The actin multigene family in Populus: organization, expression and phylogenetic analysis

Genome-Wide Profiling of the ACTIN Gene Family and Its Implications for Agronomic Traits in Brassica napus: A Bioinformatics Study

ACTINs are key structural proteins in plants, which form the actin cytoskeleton and are engaged in numerous routine cellular processes. Meanwhile, ACTIN, recognized as a housekeeping gene, has not yet been thoroughly investigated in Brassica napus. The current research has led to the detection of 69 actin genes in B. napus, which were organized into six distinct subfamilies on the basis of phylogenetic relationships. Functional enrichment analysis, along with the construction of protein interaction networks, suggested that BnACTINs play roles in Preserving cell morphology and facilitating cytoplasmic movement, plant development, and adaptive responses to environmental stress. Moreover, the BnACTIN genes presented a wide range of expression levels among different tissues, whereas the majority experienced a substantial increase in expression when subjected to various abiotic stresses, demonstrating a pronounced sensitivity to abiotic factors. Furthermore, association mapping analysis indicated that some BnACTINs potentially affected certain key agronomic traits. Overall, our research deepens the knowledge of BnACTIN genes, promotes the cultivation of improved B. napus strains, and lays the groundwork for subsequent functional research.

Research progress on the roles of actin-depolymerizing factor in plant stress responses

Actin-depolymerizing factors (ADFs) are highly conserved small-molecule actin-binding proteins found throughout eukaryotic cells. In land plants, ADFs form a small gene family that displays functional redundancy despite variations among its individual members. ADF can bind to actin monomers or polymerized microfilaments and regulate dynamic changes in the cytoskeletal framework through specialized biochemical activities, such as severing, depolymerizing, and bundling. The involvement of ADFs in modulating the microfilaments' dynamic changes has significant implications for various physiological processes, including plant growth, development, and stress response. The current body of research has greatly advanced our comprehension of the involvement of ADFs in the regulation of plant responses to both biotic and abiotic stresses, particularly with respect to the molecular regulatory mechanisms that govern ADF activity during the transmission of stress signals. Stress has the capacity to directly modify the transcription levels of ADF genes, as well as indirectly regulate their expression through transcription factors such as MYB, C-repeat binding factors, ABF, and 14-3-3 proteins. Furthermore, apart from their role in regulating actin dynamics, ADFs possess the ability to modulate the stress response by influencing downstream genes associated with pathogen resistance and abiotic stress response. This paper provides a comprehensive overview of the current advancements in plant ADF gene research and suggests that the identification of plant ADF family genes across a broader spectrum, thorough analysis of ADF gene regulation in stress resistance of plants, and manipulation of ADF genes through genome-editing techniques to enhance plant stress resistance are crucial avenues for future investigation in this field.

Four ciliate-specific expansion events occurred during actin gene family evolution of eukaryotes

Actin gene family is a divergent and ancient eukaryotic cellular cytoskeletal gene family, and participates in many essential cellular processes. Ciliated protists offer us an excellent opportunity to investigate gene family evolution, since their gene families evolved faster in ciliates than in other eukaryotes. Nonetheless, actin gene family is well studied in few model ciliate species but little is known about its evolutionary patterns in ciliates. Here, we analyzed the evolutionary pattern of eukaryotic actin gene family based on genomes/transcriptomes of 36 species covering ten ciliate classes, as well as those of nine non-ciliate eukaryotic species. Results showed: (1) Except for conventional actins and actin-related proteins (Arps) shared by various eukaryotes, at least four ciliate-specific subfamilies occurred during evolution of actin gene family. Expansions of Act2 and ArpC were supposed to have happen in the ciliate common ancestor, while expansions of ActI and ActII may have occurred in the ancestor of Armophorea, Muranotrichea, and Spirotrichea. (2) The number of actin isoforms varied greatly among ciliate species. Environmental adaptability, whole genome duplication (WGD) or segmental duplication events, distinct spatial and temporal patterns of expression might play driving forces for the increasement of isoform numbers. (3) The 'birth and death' model of evolution could explain the evolution of actin gene family in ciliates. And actin genes have been generally under strong negative selection to maintain protein structures and physiological functions. Collectively, we provided meaningful information for understanding the evolution of eukaryotic actin gene family.

An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion

Somatic mutations may alter important traits in tree fruits, such as fruit color, size and maturation date. Autumn Gala (AGala), a somatic mutation from apple cultivar Gala, matures 4 weeks later than Gala. To understand the mechanisms underlying the delayed maturation, RNA-seq analyses were conducted with fruit sampled at 13 (Gala) and 16 (AGala) time-points during their growth and development. Weighted gene co-expression network analysis (WGCNA) of 23 372 differentially expressed genes resulted in 25 WGCNA modules. Of these, modules 1 (r = -0.98, P = 2E-21) and 2 (r = -0.52, P = 0.004), which were suppressed in AGala, were correlated with fruit maturation date. Surprisingly, 77 of the 152 member genes in module 1 were harbored in a 2.8-Mb genomic region on chromosome 6 that was deleted and replaced by a 10.7-kb gypsy-like retrotransposon (Gy-36) from chromosome 7 in AGala. Among the 77 member genes, MdACT7 was the most suppressed (by 10.5-fold) in AGala due to a disruptive 2.5-kb insertion in coding sequence. Moreover, MdACT7 is the exclusive apple counterpart of Arabidopsis ACT7 known of essential roles in plant development, and the functional allele MdACT7, which was lost to the deletion in AGala, was associated with early fruit maturation in 268 apple accessions. Overexpressing alleles MdACT7 and Mdact7 in an Arabidopsis act7 line showed that MdACT7 largely rescued its stunted growth and delayed initial flowering while Mdact7 did not. Therefore, the 2.8-Mb hemizygous deletion is largely genetically causal for fruit maturation delay in AGala, and the total loss of MdACT7 might have contributed to the phenotype.

PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar

BACKGROUND

Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of habitats including highly saline ones. However, its triploid genome complicates any detailed investigation of the molecular mechanisms underlying its adaptations.

