Molecular genetics of growth and development in Populus. I. Triploidy in hybrid poplars

Polyploidy in Fruit Tree Crops of the Genus Annona (Annonaceae)

Genome duplication or polyploidy is one of the main factors of speciation in plants. It is especially frequent in hybrids and very valuable in many crops. The genus Annona belongs to the Annonaceae, a family that includes several fruit tree crops, such as cherimoya (Annona cherimola), sugar apple (Annona squamosa), their hybrid atemoya (A. cherimola × A. squamosa) or pawpaw (Asimina triloba). In this work, genome content was evaluated in several Annona species, A. triloba and atemoya. Surprisingly, while the hybrid atemoya has been reported as diploid, flow cytometry analysis of a progeny obtained from an interspecific cross between A. cherimola and A. squamosa showed an unusual ploidy variability that was also confirmed karyotype analysis. While the progeny from intraspecific crosses of A. cherimola showed polyploid genotypes that ranged from 2.5 to 33%, the hybrid atemoyas from the interspecific cross showed 35% of triploids from a total of 186 genotypes analyzed. With the aim of understanding the possible implications of the production of non-reduced gametes, pollen performance, pollen size and frequency distribution of pollen grains was quantified in the progeny of this cross and the parents. A large polymorphism in pollen grain size was found within the interspecific progeny with higher production of unreduced pollen in triploids (38%) than in diploids (29%). Moreover, using PCR amplification of selected microsatellite loci, while 13.7% of the pollen grains from the diploids showed two alleles, 41.28% of the grains from the triploids amplified two alleles and 5.63% showed up to three alleles. This suggests that the larger pollen grains could correspond to diploid and, in a lower frequency, to triploid pollen. Pollen performance was also affected with lower pollen germination in the hybrid triploids than in both diploid parents. The results confirm a higher percentage of polyploids in the interspecific cross, affecting pollen grain size and pollen performance. The occurrence of unreduced gametes in A. cherimola, A. squamosa and their interspecific progeny that may result in abnormalities of ploidy such as the triploids and tetraploids observed in this study, opens an interesting opportunity to study polyploidy in Annonaceae.

Uneven selection pressure accelerating divergence of Populus and Salix

Populus (poplars) and Salix (willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages are distinguished by two major interchromosomal and some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare the selection pressure acting on the paralogous genes resulting from salicoid duplication (PGRS) within and between the genomes of the two lineages. Purifying selection was determined to act more strongly on the PGRS in willow than on those in poplar, which would cause a faster loss of paralogous duplicates in willow. Therefore, Salix species are supposed to evolve faster than Populus species, which is consistent with the observation that the former are taxonomically and morphologically more diverse than the latter. In these two lineages, different autosomes were found to have been evolving into sex chromosomes. Examining the ω ratio and the PGRS in the sex determination regions in willow and poplar revealed higher convergent selection pressure and a faster loss of PGRS in the sex determination regions of both lineages. At the chromosome level, the sex chromosome in poplar is characterized by the lowest gene density among all chromosome members, while this feature is not observed on the sex chromosome in willow, suggesting that Populus species may inherit the more incipient sex chromosome from their progenitor. Taken together, Salix is supposed to be the nascent lineage arising from the additional round of genome reorganization that distinguishes the karyotypes of the two sister genera. In this study, assessment of ω ratios also detected a list of paralogous genes under unusual selection pressure, which could have special consequences for the adaptive evolution of Salicaceae species. In conclusion, the results of this study provide unique information for better understanding the genetic mechanism accelerating the divergence of these two closely related lineages.

Inducing triploids and tetraploids with high temperatures in Populus sect. Tacamahaca

This study is the first to report that triploids and tetraploids have been successfully produced through embryo sac and zygotic embryo chromosome doubling with high temperatures in P. simonii Carr. and its hybrid. A new synthetic polyploid induced by hybridization with unreduced gametes and heterozygotic embryo chromosome doubling can effectively combine polyploidy and heterosis, which can provide two major breeding advantages. In Populus, successfully creating and cultivating new polyploid varieties have economic and ecological production value. This was the first successful study in which embryo sac and zygotic embryo chromosome doubling was induced using high temperatures to produce triploids and tetraploids in Populus simonii Carr. and its hybrid, P. simonii × P. nigra var. Italica, of Populus sect. Tacamahaca. The relationship between flower bud morphological characteristics (time after pollination) and female meiotic stage (embryo sac and zygotic embryo development) was established to guide the induction treatment period. In the resulting progeny, 37 triploids and 12 tetraploids were obtained and identified using flow cytometry. The optimal temperatures for embryo sac and zygotic embryo chromosome doubling were 38 and 41 °C, respectively. Cytogenetic analysis revealed that 66-72 h after pollination (HAP), a period characterized by a high proportion of one-nucleate and two-nucleate embryo sacs, was the optimal period for embryo sac chromosome doubling. For zygotic embryo chromosome doubling, 168 HAP was the optimal induction period, as there was a high proportion of two-cell and four-cell proembryos. The results indicate that inducing embryo sac and zygotic embryo chromosome doubling is an ideal method for producing polyploids. The methods for inducing polyploids and for evaluating ploidy and offspring with different ploidies and heterozygosity in this study will be useful for genetic research and Populus breeding programmes.

