Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays

<p>Abstract</p> <p>Background</p> <p>Wood is the end product of secondary vascular system development, which begins from the cambium. The wood formation process includes four major stages: cell expansion, secondary wall biosynthesis, lignification, and programmed cell death. Transcriptional profiling is a rapid way to screen for genes involved in these stages and their transitions, providing the basis for understanding the molecular mechanisms that control this process.</p> <p>Results</p> <p>In this study, cDNA microarrays were prepared from a subtracted cDNA library (cambium zone <it>versus </it>leaf) of Chinese white poplar (<it>Populus tomentosa </it>Carr.) and employed to analyze the transcriptional profiles during the regeneration of the secondary vascular system, a platform established in our previous study. Two hundred and seven genes showed transcript-level differences at the different regeneration stages. Dramatic transcriptional changes were observed at cambium initiation, cambium formation and differentiation, and xylem development, suggesting that these up- or downregulated genes play important roles in these stage transitions. Transcription factors such as AUX/IAA and PINHEAD, which were previously shown to be involved in meristem and vascular tissue differentiation, were strongly transcribed at the stages when cambial cells were initiated and underwent differentiation, whereas genes encoding MYB proteins and several small heat shock proteins were strongly transcribed at the stage when xylem development begins.</p> <p>Conclusion</p> <p>Employing this method, we observed dynamic changes in gene transcript levels at the key stages, including cambium initiation, cambium formation and differentiation, and xylem development, suggesting that these up- or downregulated genes are strongly involved in these stage transitions. Further studies of these genes could help elucidate their roles in wood formation.</p

A Comparison of Hierarchical and Non-Hierarchical Bayesian Approaches for Fitting Allometric Larch (Larix.spp.) Biomass Equations

Accurate biomass estimations are important for assessing and monitoring forest carbon storage. Bayesian theory has been widely applied to tree biomass models. Recently, a hierarchical Bayesian approach has received increasing attention for improving biomass models. In this study, tree biomass data were obtained by sampling 310 trees from 209 permanent sample plots from larch plantations in six regions across China. Non-hierarchical and hierarchical Bayesian approaches were used to model allometric biomass equations. We found that the total, root, stem wood, stem bark, branch and foliage biomass model relationships were statistically significant (p-values \u3c 0.001) for both the non-hierarchical and hierarchical Bayesian approaches, but the hierarchical Bayesian approach increased the goodness-of-fit statistics over the non-hierarchical Bayesian approach. The R2 values of the hierarchical approach were higher than those of the non-hierarchical approach by 0.008, 0.018, 0.020, 0.003, 0.088 and 0.116 for the total tree, root, stem wood, stem bark, branch and foliage models, respectively. The hierarchical Bayesian approach significantly improved the accuracy of the biomass model (except for the stem bark) and can reflect regional differences by using random parameters to improve the regional scale model accuracy

Isolation and characterization of an Aux/IAA gene (LaIAA2) from Larix

The phytohormone auxin controls many aspects of plant development. Auxin/indole-3-acetic acid (Aux/IAA)  transcriptional factors are key regulators of auxin responses in plants. To investigate the effects of auxin on  gene expression during the rooting process of Larix cuttings, a subtractive cDNA library was constructed and  272 UniEST were obtained by using suppression subtractive hybridization (SSH). Based on a fragment of 272  UniEST, the full-length cDNA of LaIAA2, an Aux /IAA gene from Larix was isolated. Then, the response  expression of LaIAA2 to auxin was determined by treating with different sources and concentration of auxin and cycloheximide and the expression patterns of LaIAA2 were examined in different tissues. The results show  that LaIAA2 appears to be the first response gene of auxin and LaIAA2 gene was involved in the root  development and auxin signaling. The express pattern of LaIAA2 gene indicated that it might play a central role in root development, specially regulated lateral and adventitious root production.Key words: Aux/IAA gene family, auxin, LaIAA2, Lari

Draft genome sequence of the mulberry tree Morus notabilis

Human utilization of the mulberry–silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating the species’ spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant–herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants

Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)

While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of Larix kaempferi, a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old L. kaempferi trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from Larix embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of Larix