RESULTS

We report a haplotype-resolved genome of this triploid poplar and characterize, using reverse genetics and biochemical approaches, a MYB gene, SALT RESPONSIVE MYB TRANSCRIPTION FACTOR (SRMT), which combines NUCLEAR FACTOR Y SUBUNIT C 9 (PtoNF-YC9) and RESPONSIVE TO DESICCATION 26 (PtoRD26), to regulate an ABA-dependent salt-stress response signaling. We reveal that the salt-inducible PtoRD26 is dependent on ABA signaling. We demonstrate that ABA or salt drives PtoNF-YC9 shuttling into the nucleus where it interacts with SRMT, resulting in the rapid expression of PtoRD26 which in turn directly regulates SRMT. This positive feedback loop of SRMT-PtoRD26 can rapidly amplify salt-stress signaling. Interference with either component of this regulatory module reduces the salt tolerance of this triploid poplar.

CONCLUSION

Our findings reveal a novel ABA-dependent salt-responsive mechanism, which is mediated by the PtoNF-YC9-SRMT-PtoRD26 module that confers salt tolerance to this triploid poplar. These genes may therefore also serve as potential and important modification targets in breeding programs.

Genetic Modification of KNAT7 Transcription Factor Expression Enhances Saccharification and Reduces Recalcitrance of Woody Biomass in Poplars

The precise role of KNAT7 transcription factors (TFs) in regulating secondary cell wall (SCW) biosynthesis in poplars has remained unknown, while our understanding of KNAT7 functions in other plants is continuously evolving. To study the impact of genetic modifications of homologous and heterologous KNAT7 gene expression on SCW formation in transgenic poplars, we prepared poplar KNAT7 (PtKNAT7) overexpression (PtKNAT7-OE) and antisense suppression (PtKNAT7-AS) vector constructs for the generation of transgenic poplar lines via Agrobacterium-mediated transformation. Since the overexpression of homologous genes can sometimes result in co-suppression, we also overexpressed Arabidopsis KNAT7 (AtKNAT7-OE) in transgenic poplars. In all these constructs, the expression of KNAT7 transgenes was driven by developing xylem (DX)-specific promoter, DX15. Compared to wild-type (WT) controls, many SCW biosynthesis genes downstream of KNAT7 were highly expressed in poplar PtKNAT7-OE and AtKNAT7-OE lines. Yet, no significant increase in lignin content of woody biomass of these transgenic lines was observed. PtKNAT7-AS lines, however, showed reduced expression of many SCW biosynthesis genes downstream of KNAT7 accompanied by a reduction in lignin content of wood compared to WT controls. Syringyl to Guaiacyl lignin (S/G) ratios were significantly increased in all three KNAT7 knockdown and overexpression transgenic lines than WT controls. These transgenic lines were essentially indistinguishable from WT controls in terms of their growth phenotype. Saccharification efficiency of woody biomass was significantly increased in all transgenic lines than WT controls. Overall, our results demonstrated that developing xylem-specific alteration of KNAT7 expression affects the expression of SCW biosynthesis genes, impacting at least the lignification process and improving saccharification efficiency, hence providing one of the powerful tools for improving bioethanol production from woody biomass of bioenergy crops and trees.

Integration of genome wide association studies and co-expression networks reveal roles of PtoWRKY 42-PtoUGT76C1-1 in trans-zeatin metabolism and cytokinin sensitivity in poplar

Cytokinins are important for in vitro shoot regeneration in plants. Cytokinin N-glucosides are produced via an irreversible glycosylation pathway, which regulates the endogenous cytokinin content. Although cytokinin N-glucoside pathways have been uncovered in higher plants, no regulator has been identified to date. We performed a metabolome genome-wide association study (mGWAS), weighted gene co-expression network analysis (WGCNA), and expression quantitative trait nucleotide (eQTN) mappings to build a core triple genetic network (mGWAS-gene expression-phenotype) for the trans-zeatin N-glucoside (ZNG) metabolite using data from 435 unrelated Populus tomentosa individuals. Variation of the ZNG level in poplar is attributed to the differential transcription of PtoWRKY42, a member of WRKY multigene family group IIb. Functional analysis revealed that PtoWRKY42 negatively regulated ZNG accumulation by binding directly to the W-box of the UDP-glycosyltransferase 76C 1-1 (PtoUGT761-1) promoter. Also, PtoWRKY42 was strongly induced by leaf senescence, 6-BA, wounding, and salt stress, resulting in a reduced ZNG level. We identified PtoWRKY42, a negative regulator of cytokinin N-glucosides, which contributes to the natural variation in ZNG level and mediates ZNG accumulation by directly modulating the key glycosyltransferase gene PtoUGT76C1-1.

A Modified Actin (Gly65Val Substitution) Expressed in Cotton Disrupts Polymerization of Actin Filaments Leading to the Phenotype of Ligon Lintless-1 (Li1) Mutant

Dynamic remodeling of the actin cytoskeleton plays a central role in the elongation of cotton fibers, which are the most important natural fibers in the global textile industry. Here, a high-resolution mapping approach combined with comparative sequencing and a transgenic method revealed that a G65V substitution in the cotton actin Gh_D04G0865 (GhACT17D in the wild-type) is responsible for the Gossypium hirsutum Ligon lintless-1 (Li₁) mutant (GhACT17DM). In the mutant GhACT17DM from Li₁ plant, Gly65 is substituted with valine on the lip of the nucleotide-binding domain of GhACT17D, which probably affects the polymerization of F-actin. Over-expression of GhACT17DM, but not GhACT17D, driven by either a CaMV35 promoter or a fiber-specific promoter in cotton produced a Li₁-like phenotype. Compared with the wild-type control, actin filaments in Li₁ fibers showed higher growth and shrinkage rates, decreased filament skewness and parallelness, and increased filament density. Taken together, our results indicate that the incorporation of GhACT17DM during actin polymerization disrupts the establishment and dynamics of the actin cytoskeleton, resulting in defective fiber elongation and the overall dwarf and twisted phenotype of the Li₁ mutant.