Confirmation of Single-Locus Sex Determination and Female Heterogamety in Willow Based on Linkage Analysis

In this study, we constructed high-density genetic maps of Salix suchowensis and mapped the gender locus with an F₁ pedigree. Genetic maps were separately constructed for the maternal and paternal parents by using amplified fragment length polymorphism (AFLP) markers and the pseudo-testcross strategy. The maternal map consisted of 20 linkage groups that spanned a genetic distance of 2333.3 cM; whereas the paternal map contained 21 linkage groups that covered 2260 cM. Based on the established genetic maps, it was found that the gender of willow was determined by a single locus on linkage group LG_03, and the female was the heterogametic gender. Aligned with mapped SSR markers, linkage group LG_03 was found to be associated with chromosome XV in willow. It is noteworthy that marker density in the vicinity of the gender locus was significantly higher than that expected by chance alone, which indicates severe recombination suppression around the gender locus. In conclusion, this study confirmed the findings on the single-locus sex determination and female heterogamety in willow. It also provided additional evidence that validated the previous studies, which found that different autosomes evolved into sex chromosomes between the sister genera of Salix (willow) and Populus (poplar).

Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

BACKGROUND

Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species.

RESULTS

We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population.

CONCLUSIONS

The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.

Using Populus as a lignocellulosic feedstock for bioethanol

Populus species along with species from the sister genus Salix will provide valuable feedstock resources for advanced second-generation biofuels. Their inherent fast growth characteristics can particularly be exploited for short rotation management, a time and energy saving cultivation alternative for lignocellulosic feedstock supply. Salicaceae possess inherent cell wall characteristics with favorable cellulose to lignin ratios for utilization as bioethanol crop. We review economically important traits relevant for intensively managed biofuel crop plantations, genomic and phenotypic resources available for Populus, breeding strategies for forest trees dedicated to bioenergy provision, and bioprocesses and downstream applications related to opportunities using Salicaceae as a renewable resource. Challenges need to be resolved for every single step of the conversion process chain, i.e., starting from tree domestication for improved performance as a bioenergy crop, bioconversion process, policy development for land use changes associated with advanced biofuels, and harvest and supply logistics associated with industrial-scale biorefinery plants using Populus as feedstock. Significant hurdles towards cost and energy efficiency, environmental friendliness, and yield maximization with regards to biomass pretreatment, saccharification, and fermentation of celluloses and the sustainability of biorefineries as a whole still need to be overcome.

A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings

Background

Douglas-fir (Pseudotsuga menziesii) extends over a wide range of contrasting environmental conditions, reflecting substantial local adaptation. For this reason, it is an interesting model species to study plant adaptation and the effects of global climate change such as increased temperatures and significant periods of drought on individual trees and the forest landscape in general. However, genomic data and tools for studying genetic variation in natural populations to understand the genetic and physiological mechanisms of adaptation are currently missing for Douglas-fir. This study represents a first step towards characterizing the Douglas-fir transcriptome based on 454 sequencing of twelve cDNA libraries. The libraries were constructed from needle and wood tissue of coastal and interior provenances subjected to drought stress experiments.

Results

The 454 sequencing of twelve normalized cDNA libraries resulted in 3.6 million reads from which a set of 170,859 putative unique transcripts (PUTs) was assembled. Functional annotation by BLAST searches and Gene Ontology mapping showed that the composition of functional classes is very similar to other plant transcriptomes and demonstrated that a large fraction of the Douglas-fir transcriptome is tagged by the PUTs. Based on evolutionary conservation, we identified about 1,000 candidate genes related to drought stress. A total number of 187,653 single nucleotide polymorphisms (SNPs) were detected by three SNP detection tools. However, only 27,688 SNPs were identified by all three methods, indicating that SNP detection depends on the particular method used. The two alleles of about 60% of the 27,688 SNPs are segregating simultaneously in both coastal and interior provenances, which indicates a high proportion of ancestral shared polymorphisms or a high level of gene flow between these two ecologically and phenotypically different varieties.

