Global Transcriptomic Profile Analysis of Genes Involved in Lignin Biosynthesis and Accumulation Induced by Boron Deficiency in Poplar Roots

Su, Wanlong; Liu, Na; Mei, Li; Luo, Jie; Zhu, Yi-Jie; Zhu, Liang

doi:10.3390/biom9040156

Cited by 25 publications

(11 citation statements)

References 58 publications

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“…HISTIDINE KINASE 1 (homolog of Potri.007G056400) is believed to have a role in abscisic acid (ABA) signaling, indicated by increased sensitivity of seedlings to the effects of ABA in inhibiting germination (Tran et al ., 2007). In Populus , the putative histidine kinase Potri.007G056400 was found to be differentially expressed in Populus roots in response to boron deficiency (Su et al ., 2019) and the putative serine/threonine kinase Potri.015G105000 was previously identified in GWAS as an association with bud set and growth period (McKown et al ., 2014).…”

Section: Discussionmentioning

confidence: 99%

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Nagle

Yuan

Kaur

et al. 2022

Preprint

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Adventitious rooting is critical to the propagation, breeding, and genetic engineering or editing of trees. The capacity for plants to undergo these processes is highly heritable; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of these processes, we performed a genome-wide association study (GWAS) using 1,148 genotypes of Populus trichocarpa. GWAS are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics, and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, and reactive oxygen species signaling. Genes related to other processes with known roles in root development, and numerous genes with uncharacterized functions and/or cryptic roles, were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of adventitious rooting.

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Section: Discussionmentioning

confidence: 99%

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Nagle

Yuan

Kaur

et al. 2022

Preprint

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“…The presence of lignins limit the enzymatic degradation of cell walls and delignification could lead to the cell walls digestion [41]. MYB transcription factors have been widely reported as regulating lignin biosynthesis [42]. In addition, phenylalanine is the starting point of lignin biosynthesis, and MYB genes were reported to regulate the expression of the general phenylpropanoid biosynthetic genes and influence lignin biosynthesis [43].…”

Section: Discussionmentioning

confidence: 99%

Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp

Yun

et al. 2019

Biomolecules

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The banana is one of the most important fruits in the world. Bananas undergo a rapid ripening process after harvest, resulting in a short shelf. In this study, the mechanism underlying pulp ripening of harvested bananas was investigated using integrated transcriptomic, proteomic, and metabolomic analysis. Ribonucleic acid sequencing (RNA-Seq) revealed that a great number of genes related to transcriptional regulation, signal transduction, cell wall modification, and secondary metabolism were up-regulated during pulp ripening. At the protein level, 84 proteins were differentially expressed during pulp ripening, most of which were associated with energy metabolism, oxidation-reduction, cell wall metabolism, and starch degradation. According to partial least squares discriminant analysis, 33 proteins were identified as potential markers for separating different ripening stages of the fruit. In addition to ethylene’s central role, auxin signal transduction might be involved in regulating pulp ripening. Moreover, secondary metabolism, energy metabolism, and the protein metabolic process also played an important role in pulp ripening. In all, this study provided a better understanding of pulp ripening of harvested bananas.

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“…The adapter and low-quality reads were filtered through cutadapt (version 1.11). Clean reads were mapped to the contigs with paired-end reads by Hisat2 (version 2.1.0), allowing up to two mismatches ( Su et al, 2019 ). These genes were subjected to alignment against public protein databases: Pfam (Pfam protein families) and UniProt (Swiss-Prot).…”

Section: Methodsmentioning

confidence: 99%

Bacillus thuringiensis and Chlorantraniliprole Trigger the Expression of Detoxification-Related Genes in the Larval Midgut of Plutella xylostella

Shabbir

Yang²,

Batool

et al. 2021

Front. Physiol.

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Background: Diamondback moth (DBM), Plutella xylostella (L.), has developed resistance to many insecticides. The molecular mechanism of DBM resistance to Bt-G033A combined with chlorantraniliprole (CL) remains undefined.Methods: In this study, field-resistant strains of Plutella xylostella to three pesticides, namely, Bacillus thuringiensis (Bt) toxin (Bt-G033A), CL, and a mixture of Bt + CL, were selected to evaluate the resistance level. Additionally, transcriptomic profiles of a susceptible (SS-DBM), field-resistant (FOH-DBM), Bt-resistant (Bt-DBM), CL-resistant (CL-DBM), and Bt + CL-resistant (BtC-DBM) strains were performed by comparative analysis to identify genes responsible for detoxification.Results: The Bt-G033A was the most toxic chemical to all the DBM strains among the three insecticides. The comparative analysis identified 25,518 differentially expressed genes (DEGs) between pairs/combinations of strains. DEGs were enriched in pathways related to metabolic and catalytic activity and ABC transporter in resistant strains. In total, 17 metabolic resistance-related candidate genes were identified in resistance to Bt-G033A, CL, and Bt + CL by co-expression network analysis. Within candidate genes, the majority was upregulated in key genes including cytochrome P450, glutathione S-transferase (GST), carboxylesterase, and acetylcholinesterase in CL- and BtC-resistant strains. Furthermore, aminopeptidase N (APN), alkaline phosphatase (ALP), cadherin, trypsin, and ABC transporter genes were eminent as Bt-resistance-related genes. Expression patterns of key genes by the quantitative real-time PCR (qRT-PCR) proved the credibility of transcriptome data and suggest their association in the detoxification process.Conclusion: To date, this study is the most comprehensive research presenting functional transcriptome analysis of DBM using Bt-G033A and CL combined insecticidal activity.

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Global Transcriptomic Profile Analysis of Genes Involved in Lignin Biosynthesis and Accumulation Induced by Boron Deficiency in Poplar Roots

Cited by 25 publications

References 58 publications

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp

Bacillus thuringiensis and Chlorantraniliprole Trigger the Expression of Detoxification-Related Genes in the Larval Midgut of Plutella xylostella

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