Genetic Effects and Expression Patterns of the Nitrate Transporter (NRT) Gene Family in Populus tomentosa

Nitrate is an important source of nitrogen for poplar trees. The nitrate transporter (NRT) gene family is generally responsible for nitrate absorption and distribution. However, few analyses of the genetic effects and expression patterns of NRT family members have been conducted in woody plants. Here, using poplar as a model, we identified and characterized 98 members of the PtoNRT gene family. We calculated the phylogenetic and evolutionary relationships of the PtoNRT family and identified poplar-specific NRT genes and their expression patterns. To construct a core triple genetic network (association - gene expression - phenotype) for leaf nitrogen content, a candidate gene family association study, weighted gene co-expression network analysis (WGCNA), and mapping of expression quantitative trait nucleotides (eQTNs) were combined, using data from 435 unrelated Populus. tomentosa individuals. PtoNRT genes exhibited distinct expression patterns between twelve tissues, circadian rhythm points, and stress responses. The association study showed that genotype combinations of allelic variations of three PtoNRT genes had a strong effect on leaf nitrogen content. WGCNA produced two co-expression modules containing PtoNRT genes. We also found that four PtoNRT genes defined thousands of eQTL signals. WGCNA and eQTL provided comprehensive analysis of poplar nitrogen-related regulatory factors, including MYB17 and WRKY21. NRT genes were found to be regulated by five plant hormones, among which abscisic acid was the main regulator. Our study provides new insights into the NRT gene family in poplar and enables the exploitation of novel genetic factors to improve the nitrate use efficiency of trees.

Genetic interactions among Pto-miR319 family members and their targets influence growth and wood properties in Populus tomentosa

MicroRNAs (miRNAs) play crucial roles in all aspects of plant growth and development, but the genetic interactions of miRNAs and their target genes in woody plants are largely unknown. Here, we integrated association genetics and expression profiling to decipher the allelic variations and interactions of the Pto-MIR319 family of miRNAs and 12 putative Pto-miR319 target genes related to wood formation in 435 unrelated individuals of Populus tomentosa Carrière (Chinese white poplar). Expression pattern analysis showed that among all pairings between expressions of pre-miRNA of Pto-MIR319 members and targets, 70.0% showed negative correlation of expression levels (r = - 0.944 to 0.674, P < 0.01) in eight tissues and organs of poplar, suggesting that Pto-miR319 may participate in the regulatory network of wood formation. Single SNP-based association studies identified 137 significant associations (P < 0.01, Q < 0.1), representing 126 unique SNPs from Pto-MIR319 members and their targets, with 10 tree growth traits, revealing that these genetic factors have common roles related to wood formation. Epistasis analysis uncovered 105 significant SNP-SNP associations (P < 0.01) influencing the 10 traits, demonstrating the close genetic interactions between Pto-MIR319 family members and the 12 Pto-miR319 target genes. Notably, one common SNP, in the precursor region of Pto-MIR319e, affected the stability of Pto-MIR319e's secondary structure by altering the stem-loop structure and minimum free energy, contributing to variations in the expression of Pto-MIR319e and Pto-miR319e target genes. This study enriches the understanding of the functions of miR319 family miRNAs in poplar and exemplifies a feasible approach to exploring the genetic effects underlying miRNA-mRNA interactions related to complex traits in trees.

Efficient Agrobacterium-Mediated Transformation of the Commercial Hybrid Poplar Populus Alba × Populus glandulosa Uyeki

Transgenic technology is a powerful tool for gene functional characterization, and poplar is a model system for genetic transformation of perennial woody plants. However, the poplar genetic transformation system is limited to a number of model genotypes. Herein, we developed a transformation system based on efficient Agrobacterium-mediated transformation for the hybrid poplar Populus Alba × Populus glandulosa Uyeki, which is a fast-growing poplar species that is suitably grown in the northern part of China. Importantly, we optimized many independent factors and showed that the transformation efficiency was improved significantly using juvenile leaf explants. Explants were infected by an Agrobacterium suspension with the OD₆₀₀ = 0.6 for 15 min and then co-cultured in dark conditions for 3 days. Using the improved transformation system, we obtained the transgenic poplar with overexpression of β-glucuronidase (GUS) via direct organogenesis without callus induction. Furthermore, we analyzed the GUS gene in the transgenic poplars using PCR, qRT-PCR, and GUS staining. These analyses revealed that the GUS gene was efficiently transformed, and it exhibited various expression levels. Taken together, these results represent a simple, fast, and efficient transformation system of hybrid poplar plants. Our findings may facilitate future studies of gene functions in perennial woody plants and tree breeding via transgenic technology assisted design.

A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage

Paper mulberry (Broussonetia papyrifera) is a well-known woody tree historically used for Cai Lun papermaking, one of the four great inventions of ancient China. More recently, Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents. In this study, we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches, including Illumina and PacBio sequencing platform as well as Hi-C, optical, and genetic maps. The assembled Paper mulberry genome consists of 386.83 Mb, which is close to the estimated size, and 99.25% (383.93 Mb) of the assembly was assigned to 13 pseudochromosomes. Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine, forage, papermaking, and barkcloth making. We also identified the root-associated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation. Collectively, these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition. Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making, and as forage. These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.

Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits

Transcription factors (TFs) play crucial roles in regulating the production of the components required for photosynthesis; elucidating the mechanisms by which underlying genetic variation in TFs affects complex photosynthesis-related traits may improve our understanding of photosynthesis and identify ways to improve photosynthetic efficiency. Promoter analysis of 96 nuclear-encoded Populus tomentosa Carr. genes within this pathway revealed 47 motifs responsive to light, stress, hormones and organ-specific regulation, as well as 86 TFs that might bind these motifs. Using phenotype-genotype associations, we identified 244 single-nucleotide polymorphisms (SNPs) within 105 genes associated with 12 photosynthesis-related traits. Most (30.33%) of these SNPs were located in intronic regions and these SNPs explained 18.66% of the mean phenotypic variation in the photosynthesis-related traits. Additionally, expression quantitative trait loci (eQTL) mapping identified 216 eQTLs associated with 110 eGenes (genes regulated by eQTLs), explaining 14.12% of the variability of gene expression. The lead SNPs of 12.04% of the eQTLs also contributed to phenotypic variation. Among these, a SNP in zf-Dof 5.6 (G120_9287) affected photosynthesis by modulating the expression of a sub-regulatory network of eight other TFs, which in turn regulate 55 photosynthesis-related genes. Furthermore, epistasis analysis identified a large interacting network representing 732 SNP-SNP pairs, of which 354 were photosynthesis gene-TF pairs, emphasizing the important roles of TFs in affecting photosynthesis-related traits. We combined eQTL and epistasis analysis and found 32 TFs harboring eQTLs being epistatic to their targets (identified by eQTL analysis), of which 15 TFs were also associated with photosynthesis traits. We therefore constructed a schematic model of TFs involved in regulating the photosynthetic light reaction pathway. Taken together, our results provide insight into the genetic regulation of photosynthesis, and may drive progress in the marker-assisted selection of desirable P. tomentosa genotypes with more efficient photosynthesis.