Conclusions

We established a catalogue of PUTs and large SNP database for Douglas-fir. Both will serve as a useful resource for the further characterization of the genome and transcriptome of Douglas-fir and for the analysis of genetic variation using genotyping or resequencing methods.

Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

BACKGROUND

Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions.

RESULTS

Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'.

CONCLUSION

Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.

Forest tree genomics: growing resources and applications

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.

Population genetic relationships between Casearia sylvestris (Salicaceae) varieties occurring sympatrically and allopatrically in different ecosystems in south-east Brazil

BACKGROUND AND AIMS

Species delimitation can be problematic, and recently diverged taxa are sometimes viewed as the extremes of a species' continuum in response to environmental conditions. Using population genetic approaches, this study assessed the relationship between two Casearia sylvestris (Salicaceae) varieties, which occur sympatrically and allopatrically in the landscape of south-east Brazil, where intermediate types are also found.

METHODS

In total, 376 individuals from nine populations in four different ecosystems were sampled, and nine microsatellite markers were used to assess the relative effects of the ecosystems and varieties on the distribution of genetic diversity among populations of this species.

KEY RESULTS

As a by-product of this study, several PCR products with more than two alleles were observed. The possibility that extra bands represent non-specific amplification or PCR artefacts was discarded by sequencing a sample of these bands. We suggest that (partial) genome duplication in C. sylvestris most probably explains this phenomenon, which may be a key factor in the differentiation of the two taxa, as it was markedly more frequent in one of the varieties. AMOVA indicated that approx. 22 % of the total genetic diversity was found between the two varieties. Bayesian analysis identified varieties and ecosystems as evolutionary units, rather than the individual populations sampled.

CONCLUSIONS

The results are in agreement with field observations and support the recognition of two varieties, as well as documenting the occurrence of hybridization between them.

Coexistence of diploids and triploids in a Saharan relict olive: evidence from nuclear microsatellite and flow cytometry analyses

Polyploidy was recently reported in two endangered olive subspecies from North-West Africa. The origin of this phenomenon remains unclear. In the present study, 106 genotypes of a relict Laperrine's olive population form Hoggar (Algeria) were analysed using eight nuclear microsatellites. Diploid and triploid genetic profiles were observed. A flow cytometry analysis confirmed that trees displaying three alleles at several loci are effectively triploid. This report constitutes the first evidence for the coexistence of two ploidy types in an olive population. The triploid genotypes, probably in mean more vigorous than diploid trees, may be positively selected in the absence of sexual regeneration since a very long time, explaining their relative high frequency in the investigated population.

Five QTL hotspots for yield in short rotation coppice bioenergy poplar: the Poplar Biomass Loci

BACKGROUND

Concern over land use for non-food bioenergy crops requires breeding programmes that focus on producing biomass on the minimum amount of land that is economically-viable. To achieve this, the maximum potential yield per hectare is a key target for improvement. For long lived tree species, such as poplar, this requires an understanding of the traits that contribute to biomass production and their genetic control. An important aspect of this for long lived plants is an understanding of genetic interactions at different developmental stages, i.e. how genes or genetic regions impact on yield over time.

RESULTS

QTL mapping identified regions of genetic control for biomass yield. We mapped consistent QTL across multiple coppice cycles and identified five robust QTL hotspots on linkage groups III, IV, X, XIV and XIX, calling these 'Poplar Biomass Loci' (PBL 1-5). In total 20% of the variation in final harvest biomass yield was explained by mapped QTL. We also investigated the genetic correlations between yield related traits to identify 'early diagnostic' indicators of yield showing that early biomass was a reasonable predictor of coppice yield and that leaf size, cell number and stem and sylleptic branch number were also valuable traits.

CONCLUSION

These findings provide insight into the genetic control of biomass production and correlation to 'early diagnostic' traits determining yield in poplar SRC for bioenergy. QTL hotspots serve as useful targets for directed breeding for improved biomass productivity that may also be relevant across additional poplar hybrids.

