Spectral Pre-Processing and Multivariate Calibration Methods for the Prediction of Wood Density in Chinese White Poplar by Visible and Near Infrared Spectroscopy

Wood density is a key indicator for tree functionality and end utilization. Appropriate chemometric methods play an important role in the successful prediction of wood density by visible and near infrared (Vis-NIR) spectroscopy. The objective of this study was to select appropriate pre-processing, variable selection and multivariate calibration techniques to improve the prediction accuracy of density in Chinese white poplar (Populus tomentosa carriere) wood. The Vis-NIR spectra were de-noised using four methods (lifting wavelet transform, LWT; wavelet transform, WT; multiplicative scatter correction, MSC; and standard normal variate, SNV), and four variable selection techniques, including successive projections algorithm (SPA), uninformative variables elimination (UVE), competitive adaptive reweighted sampling (CARS) and iteratively retains informative variables (IRIV), were compared to simplify the dimension of the high-dimensional spectral matrix. The non-linear models of generalized regression neural network (GRNN) and support vector machine (SVM) were performed using these selected variables. The results showed that the best prediction was obtained by GRNN models combined with the LWT and CARS method for Chinese white poplar wood density (Rp2 = 0.870; RMSEP = 13 Kg/m3; RPDp = 2.774).

Effect of Initial Planting Density on Growth Traits and Wood Properties of Triploid Chinese White Poplar (Populus tometosa) Plantation

Planting density primarily affects the yield and wood quality of plantations. There are multiple reports on the effects of planting density on growth traits and wood properties in young triploid Chinese white poplar (Populus tomentosa) plantations. Nevertheless, assessment of the effects of initial planting density is lacking for plantations older than ten years. Here, an 11-year-old plant density trial (2490, 1665, 1110, 832, 624, 499, and 416 trees/hm2) established with four hybrid clones (S86, B301, B331 and 1316) in northern China was used to determine the effect of initial planting density on growth traits (diameter at breast height (DBH), tree height (H), stem volume (SV) and stand wood volume (SWV)), basic wood density (BWD), and fiber properties (fiber length (FL), fiber width (FW), and the ratio of fiber length to width (FL/FW)). A total of 84 trees from four clones were sampled. In this study, the initial planting density had a highly significant effect on growth traits (p < 0.001) and had a moderate effect on FL. Overall, the reduction in initial planting density led to the increase in DBH, H, SV, and FL/FW. Triploid hybrid clones planted at 416 trees/hm2 had the largest DBH, H, SV, FL/FW and the smallest SWV and FW. Clonal effects were also significant (p < 0.05) for all studied traits except for FL. Clone S86 had a higher growth rate and the largest BWD and FW. Clones–initial planting densities interaction was insignificant for all growth traits and wood properties. A weak and positive estimated correlation between BWD and growth traits (H, SV, SWV) within each planting density was seen. Our results demonstrate that an appropriate reduction in initial density in triploid Chinese white poplar plantations with long rotation is a suitable strategy to promote tree growth and retain excellent wood processing characteristics.

Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri

Type 2C protein phosphatase (PP2C) plays an essential role in abscisic acid (ABA) signaling transduction processes. In the current study, we identify 719 putative PP2C genes in eight Rosaceae species, including 118 in Chinese white pear, 110 in European pear, 73 in Japanese apricot, 128 in apple, 74 in peach, 65 in strawberry, 78 in sweet cherry, and 73 in black raspberry. Further, the phylogenetic analysis categorized PbrPP2C genes of Chinese white pear into twelve subgroups based on the phylogenic analysis. We observed that whole-genome duplication (WGD) and dispersed gene duplication (DSD) have expanded the Rosaceae PP2C family despite simultaneous purifying selection. Expression analysis finds that PbrPP2C genes have organ-specific functions. QRT-PCR validation of nine PbrPP2C genes of subgroup A indicates a role in ABA-mediated response to abiotic stress. Finally, we find that five PbrPP2C genes of subgroup A function in the nucleus. In summary, our research suggests that the PP2C family functions to modulate ABA signals and responds to abiotic stress.

