Spatiotemporal miRNA and transcriptomic network dynamically regulate the developmental and senescence processes of poplar leaves

Poplar is an important afforestation and urban greening species.Poplar leaf development occurs in stages,from young to mature and then from mature to senescent;these are accompanied by various phenotypic and physiological changes.However,the associated transcriptional regulatory network is relatively unexplored.We first used principal component analysis to classify poplar leaves at different leaf positions into two stages:developmental maturity(the stage of maximum photosynthetic capacity);and the stage when photosynthetic capacity started to decline and gradually changed to senescence.The two stages were then further subdivided into five intervals by gene expression clustering analysis:young leaves,the period of cell genesis and functional differentiation(L1);young leaves,the period of development and initial formation of photosynthetic capacity(L3-L7);the period of maximum photosynthetic capacity of functional leaves(L9-L13);the period of decreasing photosynthetic capacity of functional leaves(L15-L27);and the period of senescent leaves(L29).Using a weighted co-expression gene network analysis of regulatory genes,high-resolution spatiotemporal transcriptional regulatory networks were constructed to reveal the core regulators that regulate leaf development.Spatiotemporal transcriptome data of poplar leaves revealed dynamic changes in genes and miRNAs during leaf development and identified several core regulators of leaf development,such as GRF5 and MYB5.This in-depth analysis of transcriptional regulation during leaf development provides a theoretical basis for exploring the biological basis of the transcriptional regulation of leaf development and the molecular design of breeding for delaying leaf senescence.

Transcriptome Analysis of Auxin Drives Cone Size Regulation in Fokienia hodginsii

As the reproductive organ of the endangered species Fokienia hodginsii,the size of the cones is a constraint on the reproductive renewal of the population.In this study,the molecular basis of the influence of cone size on F.hodginsii was elucidated by comparing the phenotype,biochemistry,and transcriptome of two cultivars of F.hodginsii(‘FJ431’and‘FJ415’).The two cultivars differed significantly in cone size,with FJ431 having a significantly larger cone size and weight than FJ415,1.32 and 1.90 times that of FJ415,respectively.RNA-Seq analysis of both cultivars retrieved 75,940 genes whose approximate functions were classified as the pathway of response to endogenous stimulus and response to hormone and showed significant differences in the auxin-activated signaling pathway,particularly the MAPK signaling pathway-plant.Furthermore,the endogenous IAA content was significantly higher in FJ431 than in FJ415,and 1.58 and 1.29 times more IAA was present in immature and mature cones,respectively.Moreover,exogenous IAA treatment significantly induced the expression of the MAPK pathway-related gene TRINITY_DN10564_c0_g1 and significantly inhibited the expression of the MAPK pathwayrelated gene TRINITY_DN17056_c0_g1.Our work suggests that IAA can affect the cone size of F.hodginsii,most probably through the MAPK pathway.This has high theoretical and practical significance for the improvement of genetic breeding and the further cultivation of quality germplasm resources of F.hodginsii.

Variation in needle and cone traits in natural populations of Pinus yunnanensis

Pinus yunnanensis Franch. is a major component of coniferous forests in southwestern China. Little is known about its intraspecific variation. Morphological variations in needle and cone traits of P. yunnanensis were analyzed to quantify variability among and within natural populations. Seven traits were measured on 10 needles collected from 30 trees in each of the 18 sampled populations of P. yunna- nensis. Four cone traits were measured in 221 individual trees from nine populations. The results showed that there were significant differences （p 〈 0.01） both among popu- lations and within populations in each needle and cone trait. The proportion of phenotypic variation of nearly all needle and cone traits was over 50 % within populations, which showed trees within populations accounted for a majority of the total variation. The needle traits showed higher vari- ability within population than cone traits. Variability in theneedle traits was correlated with geo-climatic parameters （longitude, latitude, altitude, temperature, and precipitation）. Needle length and the ratio of needle length to fascicle sheath length showed clinal variation in response to latitudinal and altitudinal gradients. A hierarchical classification of all populations based on needle traits led to the formation of four major groups. The findings provide important genetic information for the evaluation of variation. Moreover, it will assist in management of genetic diversity of P. yunnanensis.

