colonization of cottonwoods by a tamarisk neighbor. Tamarisk neighbors negatively affected cottonwood specific leaf area, but not chlorophyll content, in the field. To pinpoint a mechanism for these changes, we measured soil chemistry in the field and the growth response of an EM fungus (Hebeloma crustuliniforme) to salt-amended media in the laboratory. Tamarisk increased both NO3- concentrations and electrical conductivity 2.5-fold beneath neighboring cottonwoods in the field. Salt-amended media did not affect the growth of H. crustuliniforme. Our findings demonstrate that a nonnative species, even in the early stages of invasion, can negatively affect a native species by disrupting its mycorrhizal symbioses. Some of these changes in mycorrhizal fungal communities may remain as legacy effects of invasives, even after their removal, and should be considered in management and restoration efforts.

Community genetics: what have we accomplished and where should we be going?

Research in community genetics seeks to understand how the dynamic interplay between ecology and evolution shapes simple and complex communities and ecosystems. A community genetics perspective, however, may not be necessary or informative for all studies and systems. To better understand when and how intraspecific genetic variation and microevolution are important in community and ecosystem ecology, we suggest future research should focus on three areas: (i) determining the relative importance of intraspecific genetic variation compared with other ecological factors in mediating community and ecosystem properties; (ii) understanding the importance of microevolution in shaping ecological dynamics in multi-trophic communities; and (iii) deciphering the phenotypic and associated genetic mechanisms that drive community and ecosystem processes. Here, we identify key areas of research that will increase our understanding of the ecology and evolution of complex communities but that are currently missing in community genetics. We then suggest experiments designed to meet these current gaps.

A genetic basis for the manipulation of sink-source relationships by the galling aphid Pemphigus batae

We examined how the galling aphid Pemphigus batae manipulates resource translocation patterns of resistant and susceptible narrowleaf cottonwood Populus angustifolia. Using carbon-14 ((14)C)-labeling experiments in common garden trials, five patterns emerged. First, although aphid galls on resistant and susceptible genotypes did not differ in their capacity to intercept assimilates exported from the leaf they occupied, aphids sequestered 5.8-fold more assimilates from surrounding leaves on susceptible tree genotypes compared to resistant genotypes. Second, gall sinks on the same side of a shoot as a labeled leaf were 3.4-fold stronger than gall sinks on the opposite side of a shoot, which agrees with patterns of vascular connections among leaves of the same shoot (orthostichy). Third, plant genetic-based traits accounted for 26% of the variation in sink strength of gall sinks and 41% of the variation in sink strength of a plant's own bud sinks. Fourth, tree susceptibility to aphid gall formation accounted for 63% of the variation in (14)C import, suggesting strong genetic control of sink-source relationships. Fifth, competition between two galls was observed on a susceptible but not a resistant tree. On the susceptible tree distal aphids intercepted 1.5-fold more (14)C from the occupied leaf than did basal aphids, but basal aphids compensated for the presence of a distal competitor by almost doubling import to the gall from surrounding leaves. These findings and others, aimed at identifying candidate genes for resistance, argue the importance of including plant genetics in future studies of the manipulation of translocation patterns by phytophageous insects.

Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species

Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F(1)'s. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC(1)) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC(1) revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across 'porous' species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones.

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus

BACKGROUND

Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya.

RESULTS

We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41).

CONCLUSIONS

The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 x 10-9 and 1.68 x 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.

A comparative analysis of phenylpropanoid metabolism, N utilization, and carbon partitioning in fast- and slow-growing Populus hybrid clones

The biosynthetic costs of phenylpropanoid-derived condensed tannins (CTs) and phenolic glycosides (PGs) are substantial. However, despite reports of negative correlations between leaf phenolic content and growth of Populus, it remains unclear whether or how foliar biosynthesis of CT/PG interferes with tree growth. A comparison was made of carbon partitioning and N content in developmentally staged leaves, stems, and roots of two closely related Populus hybrid genotypes. The genotypes were selected as two of the most phytochemically divergent from a series of seven previously analysed clones that exhibit a range of height growth rates and foliar amino acid, CT, and PG concentrations. The objective was to analyse the relationship between leaf phenolic content and plant growth, using whole-plant carbon partitioning and N distribution data from the two divergent clones. Total N as a percentage of tissue dry mass was comparatively low, and CT and PG accrual comparatively high in leaves of the slow-growing clone. Phenylpropanoid accrual and N content were comparatively high in stems of the slow-growing clone. Carbon partitioning within phenylpropanoid and carbohydrate networks in developing stems differed sharply between clones. The results did not support the idea that foliar production of phenylpropanoid defence chemicals was the primary cause of reduced plant growth in the slow-growing clone. The findings are discussed in the context of metabolic mechanism(s) which may contribute to reduced N delivery from roots to leaves, thereby compromising tree growth and promoting leaf phenolic accrual in the slow-growing clone.

The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome

Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info.

Extending genomics to natural communities and ecosystems

An important step in the integration of ecology and genomics is the progression from molecular studies of relatively simple model systems to complex field systems. The recent availability of sequenced genomes from key plants is leading to a new understanding of the molecular drivers of community composition and ecosystem processes. As genome sequences accumulate for species that form intimate associations in nature, a detailed view may emerge as to how these associations cause changes among species at the nucleotide level. This advance could dramatically alter views about the structure and evolution of communities and ecosystems.

Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding

Background

The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions.

Results

As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa × P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in poplar leaves attacked by forest tent caterpillars.

Conclusion

This study has generated a high-quality FLcDNA resource for poplar and the third largest FLcDNA collection published to date for any plant species. We successfully used the FLcDNA sequences to reassess gene prediction in the poplar genome sequence, perform comparative sequence annotation, and identify differentially expressed transcripts associated with defense against insects. The FLcDNA sequences will be essential to the ongoing curation and annotation of the poplar genome, in particular for targeting gaps in the current genome assembly and further improvement of gene predictions. The physical FLcDNA clones will serve as useful reagents for functional genomics research in areas such as analysis of gene functions in defense against insects and perennial growth. Sequences from this study have been deposited in NCBI GenBank under the accession numbers EF144175 to EF148838.