Sex-specific DNA methylation and gene expression in andromonoecious poplar

Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach

Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers' morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.

Methylation related genes affect sex differentiation in dioecious and gynodioecious papaya

Morphological, genic and epigenetic differences often exist in separate sexes of dioecious and trioecious plants. However, the connections and relationships among them in different breeding systems are still unclear. Papaya has three sex types, which is genetically determined and epigenetically regulated, and was chosen as a model to study sex differentiation. Bisulfite sequencing of genomic DNA extracted from early-stage flowers revealed sex-specific genomic methylation landscapes and seasonally methylome reprogramming processes in dioecious and gynodioecious papaya grown in spring and summer. Extensive methylation of sex-determining region (SDR) was the distinguishing epigenetic characteristics of nascent XY sex chromosomes in papaya. Seasonal methylome reprogramming of early-stage flowers in both dioecy and gynodioecy systems were detected, resulting from transcriptional expression pattern alterations of methylation-modification-related and chromatin-remodeling-related genes, particularly from those genes involved in active demethylation. Genes involved in phytohormone signal transduction pathway in male flowers have played an important role in the formation of male-specific characteristics. These findings enhanced the understanding of the genetic and epigenetic contributions to sex differentiation and the complexity of sex chromosome evolution in trioecious plants.

Differential DNA methylation and gene expression during development of reproductive and vegetative organs in Ilex species

Differential epigenetic (DNA cytosine methylation) and gene expression patterns were investigated in reproductive and vegetative organs from Ilex paraguariensis and I. dumosa, at distinct developmental stages. We aimed at contributing towards elucidating major molecular changes underlying the sexual differentiation processes which, in these dioecious species, are completely unknown. Simultaneously, as a first step towards the development of an early sexing system, we searched for promising molecular markers. This was assessed through Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism on cDNA (cDNA-AFLP) techniques, applying discriminant multivariate analyses, and bioinformatic characterization of differential fragments. A significant positive correlation was found between epigenetic and indirect 'genetic' information for both species, indicating influence of the genetic background on the epigenetic variation. Higher epigenetic than genetic diversities were estimated. Our outcomes showed up to 1.86 times more representation of mCG subepiloci than mCCG in all organs sampled. Along the maturing stages of floral buds, the frequency of mCG evidenced an incremental trend, whereas mCCG and unmethylated conditions showed opposite tendencies. Reproductive and vegetative samples tended to cluster apart based on epigenetic patterns; at gene expression level, organs exhibited clear-cut distinctive patterns, nonetheless profiles of young leaves and floral primordia resemble. Epigenetic and expression data allowed discrimination of I. dumosa´s samples according to the gender of the donor; more elusive patterns were observed for I. paraguariensis. In total, 102 differentially methylated and expressed fragments were characterized bioinformatically. Forty-three were annotated in various functional categories; four candidate markers were validated through qPCR, finding statistical differences among organs but not among sexes. The methylation condition of epilocus C13m33 appears as indicative of gender in both species. Thirty-three organ-specific and 34 gender-specific methylated markers were discriminated and deserve further research, particularly those expressed in leaves. Our study contributes concrete candidate markers with potential for practical application.

Long-term study of a subdioecious Populus ×canescens family reveals sex lability of females and reproduction behaviour of cosexual plants

Cosexual Populus ×canescens plants are inconstant females with life course plasticity of sex phenotype and can reproduce by selfing. Populus species are dioecious, but deviations from dioecy are reported in some cases. The objectives of this study were to investigate the phenotypic expression and the inheritance of subdioecy in a Populus ×canescens pedigree. The F₁ progeny was monitored for sex during 14 years. Thirty per cent of individuals expressed deviations from dioecy and long-term plasticity of sex. Some plants started flowering as male, then became cosexual, and finally turned female. Two cosexual individuals were self-pollinated and generated a selfed progeny markedly impaired by inbreeding depression, but able to reproduce by outcrossing. Sex segregation of the F₁ progeny statistically fitted the expected ratio 1:2:1 (female:male:cosexual). By analysis of DNA markers, the cosexual individuals were genetically clustered with the females. The segregation ratio and the genetic profile indicated that cosexual plants were female with altered sex phenotype. Linkage analysis identified a putative sex-determining region with suppressed recombination on chromosome 19 of the male Populus tremula parent. The male sex trait was linked to the pericentromeric region of the P. tremula chromosome 19, whereas the cosexual trait was linked to chromosome 19 of the female Populus alba parent. A genetic model is proposed to explain inheritance and phenotypic expression of sex.