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0.62), suggesting that the interaction of NERDL with its putative target might be involved in wood formation. We conducted association mapping in a natural population of P. tomentosa (435 unrelated individuals) to evaluate genetic variation and the interaction of the lncRNA NERDL with PtoNERD. Using additive and dominant models, we identified 30 SNPs (P < 0.01) associated with five tree growth and wood property traits. Each SNP explained 3.90-8.57% of phenotypic variance, suggesting that NERDL and its putative target play a common role in wood formation. Epistasis analysis uncovered nine SNP-SNP association pairs between NERDL and PtoNERD, with an information gain of -7.55 to 2.16%, reflecting the strong interactions between NERDL and its putative target. This analysis provides a powerful method for deciphering the genetic interactions of lncRNAs with mRNA and dissecting the complex genetic network of quantitative traits in trees.

Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa

Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development. Analysis of nucleotide diversity and LD revealed that PtoPsbW has low single-nucleotide polymorphism (SNP) diversity (π _tot = 0.0048 and θ _w = 0.0050) and relatively low average value of LD (0.1500), indicating that PtoPsbW is conserved due to its indispensable function. Using single-SNP associations in an association population of 435 individuals, we identified five significant associations at the threshold of P ≤ 0.05, explaining 3.28-15.98 % of the phenotypic variation. Haplotype-based association analyses indicated that 13 haplotypes (P ≤ 0.05) from six blocks were associated with photosynthesis, growth, and wood properties. Our work shows that identifying allelic variation and LD can help to decipher the genetic basis of photosynthesis and could potentially be applied for molecular marker-assisted selection in Populus.

Validation of Reference Genes for Gene Expression by Quantitative Real-Time RT-PCR in Stem Segments Spanning Primary to Secondary Growth in Populus tomentosa

The vertical segments of Populus stems are an ideal experimental system for analyzing the gene expression patterns involved in primary and secondary growth during wood formation. Suitable internal control genes are indispensable to quantitative real time PCR (qRT-PCR) assays of gene expression. In this study, the expression stability of eight candidate reference genes was evaluated in a series of vertical stem segments of Populus tomentosa. Analysis through software packages geNorm, NormFinder and BestKeeper showed that genes ribosomal protein (RP) and tubulin beta (TUBB) were the most unstable across the developmental stages of P. tomentosa stems, and the combination of the three reference genes, eukaryotic translation initiation factor 5A (eIF5A), Actin (ACT6) and elongation factor 1-beta (EF1-beta) can provide accurate and reliable normalization of qRT-PCR analysis for target gene expression in stem segments undergoing primary and secondary growth in P. tomentosa. These results provide crucial information for transcriptional analysis in the P. tomentosa stem, which may help to improve the quality of gene expression data in these vertical stem segments, which constitute an excellent plant system for the study of wood formation.

Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus

MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.

Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits

DNA methylation, one of the best-studied types of chromatin modification, suppresses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes. However, the extent and variation of genome-wide DNA methylation in natural populations of plants remain relatively unknown. To investigate variation in DNA methylation and whether this variation associates with important plant traits, including leaf shape and photosynthesis, 20 413 DNA methylation sites were examined in a poplar association population (505 individuals) using methylation-sensitive amplification polymorphism (MSAP) technology. Calculation of epi-population structure and kinships assigned individuals into subsets (K=3), revealing that the natural population of P. simonii consists of three subpopulations. Population epigenetic distance and geographic distance showed a significant correlation (r=0.4688, P<0.001), suggesting that environmental factors may affect epigenetics. Single-marker approaches were also used to identify significant marker-trait associations, which found 1087 high-confidence DNA methylation markers associated with different phenotypic traits explaining ~5-15% of the phenotypic variance. Among these loci, 147 differentially methylated fragments were obtained by sequencing, representing 130 candidate genes. Expression analysis of six candidate genes indicated that these genes might play important roles in leaf development and regulation of photosynthesis. This study provides association analysis to study the effects of DNA methylation on plant development and these data indicate that epigenetics bridges environmental and genetic factors in affecting plant growth and development.

Association genetics in Populus reveals the interactions between Pto-miR160a and its target Pto-ARF16

MicroRNAs (miRNAs) play important roles in the regulation of gene expression in various biological processes. However, the interactions between miRNAs and their targets are largely unknown in plants. As a powerful tool for identification of variation associated with traits, association genetics provides another strategy for exploration of interactions between miRNAs and their targets. Here, we conducted expression analysis and association mapping to evaluate the interaction between Pto-miR160a and its target Pto-ARF16 in Populus tomentosa. By examining the expression patterns of Pto-MIR160a and Pto-ARF16, we identified a significant, negative correlation between their expression levels, indicating that Pto-miR160a may affect the expression of Pto-ARF16. Among the single nucleotide polymorphisms (SNPs) identified in this study, one common SNP in the pre-miRNA region of Pto-miR160a altered its predicted secondary structure while another common SNP in the predicted miRNA target site changed the binding affinity of Pto-miR160a. Linkage disequilibrium (LD) analysis revealed low LD levels of Pto-MIR160a and Pto-ARF16, indicating that they are suitable for candidate gene-based association analysis. Single SNP-based association analysis identified 19 SNPs (false discovery rate Q < 0.05) in Pto-MIR160a and Pto-ARF16 associated with three phenotypic traits. Epistasis analysis further identified 36 SNP-SNP interactions between SNPs in Pto-MIR160a and SNPs in Pto-ARF16, reflecting the possible genetic interaction of Pto-miR160a and Pto-ARF16. Taking these results together, our study identified SNPs in Pto-MIR160a and Pto-ARF16 associated with tree growth and wood properties, providing SNPs with potential applications in marker-assisted breeding and evidence for the genetic interaction of Pto-miR160a and Pto-ARF16.

