Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

Ning, Kun; Ding, Changjun; Huang, Qinjun; Zhang, Weixi; Yang, Chengchao; Liang, Dejun; Fan, Ruting; Su, Xiaohua

doi:10.1371/journal.pone.0217066

Cited by 15 publications

(19 citation statements)

References 70 publications

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“…The plant hormone abscisic acid (ABA) is a developmental signal that responds to environmental stimuli.2C type protein phosphatases (PP2Cs) is closely related to abscisic acid (ABA) signaling pathway and play a role through the negative regulation of ABA response [51,52]. SUAR, IAA and PP2C involved in plant hormone signal transduction pathway were higher in HD than LD, which was consistent with the findings in poplar [16]. In addition, the Aux / IAA related genes were down regulated under HD when compared to LD.…”

Section: Plos Onesupporting

confidence: 80%

“…The comparative transcriptome analysis of cassava leaves under full day and natural shade conditions found that the gene expression profiles in both cases showed similar developmental changes, the expression of hormone related transcription factors and genes were influenced by shade [15]. The transcriptome analysis of poplar and maize with different densities revealed the differential expression of genes related to plant hormones, photosynthetic complexes and photosynthetic antenna proteins [16,17]. However, there are few studies on the effect of planting density on gene expression, which need more research.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis

Niu

Yin

et al. 2020

PLoS ONE

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Different densities have a great influence on the physiological process and growth of orchard plants. Exploring the molecular basis and revealing key candidate genes for different densities management of orchard has great significance for production capacity improvement. In this study, transcriptome sequencing of apple trees was carried out at three different sampling heights to determine gene expression patterns under high density (HD) and low density(LD) and the physiological indices were measured to determine the effect of density change on plants. As a result, physiological indexes showed that the content of Chlorophyll, ACC, RUBP and PEP in the LD was apparently higher than that in control group(high density, HD). While the content of PPO and AO in the LD was noticeably lower than that in the HD. There were 3808 differentially expressed genes (DEGs) were detected between HD and LD, of which 1935, 2390 and 1108 DEGs were found in the three comparisons(middle-upper, lower-outer and lower-inner), respectively. 274 common differentially expressed genes (co-DEGs) were contained in all three comparisons. Functional enrichment and KEGG pathway analysis found these genes were involved in Carbon fixation in photosynthetic organisms, Circadian rhythm, Photosynthesis − antenna proteins, Photosynthesis, chlorophyll metabolism, Porphyrin, sugar metabolism and so on. Among these genes, LHCB family participated in photosynthesis as parts of photosystem II. In addition, SPA1, rbcL, SNRK2, MYC2, BSK, SAUR and PP2C are involved in Circadian rhythm, the expression of genes related to glycometabolism and hormone signaling pathway is also changed. The results revealed that the decrease of plant density changed the photosynthetic efficiency of leaves and the expression of photosynthesis-related genes, which provide a theoretical basis for the actual production regulation of apples.

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Section: Plos Onesupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis

Niu

Yin

et al. 2020

PLoS ONE

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“…To better understand the functions of POD genes in the growth and development of Betula Platyphylla × Betula Pendula, their expression pro les in different tissues (including root, xylem, young leaf and ower) were analyzed with publicly available transcriptome data. Of the 90 BpPODs, 69 genes were expressed in one or more birch tissues, while 21 BpPOD genes exhibited no expression in various individual tissues (Relative expression value > 0 as basal expression) [40]. The heat map (Figure 7) demonstrated that most BpPODs had tissue-speci c or preferential expression patterns.…”

Section: Tissue-speci C Expression Of Bppodsmentioning

confidence: 99%

Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

Cai

Liu

Chen

et al. 2021

Preprint

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Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis, rice, poplar, maize and Chinese pear. The POD genes remain to be determined in Betula pendula.Results: A total of 90 nonredundant POD genes were identified in Betula pendula. (designated BpPODs). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPODs were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD gene family in Betula pendula. Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPODs might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD gene family in Betula pendula.

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“…Many previous studies have shown that intraspecific interactions can affect the morphological characteristics of the plant canopy (Song et al, 2016) and roots (Khan et al, 2018) as well as the plant metabolic level (Kuai et al, 2016), ultimately influencing plant growth and quality (Huang et al, 2019). The effects of intraspecific interactions on plant performance can be easily realized by altering the planting density (Broekman et al, 2019;Ning et al, 2019). A suitable density ensures the normal growth of individual plants and entire population through coordinate utilization of water, light, temperature, and nutrients (Ning et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Planting Density Affects Panax notoginseng Growth and Ginsenoside Accumulation by Balancing Primary and Secondary Metabolism

Liu

Wang

et al. 2021

Front. Plant Sci.

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Adjusting planting density is a common agricultural practice used to achieve maximum yields. However, whether the quality of medicinal herbs can be improved by implementing appropriate planting densities is still uncertain. The medicinal crop Panax notoginseng was used to analyze the effects of planting density on growth and ginsenoside accumulation, and the possible mechanisms of these effects were revealed through metabonomics. The results showed that P. notoginseng achieved high ginsenoside accumulation at high planting densities (8 × 8 and 10 × 10 cm), while simultaneously achieved high biomass and ginsenoside accumulation at moderate planting density of 15 × 15 cm. At the moderate planting density, the primary metabolism (starch and sucrose metabolism) and secondary metabolism (the biosynthesis of phytohormone IAA and ginsenoside) of the plants were significantly enhanced. However, the strong intraspecific competition at the high planting densities resulted in stress as well as the accumulation of phytohormones (SA and JA), antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the dry biomass and ginsenoside content were significantly lower at low densities (20 × 20 and 30 × 30 cm) with low intraspecific competition, which disturbed normal carbohydrate metabolism by upregulating galactose metabolism. In summary, an appropriate planting density was benefit for the growth and accumulation of ginsenosides in P. notoginseng by balancing primary metabolism and secondary metabolism.

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Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

Cited by 15 publications

References 70 publications

Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis

Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis

Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

Planting Density Affects Panax notoginseng Growth and Ginsenoside Accumulation by Balancing Primary and Secondary Metabolism

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