The distribution of epigenetic histone marks differs between the X and Y chromosomes in Silene latifolia

Contrasting patterns of histone modifications between the X and Y chromosome in Silene latifolia show euchromatic histone mark depletion on the Y chromosome and indicate hyperactivation of one X chromosome in females. Silene latifolia (white campion) is a dioecious plant with heteromorphic sex chromosomes (24, XX in females and 24, XY in males), and a genetically degenerated Y chromosome that is 1.4 times larger than the X chromosome. Although the two sex chromosomes differ in their DNA content, information about epigenetic histone marks and evidence of their function are scarce. We performed immunolabeling experiments using antibodies specific for active and suppressive histone modifications as well as pericentromere-specific histone modifications. We show that the Y chromosome is partially depleted of histone modifications important for transcriptionally active chromatin, and carries these marks only in the pseudo-autosomal region, but that it is not enriched for suppressive and pericentromere histone marks. We also show that two of the active marks are specifically enriched in one of the X chromosomes in females and in the X chromosome in males. Our data support recent findings that genetic imprinting mediates dosage compensation of sex chromosomes in S. latifolia.

The poplar pangenome provides insights into the evolutionary history of the genus

The genus Populus comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus Populus, identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism-structural variation (SNP-SV) density and indel-SV density to complement the SNP-indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.

Sex-specific polymorphism of MET1 and ARR17 genes in Populus × sibirica

The genus Populus is an effective model in tree genetics. This genus includes dioecious species and, recently, whole genome resequencing of P. trichocarpa and P. balsamifera enabled the identification of sex-linked regions and sex-associated single nucleotide polymorphisms (SNPs). These results created new opportunities to study sex determination in poplars. In the present work, we performed deep sequencing of genes encoding METHYLTRANSFERASE1 (MET1) and homolog of ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17), which are localized in a sex-linked region of Populus genome and contain a number of sex-associated SNPs. Amplicon libraries for 38 samples of P. × sibirica (19 males and 19 females) were sequenced on MiSeq Illumina (300 nt paired-end reads) and approximately 4000× coverage was obtained for each sample. In total, from 80 to 179 SNPs were detected in poplar individuals for MET1, and from 16 to 49 SNPs were detected for ARR17. We identified 17 sex-specific SNPs (11 in MET1 and 6 in ARR17) - they were present in all males but absent in all females. For identified sex-specific SNP sites, females were homozygous, while males were heterozygous. Moreover, colocation of sex-specific SNPs confirming the XY sex-determination system of poplars was revealed: in one allelic variant, males had the same nucleotides as females, while in the other, sex-specific SNPs were present. Based on the data obtained, we developed and successfully applied a high-resolution melting-based approach for sex identification in poplars. The developed molecular markers are useful for distinguishing between male and female poplars in scientific research and can also be applied to select male-only genotypes for use in city landscaping and production of paper, pulp, and biofuel.

Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression

The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7-52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression.

The association of changes in DNA methylation with temperature-dependent sex determination in cucumber

Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substantial and global impact on transposable element (TE)-related small RNA-directed DNA methylation (RdDM) mechanisms, resulting in large amounts of CHH-type cytosine demethylation. In the cucumber genome, TEs are common in regions near genes that are also subject to DNA demethylation. TE-gene interactions showed very strong reactions to LT treatment, as nearly 80% of the differentially methylated regions (DMRs) were distributed in genic regions. Demethylation near genes led to the co-ordinated expression of genes and TEs. More importantly, genome-wide de novo methylation changes also resulted in small amounts of CG- and CHG-type DMRs. Methylation changes in CG-DMRs located <600 bp from the transcription start and end sites (TSSs/TESs) negatively correlated with transcription changes in differentially expressed genes (DEGs), probably indicating epiregulation. Ethylene is called the 'sex hormone' of cucumbers. We observed the up-regulation of ethylene biosynthesis-related CsACO3 and the down-regulation of an Arabidopsis RAP2.4-like ethylene-responsive (AP2/ERF) transcription factor, demonstrating the inferred epiregulation. Our study characterized the response of the apex methylome to LT and predicted the possible epiregulation of temperature-dependent sex determination (TSD) in cucumber.