Effects of the Most Appropriate Proportion of Phytohormones on Tree-Ring Growth in Clones of Hybrid Larch

The increase in the atmospheric carbon dioxide concentration promotes its accumulation in trees by regulating the synthesis and transportation genes for endogenous hormones, such as IAA and GA, which are key factors in regulating various life activities, including growth rings. To explore the impact of changes in endogenous hormone levels such as IAA and GA on the growth of tree rings, and to provide a basis for improving the management of hybrid larch clonal forests, we investigated the effects of exogenous indole-3-acetic acid (IAA), gibberellic acid 3 (GA3), and their combination on tree-ring growth in hybrid larch. IAA, GA3, and a combination treatment were sprayed on the leaves of one clone of a hybrid larch seedling every three days. Small blocks were collected at the base stems for sequential anatomical observations. The phytohormone type, instead of the concentration, had a more significant effect on wood formation. Specifically, IAA treatment at 300 mg L−1 significantly increased latewood (LW) layers until 90 days after treatment (DAT). The 500 mg L−1 treatment significantly increased the wall radial thickness (WRT) of latewood (LW) cells. GA3 treatment at 100 mg L−1 significantly decreased the layers and width of total wood (TW), LW, and earlywood (EW). The 300 mg L−1 treatment significantly increased the WRT of EW. The IAA 100 mg L−1 + GA3 100 mg L−1 combination treatment significantly increased the layers and width of TW and LW by inducing cambium activity and increasing the rate of wood cell development. The WRT and lumen radial diameter (LRD) of EW or LW in this treatment were similar to those observed with the corresponding single phytohormone treatment. These results indicate that combination treatment at 100 mg L−1 + 100 mg L−1 was a better way to promote tree-ring growth. Our study suggests that changes in phytohormone levels and ratios are important factors that affect tree-ring formation. Hormone levels and ratios should be regarded as important indicators to guide the improvement of management practices in hybrid larch clonal plantations

Responses of the Crown Shape of <i>Larix kaempferi</i> Plantations to Site Index in Subtropical Areas of China

This study addresses how site index may affect crown shape by developing a crown shape regression model for the planted L. kaempferi at high altitudes in the subtropical climate of China. A total of 9241 branches from 78 trees, including 39 dominant trees and 39 intermediate trees, were measured in Hubei Province, southern China. The branch characteristics, including branch length, branch angle, and branch chord length of all living branches, were measured by felling trees. The models that showed good performance in crown shape modeling were used and compared in the present study. The goodness of fit statistics and stability of parameter estimation of the modified Kozak equation were better than those of the segmented polynomial equation. A nonlinear mixed-effect crown shape model was developed based on the modified Kozak equation. In addition to the tree level variables of diameter at the breast height (DBH), crown ratio (CR), and tree height-to-DBH ratio, an attempt was made to incorporate the site index into the crown shape model for the planted L. kaempferi. However, the site index was not a significant variable in the crown shape model. The purpose of our study was to lay the foundation for further study of the growth of the trees and the effects of crown morphology on stem growth in the future

Age-related trends in genetic parameters for wood properties in Larix kaempferi clones and implications for early selection

Wood properties are important traits that determine quality of structural wood. With the aim of performing efficient early selection for wood properties, we investigated genetic variation in 20 Larix kaempferi clones aged from 4 to 15 years for four quality traits: wood density, wall thickness to lumen area, microfibrillar angle (MFA) and modulus of elasticity (MOE). We observed that age-related trends in overall means varied for different traits: MFA decreased with the age, while the others generally increased with the age. Phenotypic variance always showed significant differences from the age of 8 years onward, with CVG ranging from 4% to 25%. Also, clonal repeatability increased steadily until 9 years old and then kept medium or higher intensity (0.4&#8211;0.8). After the age of 6, genetic correlations were generally higher than phenotypic correlations. Estimates of early selection efficiency suggested that the optimal selection age for wood density was at age 5&#8211;6 years, while it was 9&#8211;10 years for the other traits. In combination with previous results, we proposed a comprehensive early selection strategy for larch clonal breeding that involved selection based on nursery rooting ability, phenology, growth traits, and wood properties