Genome structure and emerging evidence of an incipient sex chromosome in Populus

The genus Populus consists of dioecious woody species with largely unknown genetic mechanisms for gender determination. We have discovered genetic and genomic features in the peritelomeric region of chromosome XIX that suggest this region of the Populus genome is in the process of developing characteristics of a sex chromosome. We have identified a gender-associated locus that consistently maps to this region. Furthermore, comparison of genetic maps across multiple Populus families reveals consistently distorted segregation within this region. We have intensively characterized this region using an F(1) interspecific cross involving the female genotype that was used for genome sequencing. This region shows suppressed recombination and high divergence between the alternate haplotypes, as revealed by dense map-based genome assembly using microsatellite markers. The suppressed recombination, distorted segregation, and haplotype divergence were observed only for the maternal parent in this cross. Furthermore, the progeny of this cross showed a strongly male-biased sex ratio, in agreement with Haldane's rule that postulates that the heterogametic sex is more likely to be absent, rare, or sterile in interspecific crosses. Together, these results support the role of chromosome XIX in sex determination and suggest that sex determination in Populus occurs through a ZW system in which the female is the heterogametic gender.

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

Cottonwoods are foundation riparian species, and hybridization among species is known to produce ecological effects at levels higher than the population, including effects on dependent species, communities and ecosystems. Because these patterns result from increased genetic variation in key cottonwood traits, novel applications of genetic tools (for example, QTL mapping) could be used to place broad-scale ecological research into a genomic perspective. In addition, linkage maps have been produced for numerous species within the genus, and, coupled with the recent publication of the Populus genome sequence, these maps present a unique opportunity for genome comparisons in a model system. Here, we conducted linkage analyses in order to (1) create a platform for QTL and candidate gene studies of ecologically important traits, (2) create a framework for chromosomal-scale perspectives of introgression in a natural population, and (3) enhance genome-wide comparisons using two previously unmapped species. We produced 246 backcross mapping (BC(1)) progeny by crossing a naturally occurring F(1) hybrid (Populus fremontii x P. angustifolia) to a pure P. angustifolia from the same population. Linkage analysis resulted in a dense linkage map of 541 AFLP and 111 SSR markers distributed across 19 linkage groups. These results compared favorably with other Populus linkage studies, and addition of SSR loci from the poplar genome project provided coarse alignment with the genome sequence. Preliminary applications of the data suggest that our map represents a useful framework for applying genomic research to ecological questions in a well-studied system, and has enhanced genome-wide comparisons in a model tree.

Adaptation of tree growth to elevated CO2: quantitative trait loci for biomass in Populus

* Information on the genetic variation of plant response to elevated CO(2) (e[CO(2)]) is needed to understand plant adaptation and to pinpoint likely evolutionary response to future high atmospheric CO(2) concentrations. * Here, quantitative trait loci (QTL) for above- and below-ground tree growth were determined in a pedigree - an F(2) hybrid of poplar (Populus trichocarpa and Populus deltoides), following season-long exposure to either current day ambient CO(2) (a[CO(2)]) or e[CO(2)] at 600 microl l(-1), and genotype by environment interactions investigated. * In the F(2) generation, both above- and below-ground growth showed a significant increase in e[CO(2)]. Three areas of the genome on linkage groups I, IX and XII were identified as important in determining above-ground growth response to e[CO(2)], while an additional three areas of the genome on linkage groups IV, XVI and XIX appeared important in determining root growth response to e[CO(2)]. * These results quantify and identify genetic variation in response to e[CO(2)] and provide an insight into genomic response to the changing environment.

The genetics and genomics of the drought response in Populus

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F(2)) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that 'genetical genomics' can be used to provide information on adaptation at the species level. The grandparents and F(2) population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.

Elucidating genomic regions determining enhanced leaf growth and delayed senescence in elevated CO2

Limited information is available on the genetic variation and control for plant growth response to elevated CO(2) (e[CO(2)]). Such information is necessary to understand plant adaptation and evolution in future rising CO(2). Here, quantitative trait loci (QTL) for leaf growth, development, quality and leaf senescence were determined in a tree pedigree - an F(2) hybrid of Populus trichocarpa T. & G and Populus deltoides Marsh, following season-long exposure to either current day ambient carbon dioxide (a[CO(2)]) or e[CO(2)] at 600 microL L(-1). Leaf growth and development differed between the grandparents such that P. trichocarpa showed greater response to e[CO(2)]. In the F(2) generation, leaf development and quality traits including leaf area, leaf shape, epidermal cell area, and stomatal number, specific leaf area (SLA), and the phenology trait, canopy senescence index, were sensitive to e[CO(2)]. Sixty-nine QTL were mapped for the 19 traits of plants in a[CO(2)] while 60 QTL were mapped for plants in e[CO(2)]. The results suggest that although many QTL mapped to common positions in a[CO(2)] and e[CO(2)], confirming their importance in determining growth, there was also differential genetic control for a number of traits including leaf senescence. Candidate genes were shown to collocate to regions where response QTL mapped. This study is the first to identify candidate genes that may be important in determining plant adaptation to future high-CO(2) world.