Transcriptome Profile Analysis from Different Sex Types of Ginkgo biloba L

In plants, sex determination is a comprehensive process of correlated events, which involves genes that are differentially and/or specifically expressed in distinct developmental phases. Exploring gene expression profiles from different sex types will contribute to fully understanding sex determination in plants. In this study, we conducted RNA-sequencing of female and male buds (FB and MB) as well as ovulate strobilus and staminate strobilus (OS and SS) of Ginkgo biloba to gain insights into the genes potentially related to sex determination in this species. Approximately 60 Gb of clean reads were obtained from eight cDNA libraries. De novo assembly of the clean reads generated 108,307 unigenes with an average length of 796 bp. Among these unigenes, 51,953 (47.97%) had at least one significant match with a gene sequence in the public databases searched. A total of 4709 and 9802 differentially expressed genes (DEGs) were identified in MB vs. FB and SS vs. OS, respectively. Genes involved in plant hormone signal and transduction as well as those encoding DNA methyltransferase were found to be differentially expressed between different sex types. Their potential roles in sex determination of G. biloba were discussed. Pistil-related genes were expressed in male buds while anther-specific genes were identified in female buds, suggesting that dioecism in G. biloba was resulted from the selective arrest of reproductive primordia. High correlation of expression level was found between the RNA-Seq and quantitative real-time PCR results. The transcriptome resources that we generated allowed us to characterize gene expression profiles and examine differential expression profiles, which provided foundations for identifying functional genes associated with sex determination in G. biloba.

Differentially methylated genomic fragments related with sexual dimorphism of rice pests, Sogatella furcifera

Sogatella furcifera (Hovarth) is a major rice pest with sexual dimorphism. The objective of the current research was to monitor differentially cytosine methylation at CCGG sequences in male and female adults of S. furcifera to determine the association between gene methylation and sexual phenotypes using methylation-sensitive representational difference analysis. After the second subtractive hybridization, four differentially methylated DNA bands were obtained and sequenced. Ten different fragments were found. One fragment from the positive hybridization was 120 bp, and highly similar to the tramtrack genes from Nasonia vitripennis. Another fragment from the reverse hybridization was 414 bp, and homologous to the 28S rRNA gene of S. furcifera with a similarity rate as high as 99%. We also discussed how DNA methylation of tramtrack and 28S rRNA genes produced effects on sexual differentiation and development. These results provide potential evidence that DNA methylation of some genes may be related to sexual phenotype variations in S. furcifera and will facilitate future studies on the epigenetic mechanisms of insect sexual dimorphism.

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)

Sex chromosomes have evolved independently in phylogenetically diverse flowering plant lineages. The genes governing sex determination in dioecious species remain unknown, but theory predicts that the linkage of genes influencing male and female function will spur the origin and early evolution of sex chromosomes. For example, in an XY system, the origin of an active Y may be spurred by the linkage of female suppressing and male promoting genes. Garden asparagus (Asparagus officinalis) serves as a model for plant sex chromosome evolution, given that it has recently evolved an XX/XY sex chromosome system. In order to elucidate the molecular basis of gender differences and sex determination, we used RNA-sequencing (RNA-Seq) to identify differentially expressed genes between female (XX), male (XY) and supermale (YY) individuals. We identified 570 differentially expressed genes, and showed that significantly more genes exhibited male-biased than female-biased expression in garden asparagus. In the context of anther development, we identified genes involved in pollen microspore and tapetum development that were specifically expressed in males and supermales. Comparative analysis of genes in the Arabidopsis thaliana, Zea mays and Oryza sativa anther development pathways shows that anther sterility in females probably occurs through interruption of tapetum development before microspore meiosis.

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.

Epi-fingerprinting and epi-interventions for improved crop production and food quality

Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.

Biochemical, physiological and gene expression analysis reveals sex-specific differences in Populus tomentosa floral development

The productivity, distribution and population structure of poplar are affected by temperature transitions. Poplar floral buds develop in a fluctuating environment and the molecular basis of temperature-dependent flowering regulation has been extensively studied, but little is known about how sex-specific floral bud development responds to temperature transitions. Here, morphological observations indicated that floral bud growth rates were affected by maximum and minimum air temperature at the later stages of enlargement (stage 4) and later stage of dormancy (stage 8), respectively. We investigated the physiological, biochemical and gene expression changes in floral development and in response to temperature treatment (heat and chilling stress). Male floral buds showed more adverse effects than female floral buds under temperature treatment. Temperature treatment experiments revealed that temperature treatment significantly increased catalase, peroxidase, superoxide dismutase activities and transcription of related genes in female floral buds, whereas malondialdehyde (MDA) significantly increased only in males. Soluble sugars and protein increased both in female and male floral buds but were higher in males. Temperature treatment also caused significant increases in Ca(2+) content and transcription of genes related to calcium transport in female flowers. These results revealed sex-specific floral developmental responses to seasonal temperature transitions and suggest that in Populus tomentosa, female floral buds possess better mechanisms for environment adaptation than do males.

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.