Transcript abundance patterns of Populus C-repeat binding factor2 orthologs and genetic association of PsCBF2 allelic variation with physiological and biochemical traits in response to abiotic stress

We conducted a candidate gene-based approach to search for genetic associations between 10 SNPs in PsCBF2 and 10 abiotic stress-related traits. The increasing incidence of abiotic stresses and the limitations of available treatments, particularly in trees, highlight the need to improve our understanding of the mechanisms of stress responses. In Arabidopsis, C-repeat binding factor 2 (CBF2) plays an important role in freezing tolerance and cold acclimation. Here, we isolated orthologs of CBF2 from five Populus species. Expression profiling revealed that the Populus CBF2s were preferentially induced in response to cold, with CBF2 transcript abundances ranging from 5.4- to 62-fold higher than in unstressed controls of the corresponding species. In addition, we used a candidate gene-based approach in Populus simonii Carr. to identify single nucleotide polymorphisms (SNPs) in PsCBF2 associated with physiological and biochemical traits. PsCBF2 showed high nucleotide diversity (π T = 0.00549, θ w = 0.01406) and low average linkage disequilibrium (r (2) = 0.061). Association studies in 528 individuals of an association population showed that nine SNPs (false discovery rate Q < 0.10) and one haplotype (Q < 0.10) were significantly associated with differences in four physiological and biochemical traits (P < 0.005), with each marker explaining 1.31-5.87 % of the total variance in the corresponding trait. PsCBF2 transcript levels differed significantly in abundance among genotypic classes for most of the significant SNPs. Identification of these significant associations will help reveal the molecular basis of physiological differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.

Methylation of microRNA genes regulates gene expression in bisexual flower development in andromonoecious poplar

Previous studies showed sex-specific DNA methylation and expression of candidate genes in bisexual flowers of andromonoecious poplar, but the regulatory relationship between methylation and microRNAs (miRNAs) remains unclear. To investigate whether the methylation of miRNA genes regulates gene expression in bisexual flower development, the methylome, microRNA, and transcriptome were examined in female and male flowers of andromonoecious poplar. 27 636 methylated coding genes and 113 methylated miRNA genes were identified. In the coding genes, 64.5% of the methylated reads mapped to the gene body region; by contrast, 60.7% of methylated reads in miRNA genes mainly mapped in the 5' and 3' flanking regions. CHH methylation showed the highest methylation levels and CHG showed the lowest methylation levels. Correlation analysis showed a significant, negative, strand-specific correlation of methylation and miRNA gene expression (r=0.79, P <0.05). The methylated miRNA genes included eight long miRNAs (lmiRNAs) of 24 nucleotides and 11 miRNAs related to flower development. miRNA172b might play an important role in the regulation of bisexual flower development-related gene expression in andromonoecious poplar, via modification of methylation. Gynomonoecious, female, and male poplars were used to validate the methylation patterns of the miRNA172b gene, implying that hyper-methylation in andromonoecious and gynomonoecious poplar might function as an important regulator in bisexual flower development. Our data provide a useful resource for the study of flower development in poplar and improve our understanding of the effect of epigenetic regulation on genes other than protein-coding genes.

Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq

BACKGROUND

Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing to characterize cDNA libraries of mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW), in the industrial tree species Populus tomentosa.

RESULTS

Our sequencing generated 140,978,316 (TW), 128,972,228 (OW), and 117,672,362 (NW) reads, corresponding to 10,127 (TW), 10,129 (OW), and 10,129 (NW) unique genes. Of these, 361 genes were differentially transcribed between TW and OW (log2FC ≥ 1 or ≤ -1, FDR < 0.05), 2,658 differed between OW and NW, and 2,417 differed between TW and NW. This indicates that NW differs significantly from the wood in branches; GO term analysis also indicated that OW experienced more transcriptome remodeling. The differentially expressed genes included 97 encoding transcription factors (TFs), 40 involved in hormone signal transduction, 33 in lignin biosynthesis, 21 in flavonoid biosynthesis, and 43 in cell wall metabolism, including cellulose synthase, sucrose synthase, and COBRA. More than half of the differentially expressed TF showed more than 4-fold lower transcript levels in NW compared with TW or OW, indicating that TF abundances differed dramatically in different wood types and may have important roles in the formation of reaction wood. In addition, transcripts of most of the genes involved in lignin biosynthesis were more abundant in OW compared with TW, consistent with the higher lignin content of OW. We constructed two transcriptomic networks for the regulation of lignin and cellulose biosynthesis, including TFs, based on the co-expression patterns of different genes. Lastly, we used reverse transcription quantitative PCR to validate the differentially expressed genes identified.

CONCLUSIONS

Here, we identified the global patterns and differences in gene expression among TW, OW, and NW, and constructed two transcriptomic regulatory networks involved in TW formation in P. tomentosa. We also identified candidate genes for molecular breeding of wood quality, and provided a starting point to decipher the molecular mechanisms of wood formation in Populus.

Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†

Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq

Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus.

Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa

In plants, the composition and organization of the cell wall determine cell shape, enable cell expansion, and affect the properties of woody tissues. Cellulose synthase (CesA) genes encode the enzymes involved in the synthesis of cellulose which is the major component of plant primary and secondary cell walls. Here, we isolated a full-length PtoCesA3 cDNA from the stem cambium tissue of Populus tomentosa. Tissue-specific expression profiling showed that PtoCesA3 is highly expressed during primary cell wall formation. Estimation of single nucleotide polymorphism (SNP) diversity and linkage disequilibrium (LD) revealed that PtoCesA3 harbors high SNP diversity (π(T) = 0.00995 and θ(w) = 0.0102) and low LD (r(2) ≥ 0.1, within 1,280 bp). Association analysis in a P. tomentosa association population (460 individuals) showed that seven SNPs (false discovery rate Q < 0.10) and five haplotypes (Q < 0.10) were significantly associated with growth and wood properties, explaining 4.09-7.02% of the phenotypic variance. All significant marker-trait associations were validated in at least one of the three smaller subsets (climatic regions) while five associations were repeated in the linkage population. Variation in RNA transcript abundance among genotypic classes of significant loci was also confirmed in the association or linkage populations. Identification of PtoCesA3 and examining its allelic polymorphisms using association studies open an avenue to understand the mechanism of cellulose synthesis in the primary cell wall and its effects on the properties of woody tissues.