High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis

We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species,Eucommia ulmoides,which is known for its rubber biosynthesis and medicinal applications.The assembly was obtained by applying PacBio and Hi–C technologies to a haploid that we specifically generated.Compared to the initial genome release,this one has significantly improved assembly quality.The scaffold N50(53.15 MB)increased 28-fold,and the repetitive sequence content(520 Mb)increased by 158.24 Mb,whereas the number of gaps decreased from 104,772 to 128.A total of 92.87%of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes.A new whole-genome duplication event was superimposed on the earlierγpaleohexaploidization event,and the expansion of long terminal repeats contributed greatly to the evolution of the genome.The more primitive rubber biosynthesis of this species,as opposed to that in Hevea brasiliensis,relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate,as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels.Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark.This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution,gene mapping,epigenetic analysis and functional genomics but also efforts to improve E.ulmoides for industrial and medical uses through genetic engineering.

The diverse roles of cytokinins in regulating leaf development

Leaves provide energy for plants,and consequently for animals,through photosynthesis.Despite their important functions,plant leaf developmental processes and their underlying mechanisms have not been well characterized.Here,we provide a holistic description of leaf developmental processes that is centered on cytokinins and their signaling functions.Cytokinins maintain the growth potential(pluripotency)of shoot apical meristems,which provide stem cells for the generation of leaf primordia during the initial stage of leaf formation;cytokinins and auxins,as well as their interaction,determine the phyllotaxis pattern.The activities of cytokinins in various regions of the leaf,especially at the margins,collectively determine the final leaf morphology(e.g.,simple or compound).The area of a leaf is generally determined by the number and size of the cells in the leaf.Cytokinins promote cell division and increase cell expansion during the proliferation and expansion stages of leaf cell development,respectively.During leaf senescence,cytokinins reduce sugar accumulation,increase chlorophyll synthesis,and prolong the leaf photosynthetic period.We also briefly describe the roles of other hormones,including auxin and ethylene,during the whole leaf developmental process.In this study,we review the regulatory roles of cytokinins in various leaf developmental stages,with a focus on cytokinin metabolism and signal transduction processes,in order to shed light on the molecular mechanisms underlying leaf development.

Comparative microsporogenesis and flower development in Eucalyptus urophylla×E.grandis

Microsporogenesis and flower development in Eucalyptus urophylla × E. grandis were examined using chromosome tableting to provide a method to predict the meiotic stages in this species. Although microsporogenesis was normal, cytokinesis during meiosis of pollen mother cells occurred simultaneously, with strong asynchronism observed in the two different lengths of stamens in a flower bud. In a single flower, the developmental period of microsporogenesis in anthers on the longer stamens was always ahead of those on the shorter stamens. Flower development was also asynchronous at different locations on a branch. Flower buds on the upper side of the branch were larger in diameter than those on the lower side. In addition, a correlation was observed between microsporogenesis development and flower bud diameter growth. The pachy- tene stage was first observed when the diameter of the flower buds increased to 3.0 mm, and the majority of the meiotic stages were observed when bud diameters ranged from 3.5 to 5.0 mm. This study showed that the developmental stages of microsporogenesis in Eucalyptus urophylla × E. grandis could be distinguished readily, which may be applicable to future breeding studies.

Breeding polyploid Populus:progress and perspective

Populus is a genus of 25−30 species of deciduous flowering plants in the family Salicaceae,which are primarily planted in short-rotation planations for producing timber,pulpwood,wooden products as well as bioenergy feedstock;they are also widely planted in agricultural fields and along roadsides as shelter forest belts for windbreak,decoration,and reduction of pollutants and noise.Moreover,their fast-growth and good adaptation to marginal lands enable them to provide some critical ecosystem services at various phytoremediation sites for land restoration and reclaimation.Thanks to their important roles,breeding for fast growing poplar trees has been one of the most important objectives for nearly a century.One of the most demonstrated,documented achievements in this aspect is polyploid breeding,especially triploid breeding.This paper critically reviews the various techniques used in inducing triploid plants,including natural 2n formation,artificial induction of 2n male and female gemmates through chemical or physical treatments,trait characterization of the triploid and tetraploid breeding populations,unveiling the molecular mechanisms underpinning the significantly improved traits,and identification and selection of the best triploid progenies.This review also recapitulated the challenges and strategies facing the future of triploid breeding in Populus,including amelioration of 2n gamete induction techniques and efficiency,selection of the best parents and identification of the best progrenies,utilization of the huge amount of genomic,transcriptomic,proteomic,metabolomic,and other omics data for selecting parents for improving target traits.

Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution

in this report, we compared transcriptomic differ- ences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids （SDR-H） and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expres- sion between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes （DEGs） between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigorallotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.