Phylogeny of Pyrus and their relationships inferred from sequences of nuclear NIA-i3 intron and chloroplast ndhC-trnV and trnR-atpA

Background: Pear (Pyrus L.) belongs to subtribe Malinae, tribe Maleae, family Rosaceae. According to the geography distribution, it could be divided into Oriental pear and Occidental pear. Though the phylogeny of Pyrus was complicate, previous study referring to morphology, nuclear genes and chloroplast genes made the relationships clear gradually. However, they had lower sequence divergence and less information, therefore it hardly solved the phylogeny of Pyrus. Results: A total of 100 accessions from Oriental and Occidental pears were used to elucidate the phylogeny of Pyrus by one nuclear NIA-i3 intron and two chloroplast regions (ndhC-trnV and trnR-atpA) with higher polymorphism. The Neighbor-Net phylogenetic network indicated that the phylogenetic relationships were complicate based on ndhC-trnV and trnR-atpA. Oriental pear and Occidental pear were separated in the tree of NIA-i3, P. betulaforlia, P. pashia (except P. pashia ‘P10-3’_1 and P. pashia ‘P23-4’_1) were monophyly; several P. ussuriensis were closely related with P. xerophila. However, the phylogenetic relationships of Chinese White Pear, P. pyrifolia and some P. ussuriensis still could not be well solved; West Asian species and European species were mingled together. Occidental pear P. caucasica 684，P. pyraster 989，P. elaeagrifolia 2817 might be hybrids between Oriental pear and Occidental pear.Conclusions: The phylogenetic relationships of Pyrus were still complicate because interspecies and intraspecies of Oriental pear and Occidental pear respectively were intercrossed. More genes and more accessions were needed to solve the phylogenetic relationships in Pyrus and to explore the possible parents.

Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

Background Heterotrimeric G-proteins, composed of Gα, Gβ and Gγ subunits, are important signal transmitters, mediating the cellular response to multiple stimuli in animals and plants. The Gγ subunit is an essential component of the G-protein, providing appropriate functional specificity to the heterotrimer complex and has been well studied in many species. However, the evolutionary history, expression pattern and functional characteristics of Gγ subunits has not been explored in the Rosaceae, representing many important fruit crops. Results In this study, 35 Gγ subunit genes were identified from the eight species belonging to the Rosaceae family. Based on the structural gene characteristics, conserved protein motifs and phylogenetic analysis of the Gγ subunit genes, the genes were classified into three clades. Purifying selection was shown to play an important role in the evolution of Gγ subunit genes, while a recent whole-genome duplication event was the principal force determining the expansion of the Gγ subunit gene family in the subfamily Maloideae. Gγ subunit genes exhibited diverse spatiotemporal expression patterns in Chinese white pear, including fruit, root, ovary and bud, and under abiotic stress conditions, the relative expression of Gγ subunit genes were up-regulated or down-regulated. In addition, seven of the Gγ subunit proteins in pear were located on the plasma membrane, in the cytoplasm or nucleus. Conclusion Overall, this study of the Gγ subunit gene family in eight Rosaceae species provided useful information to better understand the evolution and expression of these genes and facilitated further exploration of their functions in these important crop plants.

Genome-Wide Identification of the 1-Aminocyclopropane-1-carboxylic Acid Synthase (ACS) Genes and Their Possible Role in Sand Pear (Pyrus pyrifolia) Fruit Ripening

Ethylene production is negatively associated with storage life in sand pear (Pyrus pyrifoliaNakai), particularly at the time of fruit harvest. 1-Aminocyclopropane-1-carboxylic acid synthase (ACS) is the rate-limiting enzyme in ethylene biosynthesisand is considered to be important for fruit storage life. However, the candidate ACS genes and their roles in sand pear remain unclear. The present study identified 13ACS genes from the sand pear genome.Phylogenetic analysiscategorizedthese ACS genesinto four subgroups (type Ⅰ, type Ⅱ, type Ⅲ and putative AAT), and indicated a close relationship between sand pear and Chinese white pear (P. bretschneideri). According to the RNA-seq data and qRT-PCR analysis, PpyACS1, PpyACS2, PpyACS3, PpyACS8, PpyACS9, PpyACS12 and PpyACS13 were differently expressed in climacteric and non-climacteric-typepear fruits,‘Ninomiyahakuri’ and ‘Eli No.2′, respectively, during fruit ripening. In addition, the expressions of PpyACS2, PpyACS8, PpyACS12 and PpyACS13 werefound to be associated with system 1 of ethylene production, while PpyACS1, PpyACS3, and PpyACS9 werefound to be associated with system 2, indicating that these ACS genes have different roles in ethylenebiosynthesis during fruit development. Overall, our study provides fundamental knowledge onthe characteristics of the ACS gene family in sand pear, in addition to their possible roles infruit ripening.

Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

Background In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. Results In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. Conclusions Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.