Association of allelic variation in PtoXET16A with growth and wood properties in Populus tomentosa

Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θ_w = 0.01392) and low linkage disequilibrium (r² ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%–10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus.

Selection of suitable soybean EF1α genes as internal controls for real-time PCR analyses of tissues during plant development and under stress conditions

KEY MESSAGE

The EF1α genes were stable in the large majority of soybean tissues during development and in specific tissues/conditions under stress. Quantitative real-time PCR (qPCR) analysis strongly depends on transcript normalization using stable reference genes. Reference genes are generally encoded by multigene families and are used in qPCR normalization; however, little effort has been made to verify the stability of different gene members within a family. Here, the expression stability of members of the soybean EF1α gene family (named EF1α 1a1, 1a2, 1b, 2a, 2b and 3) was evaluated in different tissues during plant development and stress exposure (SA and PEG). Four genes (UKN1, SKIP 16, EF1β and MTP) already established as stably expressed were also used in the comparative analysis. GeNorm analyses revealed different combinations of reference genes as stable in soybean tissues during development. The EF1α genes were the most stable in cotyledons (EF1α 3 and EF1α 1b), epicotyls (EF1α 1a2, EF1α 2b and EF1α 1a1), hypocotyls (EF1α 1a1 and EF1β), pods (EF1α 2a and EF1α 2b) and roots (EF1α 2a and UKN1) and less stable in tissues such as trifoliate and unifoliate leaves and germinating seeds. Under stress conditions, no suitable combination including only EF1α genes was found; however, some genes were relatively stable in leaves (EF1α 1a2) and roots (EF1α 1a1) treated with SA as well as in roots treated with PEG (EF1α 2b). EF1α 2a was the most stably expressed EF1α gene in all soybean tissues under stress. Taken together, our data provide guidelines for the selection of EF1α genes for use as reference genes in qPCR expression analyses during plant development and under stress conditions.

Vernalization of Oriental hybrid lily 'Sorbonne': changes in physiology metabolic activity and molecular mechanism

Oriental hybrid lily 'Sorbonne' was used to investigate molecular changes during the storage at 4 °C for dormancy-release besides physiology metabolic activity observations. In physiological mechanism, endogenous abscisic acid (ABA) concentration level of lily bulbs decreased as the cold preservation time increased, and it kept at a stable level after being preserved for 35 days. The level of soluble sugars concentrations also changed during the cold preservation time, and it increased as the cold preservation time raised to 49 days then decreased afterward. On molecule level, a new transcriptome providing comprehensive sequence profiling data of variation during dormancy-release in lily was constructed. 34,367 unigenes expressed differentially between the control and the treatment was analyzed. 14 genes including 8 MADS-box family genes, 4 genes related to plant hormone, and 2 DNA methylation genes were selected to identify the levels of their expression by qRT-PCR. Our results show that the decrease of ABA level during cold storage, as well as changes in plant hormone genes was correlated with dormancy-release; MADS-box family genes VRN2, FLC, FT, SOC1 a, as well as LFY, MIKC and ARF, MYB transcription factor were included in lily floral induction and DNA methylation was correlated to lily vernalization under low temperature. According to the results of the present studies, we predicted that plant hormone pathway, energy metabolic pathway, vernalization pathway, and DNA methylation played important roles during vernalization; these data provided the foundation for future studies of vernalization to induce flowering of lily.

Allelic variation within the S-adenosyl-L-homocysteine hydrolase gene family is associated with wood properties in Chinese white poplar (Populus tomentosa)

Background

S-adenosyl-l-homocysteine hydrolase (SAHH) is the only eukaryotic enzyme capable of S-adenosyl-l-homocysteine (SAH) catabolism for the maintenance of cellular transmethylation potential. Recently, biochemical and genetic studies in herbaceous species have obtained important discoveries in the function of SAHH, and an extensive characterization of SAHH family in even one tree species is essential, but currently lacking.

Results

Here, we first identified the SAHH family from Populus tomentosa using molecular cloning method. Phylogenetic analyses of 28 SAHH proteins from dicotyledons, monocotyledons, and lower plants revealed that the sequences formed two monophyletic groups: the PtrSAHHA with PtoSAHHA and PtrSAHHB with PtoSAHHB. Examination of tissue-specific expression profiles of the PtoSAHH family revealed similar expression patterns; high levels of expression in xylem were found. Nucleotide diversity and linkage disequilibrium (LD) in the PtoSAHH family, sampled from P. tomentosa natural distribution, revealed that PtoSAHH harbors high single-nucleotide polymorphism (SNP) diversity (π=0.01059±0.00122 and 0.00930±0.00079,respectively) and low LD (r² > 0.1, within 800 bp and 2,200 bp, respectively). Using an LD-linkage analysis approach, two noncoding SNPs (PtoSAHHB_1065 and PtoSAHHA_2203) and the corresponding haplotypes were found to significantly associate with α-cellulose content, and a nonsynonymous SNP (PtoSAHHB_410) within the SAHH signature motifs showed significant association with fiber length, with an average of 3.14% of the phenotypic variance explained.

Conclusions

The present study demonstrates that PtoSAHHs were split off prior to the divergence of interspecies in Populus, and SAHHs may play a key role promoting transmethylation reactions in the secondary cell walls biosynthesis in trees. Hence, our findings provide insights into SAHH function and evolution in woody species and also offer a theoretical basis for marker-aided selection breeding to improve the wood quality of Populus.

Effects of high temperature on photosynthesis and related gene expression in poplar

BACKGROUND

High temperature, whether transitory or constant, causes physiological, biochemical and molecular changes that adversely affect tree growth and productivity by reducing photosynthesis. To elucidate the photosynthetic adaption response and examine the recovery capacity of trees under heat stress, we measured gas exchange, chlorophyll fluorescence, electron transport, water use efficiency, and reactive oxygen-producing enzyme activities in heat-stressed plants.