Transcriptome profiling reveals differential transcript abundance in response to chilling stress in Populus simonii

We report global gene expression patterns of poplar in response to chilling stress. A total of 1,085 significantly differentially expressed genes, involved in photosynthesis, signal transduction, and regulation of transcription, were identified. To understand the gene network underlying the response to chilling stress in the poplar, Populus simonii, we determined the genome transcript expression profile using an Affymetrix GeneChip with 56,000 genes. Our results revealed 11,626 cold-responsive genes, with 5,267 upregulated and 6,359 downregulated. In terms of biological processes, gene ontology (GO) analysis indicated that cold-induced genes were enriched in response to temperature stimulus, reactive oxygen species, and hormone stimulus. GO terms including cellular nitrogen compound metabolic processes, photosynthesis, and generation of precursor metabolites and energy were enriched in the cold-repressed genes. The functional annotation of differentially expressed genes revealed genes involved in photosynthesis, calcium/calmodulin-mediated signal transduction, abscisic acid (ABA) homeostasis and transport, and antioxidant defense systems. Gene expression analysis showed that the majority of genes involved in photosynthesis were repressed, but the THF1 gene was induced, suggesting that it may play an important role in the production of vesicles for leaf development under low-temperature conditions. Several genes involved in calcium/calmodulin-mediated signal transduction, ABA homeostasis and transport, and antioxidant defense systems were significantly induced under chilling stress, suggesting that they may act as positive regulators in the enhanced low-temperature tolerance of poplar. Several transcription factors had divergent expression patterns, suggesting they have variable functional responses to abiotic stress. This profile of global gene expression patterns during chilling stress will be valuable for future studies on the molecular mechanisms of chilling tolerance in woody plants.

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.

Sexual dimorphism floral microRNA profiling and target gene expression in andromonoecious poplar (Populus tomentosa)

Although the molecular basis of poplar sex-specific flower development remains largely unknown, increasing evidence indicates an essential role for microRNAs (miRNAs). The specific miRNA types and precise miRNA 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. This system, combined with high-throughput sequencing and computational analysis, allowed us to characterize sex-specific miRNAomes from female and male flowers. Comparative miRNAome analysis combined with quantitative real-time PCR revealed the expression patterns of 27 miRNAs in poplar flower and showed that the targets of these miRNAs are involved in flower organogenesis, Ca(2+) transport, phytohormone synthesis and metabolism, and DNA methylation. This paper describes a complex regulatory network consisting of these miRNAs expressed in sex-specific flower development in a dioecious plant. The conserved and novel miRNA locations were annotated in the Populus trichocarpa genome. Among these, miRNA Pto-F70 and 4 targets are located in the sex-determination regions of chromosome XIX. Furthermore, two novel miRNAs, Pto-F47 and Pto-F68, were shown for the first time to be regulatory factors in phytohormone interactions. To our knowledge, this report is the first systematic investigation of sex-specific flower-related miRNAs and their targets in poplar, and it deepens our understanding of the important regulatory functions of miRNAs in female and male flower development in this dioecious plant.

The low fertility of Chinese white poplar: dynamic changes in anatomical structure, endogenous hormone concentrations, and key gene expression in the reproduction of a naturally occurring hybrid

KEY MESSAGE : We report that low fertility during intraspecific hybridization in Chinese white poplar was caused by prefertilization barriers, reduced ovules, and embryonic abortion. Hormone concentrations and gene expression patterns were also evaluated during the fertilization process. Hybrid vigor holds tremendous potential for yield increases and trait improvement; however, some hybridization combinations within Populus show very low fertility. To explore the causes of this low fertility in intraspecific hybridization of Chinese white poplar, we examined anatomical structure, hormone levels and expression of key genes in two unique crossing combinations of Populus × tomentosa "Pt02" × P. × tomentosa "LM50", and (P. × tomentosa × P. alba cv. bolleana "Ptb") × P. × tomentosa "LM50". The seed set potential in the intraspecific hybridization P. × tomentosa "Pt02" × P. × tomentosa "LM50" was quite low, which was likely caused by prefertilization barriers, reduced ovule numbers, and embryonic abortion in ovaries. During intraspecific hybridization, we found reduced indoleacetic acid (IAA) in pistils, which may cause pollen tube deformations and increased IAA in heart-stage embryos, which may affect embryo development. Gibberellin A3 (GA3) decreased from the zygote dormancy stage to globular-stage embryos, which may be caused by failure of fertilization in specific embryos. The maximum zeatin (Z) concentration was found in heart-stage embryos, but Z concentrations quickly decreased, which may affect endosperm development. Increasing concentrations of abscisic acid (ABA) during zygote dormancy and eight-cell proembryo stages likely induced abscission of the infructescence. High ABA concentrations also regulated embryo maturity. Measurement of genes expression showed that high expression of SRK and/or SLG may result in rejection of pollen by stigmatic papillae through a mechanism, reminiscent of self-incompatibility. Also, low expression of LEC1 and FUS3 may cause embryonic abortion. Identification and eventual bypassing of these barriers may allow future genetic improvement of this key woody crop species.