Targeted Metabolic and Transcriptomic Analysis of Pinus yunnanensis var. pygmaea with Loss of Apical Dominance

Xiao, Feng; Yang, Zhao; Wang, Xiurong; Yao, Yang

doi:10.3390/cimb44110371

Cited by 7 publications

(9 citation statements)

References 39 publications

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“…P. pygmaea exhibit a clear absence of apical dominance with an inconspicuous main trunk. The base is multi-branched, clumped, with a height range of 40–50 cm to 1–2 m. Leaves grow short and upright while its seed cones cluster together [ 3 ]. Tracheid length of P. pygmaea is shortened, resin canals increase and more or less concentrate in the late wood [ 7 ].…”

Section: Methodsmentioning

confidence: 99%

“…The broad distribution and diverse uses make P. massoniana pivotal for sustainable forestry production and ecological environment construction [ 2 ]. Compared with Pinus elliottii ( P. elliottii ), P. massoniana grows slower in the early stage (10–15 years) and faster in the later stage (> 15 years) [ 3 ]. P. elliottii is an important timber and resin-producing species grown worldwide [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

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Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea

Xiao,

Zhao,

Wang

et al. 2024

BMC Genomics

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Drought stress can significantly affect plant growth, development, and yield. Fewer comparative studies have been conducted between different species of pines, particularly involving Pinus yunnanensis var. pygmaea (P. pygmaea). In this study, the physiological indices, photosynthetic pigment and related antioxidant enzyme changes in needles from P. pygmaea, P. elliottii and P. massoniana under drought at 0, 7, 14, 21, 28 and 35 d, as well as 7 days after rehydration, were measured. The PacBio single-molecule real-time (SMRT) and Illumina RNA sequencing were used to uncover the gene expression differences in P. pygmaea under drought and rehydration conditions. The results showed that the total antioxidant capacity (TAOC) of P. pygmaea was significantly higher than P. massoniana and P. elliottii. TAOC showed a continuous increase trend across all species. Soluble sugar (SS), starch content and non-structural carbohydrate (NSC) of all three pines displayed a "W" pattern, declining initially, increasing, and then decreasing again. P. pygmaea exhibits stronger drought tolerance and greater recovery ability under prolonged drought conditions. Through the PacBio SMRT-seq, a total of 50,979 high-quality transcripts were generated, and 6,521 SSR and 5,561 long non-coding RNAs (LncRNAs) were identified. A total of 2310, 1849, 5271, 5947, 7710, and 6854 differentially expressed genes (DEGs) were identified compared to the control (Pp0D) in six pair-wise comparisons of treatment versus control. bHLH, NAC, ERF, MYB_related, C3H transcription factors (TFs) play an important role in drought tolerance of P. pygmaea. KEGG enrichment analysis and Gene set enrichment analysis (GSEA) analysis showed that P. pygmaea may respond to drought by enhancing metabolic processes such as ABA signaling pathway, alpha-linolenic acid. Weighted gene co-expression network analysis (WGCNA) revealed GST, CAT, LEC14B, SEC23 were associated with antioxidant enzyme activity and TAOC. This study provides a basis for further research on drought tolerance differences among coniferous species.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea

Xiao,

Zhao,

Wang

et al. 2024

BMC Genomics

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“…fera) were quantified via tandem mass spectrometry combined with liquid chromatography (LC-MS/MS). The workflow and methodology used to conduct the LC-MS/MS analyses were based on a previous report [35].…”

Section: Determination Of Hormone Contentsmentioning

confidence: 99%

The Effects of Homologous and Heterologous Grafting on the Growth of Gleditsia sinensis Scions

