- Plant Science, Bioenergy (Biology), Climate change biology, Crop genetic diversity, Molecular Markers, Synthetic Biology, and 17 moreFunctional Genomics, Genetic Diversity, Adaptation to Climate Change, Species Distribution Models, Indigenous ecological knowledges and practices, Palaeobotany, Quantitative Genetics, Evolutionary Biology, Forestry, Plant Molecular Biology, Genome Wide Association Studies (GWAS), Wood Science, Speciation, Wood chemistry, Genetics, Bioenergy, and Population Geneticsedit
The evolution of sexual dimorphism and expansion of sex chromosomes are both driven through sexual conflict, arising from differing fitness optima between males and females. Here, we pair work in poplar (Populus) describing one of the... more
The evolution of sexual dimorphism and expansion of sex chromosomes are both driven through sexual conflict, arising from differing fitness optima between males and females. Here, we pair work in poplar (Populus) describing one of the smallest sex-determining regions known thus far in complex eukaryotes (~100 kbp) with comprehensive tests for sexual dimorphism using >1300 individuals from two Populus species and assessing 96 non-reproductive functional traits. Against expectation, we found sexual homomorphism (no non-reproductive trait differences between the sexes), suggesting that gender is functionally neutral with respect to non-reproductive features that affect plant survival and fitness. Combined with a small sex-determining region, we infer that sexual conflict may be effectively stymied or non-existent within these taxa. Both sexual homomorphism and the small sex-determining region occur against a background of strong environmental selection and local adaptation in Populu...
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In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies... more
In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P = 0.004) of the negativ...
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The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental... more
The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, R. molle. Comparative genomics found recent proliferation of LTR-RTs, especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13402) and pseudogenes (17437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 a...
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Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among... more
Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits. Here, we revisited leaf morphology in two European sympatric white oaks (Quercus petraea (Matt.) Liebl. and Quercus robur L.), sampling 2098 individuals, across much of their geographical distribution ranges. At the phenotypic level, leaf morphology traditionally encompasses discriminant attributes among different oak species. Here, we estimated in situ heritability, genetic correlation, and integration across such attributes. Also, we performed Selection Response Decomposition to test these traits for potential differences in oak species' evolutionary r...
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Among the R2R3 MYB transcription factors that involve in the regulation of secondary cell wall formation in
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The development of reproductive structures is still poorly studied in gymnosperms due to limited genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less... more
The development of reproductive structures is still poorly studied in gymnosperms due to limited genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less studied aspect of seed plant evolution.
To extend our understanding regarding the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed by RNA-seq.
Results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous.
This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.
To extend our understanding regarding the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed by RNA-seq.
Results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous.
This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.
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Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most... more
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.
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Water stress affecting long-lived trees is an important challenge in forestry. Due to global climate change, forest trees will be threatened by extreme conditions like flooding or drought. It is necessary to understand differences in... more
Water stress affecting long-lived trees is an important challenge in forestry. Due to global climate change, forest trees will be threatened by extreme conditions like flooding or drought. It is necessary to understand differences in stress tolerance within certain species and to investigate putative relations on genomic level. In this study, osmotic stress induced genes of Quercus ssp. were positioned on two genetic linkage maps of oak. An intra-specific cross 3P*A4 of Quercus robur consisting of 88 offspring and an inter-specific cross 11P*QS29 of Q. robur and Q. petraea comprising 72 full-sibs were analyzed for the inheritance of 14 loci represented by 34 individual single nucleotide polymorphisms. Seven genes in the intra-cross, as well as other six genes in the inter-cross could be mapped and one gene could not be localised due to the severe distortion of the segregation. The collection of expressed sequences involved ribosomal proteins, members of the oxylase/oxygenase gene family, betaine aldehyde dehydrogenase, Dc3 promoter-binding factor, a putative member of the nodulin family, glutathione-S-transferase and proteins with unknown functions. In the inter-cross, two linked markers exhibited 89% deficiency of heterozygosity. Thirteen genes were positioned on ten different oak chromosomes and can serve as orthologous markers in comparative mapping studies within Fagaceae.
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Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently... more
Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits.Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29 233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations.The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3–7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation.Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
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In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait... more
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions.We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes).The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
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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... more
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.
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The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood... more
The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations.Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy–Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits.The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified.The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.