Genetic architecture of qualitative and quantitative Melampsora larici-populina leaf rust resistance in hybrid poplar: genetic mapping and QTL detection

In order to elucidate the genetic control of resistance to Melampsora larici-populina leaf rust in hybrid poplars, a Populus deltoides x P. trichocarpa F(1) progeny was analysed for qualitative and quantitative rust resistances. This progeny was evaluated for three components of quantitative resistance (latent period, uredinia number and uredinia size) to seven M. larici-populina strains in controlled conditions, and for one component of field susceptibility (rust colonization on the most infected leaf). One qualitative resistance locus inherited from P. deltoides, R(1), was localized on the genetic map. It segregates 1 : 1 in the F(1) progeny and is effective against four of the studied strains. QTL analysis was performed separately on R(1) and r(1) genotype subsets. An additional detection was conducted on the entire F(1) progeny for the three strains able to overcome R(1) and for MAX2. A total of nine QTLs were detected. Two had large, broad-spectrum effects. One (R(US)) is inherited from the P. trichocarpa parent; the other is inherited from P. deltoides and colocalized with R(1). Seven QTLs had only limited and specific effects. Significant interaction effects were detected mainly between the two major QTLs. Implications of these results for durable resistance breeding strategies, and possible benefits from the Populus genome sequence, are discussed.

Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map

We report the most complete genetic map to have been constructed for the genus Populus. This map includes 544 markers mapped onto 19 linkage groups, equivalent to the Populus chromosome number, with all markers displaying internally consistent linkage patterns. We estimate the genome length to be between 2,300 and 2,500 cM, based both on the observed number of crossovers in the maternal haplotypes, as well as the total observed map length. Genome coverage was estimated to be greater than 99.9% at 20 cM per marker. We did not detect obvious recombination repression in the maternal tree (a hybrid of Populus trichocarpa Hooker x P. deltoides Marsh.) compared to the paternal tree (pure P. deltoides). Finally, most markers exhibiting segregation distortion were derived from the donor parent in this backcross, and generally occurred in large contiguous blocks on two linkage groups. We hypothesize that divergent selection has occurred on chromosomal scales among the parental species used to create this pedigree, and explore the evolutionary implications of this observation. This genetic linkage map provides the most comprehensive view of the Populus genome reported to date and will prove invaluable for future inquiries into the structural and functional genomics, evolutionary biology, and genetic improvement of this ecologically important model species.

Partial Resistance to Melampsora larici-populina Leaf Rust in Hybrid Poplars: Genetic Variability in Inoculated Excised Leaf Disk Bioassay and Relationship with Complete Resistance

ABSTRACT Inoculated excised leaf disk technique allows decomposition of poplar partial resistance to Melampsora larici-populina leaf rust into key epidemiological components such as latent period (LP), uredinia number (UN), uredinia size (US), and spore production (SP) for a given M. larici-populina strain under controlled environmental conditions. Three hundred thirty-six genotypes from an interspecific Populus deltoides x P. trichocarpa F(1) progeny segregating for complete resistance to M. larici-populina strain 93ID6 were inoculated with M. larici-populina strain 93CV1. This strain was able to infect the whole family, except few probable recombinants. LP, final UN, and final US after one infectious cycle proved to be relevant complementary descriptors of partial resistance. Area under the disease progress curve and other parameters of uredinia appearance dynamics did not yield additional information. Indirect assessment of SP by US scoring was reliable and easy to access compared with direct spore counting. UN was the only trait for which a doubling of the inoculum pressure level had a significant effect, leading to greater differentiation between genotypes. Consistent with previous studies is the clear relationship between presence of complete resistance against M. larici-populina strain 93ID6 and higher partial resistance to M. larici-populina strain 93CV1 (32% longer LP, 76% smaller UN, and 34% smaller US). In the subpopulation compatible with 93ID6, bimodal distribution of genotypic means for US suggested implication of a major gene inherited from the P. trichocarpa parent. Residual variation was noted for the three epidemiological components, suggesting that additional genes might condition these quantitative traits.

Molecular linkage maps of the Populus genome

We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification.