Xiao,

Zhao,

Wang

et al. 2023

Forests

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Gleditsia sinensis Lam. (Fam. Leguminosae; Gen.: Gleditsia) has various uses, including for medicinal, edible, chemical, and material purposes, and is widely distributed in China. However, the extent of graft compatibility and its impact on growth when using different Gleditsia species as rootstocks for grafting G. sinensis scions is not yet clear. This study examined homologous and heterologous grafting between different Gleditsia species, measuring the survival rate, morphology, photosynthesis, physiology, and hormones of the grafted plants. The results showed that G. sinensis and other Gleditsia seedlings have survival rates of over 86%. The more distant the genetic relationship between species, the lower the grafting survival rate. The grafting of fast-growing G. fera as a rootstock increased the accumulation of photosynthetic products in the grafted plants, while the grafting of slow-growing G. microphylla as a rootstock slowed down the growth rate of the longitudinal extension of the leaves of the grafted plants. Heterografted rootstocks increased the contents of IPA, PP333, ACC, and DZ but decreased the levels of GA4, iP, and SA hormones. Some hormone levels that can be highly expressed in seedlings were used as rootstocks, and the corresponding hormone levels in the grafted seedlings were still highly expressed. This study lays a material and theoretical basis for the development of new resources for the breeding and rootstock selection of G. sinensis.

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“…Consequently, researchers selected various plant varieties to investigate aspects such as plant height regulation, phytohormone biosynthesis and signal transduction, etc. [3,11,12].…”

Section: Introductionmentioning

confidence: 99%

Endogenous Phytohormone and Transcriptome Analysis Provided Insights into Seedling Height Growth of Pinus yunnanensis

Lu,

Wang,

Yang

et al. 2024

Forests

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Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the phenotypes of P. yunnanensis seedlings with different plant heights were quite different at their seedling stage, the molecular mechanisms controlling the seedling differentiation remain poorly understood. This study is aimed to investigate the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The P. yunnanensis seedlings were categorized into three grades, i.e., Grades A, B, and C, by mean ± 1/2 standard deviation method (H ± 1/2σ), and the seedling height and ground diameter were measured. We conducted the measurements of endogenous hormone levels in the young shoot apexes of seedlings at different grades during the fast-growth period (March). The DEGs were identified through transcriptome sequencing and analyzed by qRT-PCR validation. Significant differences were observed in the content and ratio of endogenous phytohormones among various grades of P. yunnanensis seedlings (p < 0.05). The ABA content in Grade A was prominently more than that in Grades B and C, and the order of the content of auxins was Grade B > C > A. Furthermore, when compared to Grade A, the ratios of auxins/CTKs, auxins/ABA, CTKs/ABA, and (auxins + CTKs)/ABA exhibited significant increases in Grades B and C. Moreover, GO functional annotation analysis indicated the more pronounced enrichment of DEGs in molecular functions. KEGG metabolic pathway analysis revealed notable differences in enrichment pathways between the pairwise comparisons. The “plant hormone signal transduction” pathway exhibited enrichment in the two groups, followed by “plant–pathogen interaction” pathway in the organism system that was enriched in the three groups. In addition, the results for endogenous phytohormone metabolism pathways indicate a significant up-regulation in the expression of AUX1, while AHP and PP2C exhibited significant down-regulation. To sum up, we aimed at investigating the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The results suggested that individual phytohormones have a limited capacity to regulate gene expression, and seedling differentiation results from the combined regulation of multiple hormones. In addition, several candidate genes associated with phytohormone biosynthesis and signal transduction pathways were identified, including AUX1, GH3, AHP, B-ARR, PP2C, etc., which provided candidate genes for the following hormone-related gene overexpression and knockout experiments. These findings provide insights into the molecular genetic control of seedling height growth of P. yunnanensis.

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Targeted Metabolic and Transcriptomic Analysis of Pinus yunnanensis var. pygmaea with Loss of Apical Dominance

Cited by 7 publications

References 39 publications

Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea

Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea

The Effects of Homologous and Heterologous Grafting on the Growth of Gleditsia sinensis Scions

Endogenous Phytohormone and Transcriptome Analysis Provided Insights into Seedling Height Growth of Pinus yunnanensis

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