RESULTS

We found that photosynthesis could completely recover after less than six hours of high temperature treatment, which might be a turning point in the photosynthetic response to heat stress. Genome-wide gene expression analysis at six hours of heat stress identified 29,896 differentially expressed genes (15,670 up-regulated and 14,226 down-regulated), including multiple classes of transcription factors. These interact with each other and regulate the expression of photosynthesis-related genes in response to heat stress, controlling carbon fixation and changes in stomatal conductance. Heat stress of more than twelve hours caused reduced electron transport, damaged photosystems, activated the glycolate pathway and caused H2O2 production; as a result, photosynthetic capacity did not recover completely.

CONCLUSIONS

This study provides a systematic physiological and global gene expression profile of the poplar photosynthetic response to heat stress and identifies the main limitations and threshold of photosynthesis under heat stress. It will expand our understanding of plant thermostability and provides a robust dataset for future studies.

Single-nucleotide polymorphisms in PtoCesA7 and their association with growth and wood properties in Populus tomentosa

Cellulose synthase (CesA) genes encode the enzymes that synthesize cellulose; therefore, CesAs play central roles in plant development and affect the yield and quality of wood, essential properties for industrial applications of plant biomass. To effectively manipulate wood biosynthesis in trees and improve wood quality, we thus require a better understanding of the natural variation in CesAs. Association studies have emerged as a powerful tool for identification of variation associated with quantitative traits. Here, we used a candidate gene-based association mapping approach to identify PtoCesA7 allelic variants that associate with growth and wood quality traits in Populus tomentosa. We isolated a full-length PtoCesA7 cDNA and observed high PtoCesA7 expression in xylem, consistent with the xylem-specific expression of CesA7. Nucleotide diversity and linkage disequilibrium (LD) in PtoCesA7, sampled from the P. tomentosa natural distribution, revealed that PtoCesA7 harbors high nucleotide diversity (π(T) = 0.0091) and low LD (r(2) ≥ 0.1, within 800 bp). By association analysis, we identified seven single-nucleotide polymorphisms (SNPs) (false discovery rate Q < 0.10) and 12 haplotypes (Q < 0.10) that associated with growth and wood properties, explaining 3.62-10.59 % of the phenotypic variance. We also validated 9 of the 10 significant marker-trait associations in at least one of three smaller subsets (climatic regions) or in a linkage-mapping population. Thus, our study identified functional PtoCesA7 allelic variants associated with growth and wood quality traits, giving new insights into genes affecting wood quality and quantity. From an applied perspective, the SNPs revealed in this study have potential applications in marker-assisted breeding.

Sexual dimorphic floral development in dioecious plants revealed by transcriptome, phytohormone, and DNA methylation analysis in Populus tomentosa

Dioecious plants have evolved sex-specific floral development mechanisms. However, the precise gene expression patterns in dioecious plant flower development remain unclear. Here, we used andromonoecious poplar, an exceptional model system, to eliminate the confounding effects of genetic background of dioecious plants. Comparative transcriptome and physiological analysis allowed us to characterize sex-specific development of female and male flowers. Transcriptome analysis identified genes significantly differentially expressed between the sexes, including genes related to floral development, phytohormone synthesis and metabolism, and DNA methylation. Correlation analysis revealed a significant correlation between phytohormone signaling and gene expression, identifying specific phytohormone-responsive genes and their cis-regulatory elements. Two genes related to DNA methylation, METHYLTRANSFERASE1 (MET1) and DECREASED DNA METHYLATION 1 (DDM1), which are located in the sex determination region of Chromosome XIX, have differential expression between female and male flowers. A time-course analysis revealed that MET1 and DDM1 expression may produce different DNA methylation levels in female and male flowers. Understanding the interactions of phytohormone signaling, DNA methylation and target gene expression should lead to a better understanding of sexual differences in floral development. Thus, this study identifies a set of candidate genes for further studies of poplar sexual dimorphism and relates sex-specific floral development to physiological and epigenetic changes.

Allelic variation in a cellulose synthase gene (PtoCesA4) associated with growth and wood properties in Populus tomentosa

Lignocellulosic biomass from trees provides a renewable feedstock for biofuels, lumber, pulp, paper, and other uses. Dissecting the mechanism underlying natural variation of the complex traits controlling growth and lignocellulose biosynthesis in trees can enable marker-assisted breeding to improve wood quality and yield. Here, we combined linkage disequilibrium (LD)-based association analysis with traditional linkage analysis to detect the genetic effect of a Populus tomentosa cellulose synthase gene, PtoCesA4. PtoCesA4 is strongly expressed in developing xylem and leaves. Nucleotide diversity and LD in PtoCesA4, sampled from the P. tomentosa natural distribution, revealed that PtoCesA4 harbors high single nucleotide polymorphism (SNP) diversity (πT = 0.0080 and θw = 0.0098) and low LD (r(2) ≥ 0.1, within 1400 bp), demonstrating that the potential of a candidate-gene-based LD approach in understanding the molecular basis underlying quantitative variation in this species. By combining single SNP, multi-SNP, and haplotype-based associations in an association population of 460 individuals with single SNP linkage analysis in a family-based linkage populations (1200 individuals), we identified three strong associations (false discovery rate Q < 0.05) in both populations. These include two nonsynonymous markers (SNP49 associated with α-cellulose content and SNP59 associated with fiber width) and a noncoding marker (SNP18 associated with α-cellulose content). Variation in RNA transcript abundance among genotypic classes of SNP49 was confirmed in these two populations. Therefore, combining different methods allowed us to examine functional PtoCesA4 allelic variation underlying natural variation in complex quantitative traits related to growth and lignocellulosic biosynthesis.

The SUPERMAN gene family in Populus: nucleotide diversity and gene expression in a dioecious plant

SUP gene family expression and regulation patterns reported in dioecious woody plant. Phylogenetic and nucleotide diversity analysis indicated PtoSUP1 is highly conserved and has undergone strong purifying selection. The molecular basis of SUPERMAN (SUP) regulation during floral development in monoecious plants has been extensively studied, but little is known of the SUP gene family in dioecious woody plants. In this study, we systematically examined the diversification of the SUP gene family in Populus, integrating genomic organization, expression, and phylogeny data. SUP family members showed sex-specific expression throughout flower development. Transcript profiling of rare gynomonoecious poplar flowers revealed that a significant reduction in PtoSUP1 mRNA might be important for stamen development in gynomonoecious poplar flowers. We found that the coding regions of Populus SUP genes are very highly conserved and that synonymous sites in exon regions have undergone strong purifying selection during SUP evolution in Populus. These results indicate that SUP genes play an important role in floral development of dioecious plants. Expression analysis of SUP suggested possible regulatory mechanisms for gynomonoecious poplar flower development. These findings provide an important insight into the mechanisms of the evolution of SUP function and may help enable engineered regulation of flower development for breeding improved tree varieties.