Unravelling cell wall formation in the woody dicot stem

Populus is presented as a model system for the study of wood formation (xylogenesis). The formation of wood (secondary xylem) is an ordered developmental process involving cell division, cell expansion, secondary wall deposition, lignification and programmed cell death. Because wood is formed in a variable environment and subject to developmental control, xylem cells are produced that differ in size, shape, cell wall structure, texture and composition. Hormones mediate some of the variability observed and control the process of xylogenesis. High-resolution analysis of auxin distribution across cambial region tissues, combined with the analysis of transgenic plants with modified auxin distribution, suggests that auxin provides positional information for the exit of cells from the meristem and probably also for the duration of cell expansion. Poplar sequencing projects have provided access to genes involved in cell wall formation. Genes involved in the biosynthesis of the carbohydrate skeleton of the cell wall are briefly reviewed. Most progress has been made in characterizing pectin methyl esterases that modify pectins in the cambial region. Specific expression patterns have also been found for expansins, xyloglucan endotransglycosylases and cellulose synthases, pointing to their role in wood cell wall formation and modification. Finally, by studying transgenic plants modified in various steps of the monolignol biosynthetic pathway and by localizing the expression of various enzymes, new insight into the lignin biosynthesis in planta has been gained.

Preliminary interspecific genetic maps of the Populus genome constructed from RAPD markers

We have constructed RAPD-based linkage maps for an interspecific cross between two species of the genus Populus (P. adenopoda and P. alba), based on a double pseudo-test-cross strategy. Of a total of 360 polymorphic fragments scored, 290 showed a test-cross configuration, corresponding to DNA polymorphisms heterozygous in one parent and null in the other. In the female parent, P. adenopoda, 82 markers were grouped in 19 different linkage groups (553 cM), whereas in the male parent P. alba, 197 markers established a much more complete framework map with an observed genome length of 2300 cM covering 87% of the total P. alba genome. The larger number of test-cross markers detected for the P. alba parent than for the P. adenopoda parent might be due to a higher level of heterozygosity in the former than in the latter. In this study, we detected only a small percentage (2%) of the intercross dominant markers heterozygous in both parents and segregating 3:1 in the progeny. The further focus in this mapping study should be on the identification of more intercross markers, to align the two parent-specific maps into a consensus map for mapping important genes causing species differentiation during long evolutionary divergences.Key words: interspecific hybrids, linkage map, poplar, pseudo-testcross mapping strategy.

Hybrid populations selectively filter gene introgression between species

Hybrids have long been recognized as a potential pathway for gene flow between species that can have important consequences for evolution and conservation biology. However, few studies have demonstrated that genes from one species can introgress or invade another species over a broad geographic area. Using 35 genetically mapped restriction fragment length polymorphism (RFLP) markers of two species of cottonwoods (Populus fremontii x P. angustifolia) and their hybrids (n = 550 trees), we showed that the majority of the genome is prohibited from introgressing from one species into the other. However, this barrier was not absolute; Fremont cpDNA and mtDNA were found throughout the geographic range of narrowleaf cottonwood, and 20% of the nuclear markers of Fremont cottonwood introgressed varying distances (some over 100 km) into the recipient species' range. Rates of nuclear introgression were variable, but two nuclear markers introgressed as fast as the haploid, cytoplasmically inherited chloroplast and mitochondrial markers. Our genome-wide analysis provides evidence for positive, negative, and neutral effects of introgression. For example, we predict that DNA fragments that introgress through several generations of backcrossing will be small, because small fragments are less likely to contain deleterious genes. These results argue that recombination will be important, that introgression can be very selective, and that evolutionary forces within the hybrid population to effectively "filter" gene flow between species. A strong filter may make introgression adaptive, prevent genetic assimilation, lead to relaxed isolating mechanisms, and contribute to the stability of hybrid zones. Thus, rather than hybridization being a negative factor as is commonly argued, natural hybridization between native species may provide important genetic variation that impacts both ecological and evolutionary processes. Finally, we propose two hypotheses that contrast the likelihood of contemporary versus ancient introgression in this system.

A DEFICIENS homolog from the dioecious tree black cottonwood is expressed in female and male floral meristems of the two-whorled, unisexual flowers

We isolated PTD, a member of the DEFICIENS (DEF) family of MADS box transcription factors, from the dioecious tree, black cottonwood (Populus trichocarpa). In females, in situ hybridization experiments showed that PTD mRNA was first detectable in cells on the flanks of the inflorescence meristem, before differentiation of individual flowers was visually detectable. In males, the onset of PTD expression was delayed until after individual flower differentiation had begun and floral meristems were developing. Although PTD was initially expressed throughout the inner whorl meristem in female and male flowers, its spatial expression pattern became sex-specific as reproductive primordia began to form. PTD expression was maintained in stamen primordia, but excluded from carpel primordia, as well as vegetative tissues. Although PTD is phylogenetically most closely related to the largely uncharacterized TM6 subfamily of the DEF/APETELA3(AP3)/TM6 group, its spatio-temporal expression patterns are more similar to that of DEF and AP3 than to other members of the TM6 subfamily.