Dynamic actin gene family evolution in primates

Actin is one of the most highly conserved proteins and plays crucial roles in many vital cellular functions. In most eukaryotes, it is encoded by a multigene family. Although the actin gene family has been studied a lot, few investigators focus on the comparison of actin gene family in relative species. Here, the purpose of our study is to systematically investigate characteristics and evolutionary pattern of actin gene family in primates. We identified 233 actin genes in human, chimpanzee, gorilla, orangutan, gibbon, rhesus monkey, and marmoset genomes. Phylogenetic analysis showed that actin genes in the seven species could be divided into two major types of clades: orthologous group versus complex group. Codon usages and gene expression patterns of actin gene copies were highly consistent among the groups because of basic functions needed by the organisms, but much diverged within species due to functional diversification. Besides, many great potential pseudogenes were found with incomplete open reading frames due to frameshifts or early stop codons. These results implied that actin gene family in primates went through “birth and death” model of evolution process. Under this model, actin genes experienced strong negative selection and increased the functional complexity by reproducing themselves.

The UDP-glucuronate decarboxylase gene family in Populus: structure, expression, and association genetics

In woody crop plants, the oligosaccharide components of the cell wall are essential for important traits such as bioenergy content, growth, and structural wood properties. UDP-glucuronate decarboxylase (UXS) is a key enzyme in the synthesis of UDP-xylose for the formation of xylans during cell wall biosynthesis. Here, we isolated a multigene family of seven members (PtUXS1-7) encoding UXS from Populus tomentosa, the first investigation of UXSs in a tree species. Analysis of gene structure and phylogeny showed that the PtUXS family could be divided into three groups (PtUXS1/4, PtUXS2/5, and PtUXS3/6/7), consistent with the tissue-specific expression patterns of each PtUXS. We further evaluated the functional consequences of nucleotide polymorphisms in PtUXS1. In total, 243 single-nucleotide polymorphisms (SNPs) were identified, with a high frequency of SNPs (1/18 bp) and nucleotide diversity (π_T = 0.01033, θ_w =0.01280). Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r²<0.1, P<0.001, within 700 bp). SNP- and haplotype-based association analysis showed that nine SNPs (Q <0.10) and 12 haplotypes (P<0.05) were significantly associated with growth and wood property traits in the association population (426 individuals), with 2.70% to 12.37% of the phenotypic variation explained. Four significant single-marker associations (Q <0.10) were validated in a linkage mapping population of 1200 individuals. Also, RNA transcript accumulation varies among genotypic classes of SNP10 was further confirmed in the association population. This is the first comprehensive study of the UXS gene family in woody plants, and lays the foundation for genetic improvements of wood properties and growth in trees using genetic engineering or marker-assisted breeding.

Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa

Chinese white poplar (Populus tomentosa), an important commercial tree species for timber and pulp production in northern China, has been used to examine the individual genes and allelic diversity responsible for complex traits controlling growth and lignocellulosic biosynthesis. Taking advantage of the low degree of linkage disequilibrium (LD) within P. tomentosa association populations, we examined associations between 15 cellulose synthase (PtoCesA) genes and traits including growth and wood properties. Thirty-six novel simple sequence repeat (SSR) markers within PtoCesA genes were detected by re-sequencing and genotyped in an association population (460 individuals). Single-marker and haplotype-based LD approaches were used to identify significant marker-trait associations. Family-based linkage studies and real-time PCR testing were conducted to validate the functional significance of SSR variation. Fifteen single-marker associations from seven PtoCesA genes and nine haplotype-based associations within six genes were identified in the association population (false discovery rate Q < 0.05). Next, five SSR marker-trait associations (Q < 0.05) from four PtoCesA genes were successfully validated in a linkage mapping population (1200 individuals). The results imply a functional role for these genes in mediating wood properties, demonstrating the potential of combining single-marker and haplotype-based LD approaches to detect functional allelic variation underlying quantitative traits in a low-LD population.

Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.)

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.

Sex-specific DNA methylation and gene expression in andromonoecious poplar

The andromonoecious poplar is an exceptional model system for studying sex-specific flower development in dioecious plants. There is increasing evidence that epigenetic regulation, particularly DNA methylation, is an important regulatory factor during flower development. Here, methylation-sensitive amplified polymorphism (MSAP) was used to screen for sex-specific DNA methylation alterations in the andromonoecious poplar. The sequences of 27 sex-specific amplified fragments were obtained from DNA prepared from sex-specific flower tissues. PtGT2, PtPAL3, and PtCER4, which are homologous to MF26, MF29, and MF35, respectively, were cloned as candidate genes. Expression analysis and DNA methylation pattern profiling of the three candidate genes revealed that gene expression upregulation was always associated with gene body methylation. The results suggested that DNA methylation sites have the potential to regulate the genes' transcript levels. These three genes were shown to play important roles during different phases of flower development. This study will help to provide candidates for future experiments aimed at understanding the mechanism, whereby DNA methylation regulates gene expression in poplar.

KEY MESSAGES

We report the first screen for sex-specific DNA methylation alterations in the andromonoecious poplar. 27 sex-specific methylation sites were identified. The gene expression levels and DNA methylation patterns were detected for three candidate genes.

Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis

BACKGROUND

Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.

RESULTS

Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.

CONCLUSION

The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.

Multiple actin isotypes in plants: diverse genes for diverse roles?

Plant actins are encoded by a gene family. Despite the crucial significance of the actin cytoskeleton for plant structure and function, the importance of individual actin isotypes and their specific roles in various plant tissues or even single cells is rather poorly understood. This review summarizes our current knowledge about the plant actin gene family including its evolution, gene and protein structure, and the expression profiles and regulation. Based on this background information, we review mutant and complementation analyses in Arabidopsis to draw an emerging picture of overlapping and specific roles of plant actin isotypes. Finally, we examine hypotheses explaining the mechanisms of isotype-specific functions.