Gene discovery in the wood-forming tissues of poplar: analysis of 5, 692 expressed sequence tags

A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue. To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L. x tremuloides Michx. and Populus trichocarpa 'Trichobel.' The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries. Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs showed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

Association of Mmd1, a Major Gene for Resistance to Melampsora medusae f. sp. deltoidae, with Quantitative Traits in Poplar Rust

ABSTRACT A single gene, Mmd1, which conditions resistance and a necrotic flecking response to a monouredinial isolate of Melampsora medusae f. sp. deltoidae and is presumed to possess the corresponding avirulence gene, was previously shown to segregate 3:1 (resistant to susceptible) in an interspecific hybrid poplar F(2) progeny. Some inoculated clones of the resistant phenotypic class of this progeny were completely resistant and bore no uredinia, but most bore some sporulating uredinia with accompanying necrotic flecking. The dominant allele at the Mmd1 locus in these incompletely resistant clones was significantly associated with reduced uredinial density and diameter and longer latent period in a growth-room assay and with reduced disease incidence and infection efficiency and longer latent period in a leaf-disk assay. However, high clone-mean heritabilities within the susceptible phenotypic class indicated that genes other than Mmd1 also contribute to control of quantitative traits. Leaf age had a significant effect on uredinial density and latent period but not on uredinial diameter in the growth-room assay. All quantitative traits were intercorrelated to varying extents. A principal components analysis (PCA) demonstrated that uncorrelated components associated with uredinial diameter and uredinial density explained two-thirds of the total variation. Since uredinial diameter (PC1) and necrotic flecking are the visual components of an infection-type rating scale, genetic analyses of poplar rust should be based on infection type. Mmd1 is a major gene for resistance associated with a significant effect on all quantitative traits measured. Gene complexes in domesticated, agricultural rust pathosystems known to provide durable resistance consist of similar "pivotal" major genes and inferred ancillary genes or quantitative trait loci.

4-Coumarate:coenzyme A ligase in hybrid poplar. Properties of native enzymes, cDNA cloning, and analysis of recombinant enzymes

The enzyme 4-coumarate:coenzyme A ligase (4CL) is important in providing activated thioester substrates for phenylpropanoid natural product biosynthesis. We tested different hybrid poplar (Populus trichocarpa x Populus deltoides) tissues for the presence of 4CL isoforms by fast-protein liquid chromatography and detected a minimum of three 4CL isoforms. These isoforms shared similar hydroxycinnamic acid substrate-utilization profiles and were all inactive against sinapic acid, but instability of the native forms precluded extensive further analysis. 4CL cDNA clones were isolated and grouped into two major classes, the predicted amino acid sequences of which were 86% identical. Genomic Southern blots showed that the cDNA classes represent two poplar 4CL genes, and northern blots provided evidence for their differential expression. Recombinant enzymes corresponding to the two genes were expressed using a baculovirus system. The two recombinant proteins had substrate utilization profiles similar to each other and to the native poplar 4CL isoforms (4-coumaric acid > ferulic acid > caffeic acid; there was no conversion of sinapic acid), except that both had relatively high activity toward cinnamic acid. These results are discussed with respect to the role of 4CL in the partitioning of carbon in phenylpropanoid metabolism.

A quantitative genetic model for mixed diploid and triploid hybrid progenies in tree breeding and evolution

Interspecific hybridization has played a critical role in tree evolution and breeding. The findings of triploidy in forest trees stimulate the development of a quantitative genetic model to estimate the nature of gene action. The model is based on clonally replicated triploid progenies derived from a two-level population and individual-within-population mating design in which offspring have a double dose of alleles from the parent and a single dose of alleles from the other parent. With the same genetic assumptions of a diploid model, except non-Mendelian behavior at meiosis, and the experimental variances estimated from a linear statistical model, total genetic variances in the triploid progenies are separated into additive, dominance, and epistatic components. In addition, by combining the new model with the already existing model based on disomic expression, the partitioning of additive, dominant, and epistatic variances can be obtained for a mixed diploid/triploid F1 progeny population. This paper provides an alternative technique to study the modes of quantitative inheritance for outcrossing, long-lived forest trees in which inbred lines cannot be easily generated. The accuracy for estimating gene action using this technique is discussed.

Quantitative genetics of growth and development in Populus. I. A three-generation comparison of tree architecture during the first 2 years of growth

One approach to gain an insight into the genetics of tree architecture is to make use of morphologically divergent parents and study their segregating progeny in the F2 and backcross (B1) generations. This approach was chosen in the present study in which material of a three-generation pedigree growing side by side in a replicated plantation, was analyzed. The pedigree included Populus trichocarpa (T) and P. deltoides (D) parents, their F1 and F2 hybrids and their B1 hybrids to the D parent. The trees were grown in the environment of the T parent and measured for the first 2 years of growth. Nine quantitative traits were studied at the stem, branch and leaf levels of tree architecture, in which the original parents differed. Strong F1 hybrid vigor relative to the better parent (T) was expressed in growth and its components. Most quantitative traits in the F2 and B1 hybrids were intermediate between the T and D parents but displayed a wide range of variation due to segregation. The results from the analysis of variance indicated that all morphometric traits were significantly different among F2 and B1 clones, but the B1 hybrids were more sensitive to replicates than the F2. Broad-sense heritabilities (H (2)) based on clonal means ranged from moderately high to high (0.50-0.90) for the traits studied, with H (2) values varying over age. The H (2) estimates reflected greater environmental "noise" in the B1 than in the F2, presumably due to the greater proportion of maladaptive D alleles in those hybrids. In both families, sylleptic branch number and length, and leaf size on the terminal, showed strong genetic correlations with stem growth. The large divergence between the two original parents in the traits studied, combined with the high chromosome number in Populus (2n=38), makes this pedigree well suited for the estimation of the number of quantitative trait loci (QTLs) underlying quantitative variation by Wright's biometric method (1968). Variation in several traits was found to be under the control of surprisingly few major QTLs: 3-4 in 2nd-year height and diameter growth, a single QTL in stem diameter/height ratio.

Molecular genetics of growth and development in Populus. II. Segregation distortion due to genetic load

Distortion of expected Mendelian segregation ratios, commonly observed in many plant taxa, has been detected in an experimental three-generation inbred pedigree of Populus founded by interspecific hybridization between P. trichocarpa and P. deltoides. An RFLP linkage map was constructed around a single locus showing severe skewing of segregation ratio against F2 trees carrying the P. trichocarpa allele in homozygous form. Several hypotheses for the mechanism of segregation distortion at this locus were tested, including directional chromosome loss, segregation of a pollen lethal allele, conflicts between genetic factors that isolate the parental species, and inbreeding depression as a result of genetic load. Breeding experiments to produce inbred and outcrossed progenies were combined with PCR-based detection of RFLPs to follow the fate of the deficient allele throughout embryo and seedling development. A recessive lethal allele, lth, inherited from the P. trichocarpa parent, was found to be tightly linked to the RFLP marker locus POP1054 and to cause embryo and seedling mortality. Heterozygotes (lth/+) appear to be phenotypically normal as embryos, seedlings, and young trees.

Molecular genetics of growth and development in Populus. III. A genetic linkage map of a hybrid poplar composed of RFLP, STS, and RAPD markers

We have evaluated three DNA-based marker types for linkage map construction in Populus: RFLPs detected by Southern blot hybridization, STSs detected by a combination of PCR and RFLP analysis, and RAPDs. The mapping pedigree consists of three generations, with the F1 produced by interspecific hybridization between a P. trichocarpa female and a P. deltoides male. The F2 generation was made by inbreeding to the maximum degree permitted by the dioecious mating system of Populus. The applicability of STSs and RAPDs outside the mapping pedigree has been investigated, showing that these PCR-based marker systems are well-suited to breeding designs involving interspecific hybridization. A Populus genome map (343 markers) has been constructed from a combination of all three types. The length of the Populus genome is estimated to be 2400-2800 cM.

Intra- and interspecific inheritance of some components of the resistance to leaf rust (Melampsora larici-populina Kleb.) in poplars

Clonal variation for rust resistance was studied in a factorial mating design of Populus trichocarpa and P. deltoides with 17 intraspecific and 15 interspecific progenies. Susceptibility to Melampsora larici-populina was assessed both under natural conditions in the nursery and after leaf-disk inoculation with two pathogen races in a controlled environment. Different components of the resistance were taken into account: immunity in the field or in the laboratory, latent period, number and size of uredia in the laboratory, and field resistance at the end of the growing season. Genes controlling immunity were contributed only by the P. deltoides parents. The distributions of clonal means within each family suggested a polygenic inheritance of field resistance in the P. trichocarpa x P. trichocarpa crosses, but major gene effects were suspected in the interspecific progenies. Inefficiency of the quantitative mechanisms of resistance in the interspecific F1 hybrids might have important implications for future breeding strategies. Field and laboratory trials complemented each other well, and a combined selection approach is proposed.