The bZIP53–IAA4 module inhibits adventitious root development in Populus

Zhang, Yan; Yang, Xiaoqing; Cao, Pei; Xiao, Zheng’ang; Zhan, Chengjun; Liu, Meifeng; Nvsvrot, Tashbek; Wang, Nian

doi:10.1093/jxb/eraa096

Cited by 34 publications

(26 citation statements)

References 64 publications

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“…In arabidopsis hypocotyls it has been shown that ARF7 act together with ARF19 as positive AR regulators by activating the downstream transcription factors ORGAN BOUNDARIES DOMAIN ( LBD ) LBD16 and LBD18 ( Lee et al, 2019 ). Recently, Zhang et al (2020) showed that the overexpression of the poplar bZIP53 transcription factor had a negative effect on AR development by controlling the expression of IAA4-1 and IAA4-2 ( Figure 1 ). bZIP53 was shown to bind to the promoter of IAA4-1 and IAA4-2 and activate their expression.…”

Section: Endogenous Factors Influencing Rooting Of Cuttingsmentioning

confidence: 99%

Adventitious Rooting in Populus Species: Update and Perspectives

Bannoud

Bellini

2021

Front. Plant Sci.

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Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.

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Section: Endogenous Factors Influencing Rooting Of Cuttingsmentioning

confidence: 99%

Adventitious Rooting in Populus Species: Update and Perspectives

Bannoud

Bellini

2021

Front. Plant Sci.

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“…For example, poplar PtabZIP1L is mainly expressed in roots and can mediate the development of lateral roots and drought resistance by regulating various metabolic pathways [ 12 ]. Poplar bZIP53 is inducible in gene expression by salt stress and negatively regulates the development of adventitious roots [ 13 ]. The poplar AREB1 can regulate drought responses and tolerance of Populus trichocarpa by affecting histone acetylation [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis and expression profile of the bZIP gene family in poplar

et al. 2021

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Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

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“…As for the up-regulated genes, EAT-UpTF identified LATERAL ORGAN BOUNDARIES DOMAIN 19 (LBD19), LBD18 and LBD16 as upstream regulators, which are involved in auxin-dependent lateral root emergence ( Feng et al, 2012 ) ( Table 3 ). Meanwhile, BASIC REGION/LEUCINE ZIPPER MOTIF 53 (bZIP53) and bZIP11, which negatively regulate adventitious root formation and primary root growth in an auxin-dependent pathway ( Weiste et al, 2017 ; Zhang et al, 2020 ), were retrieved as overrepresented upstream TFs for the IAA-repressed genes ( Table 4 ). Overall, the EAT-UpTF analysis reliably identified upstream TFs for a group of GOIs.…”

Section: Resultsmentioning

confidence: 99%

EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes

Shim

Seo

2020

Front. Genet.

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EAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a group of plant genes) is an open-source Python script that analyzes the enrichment of upstream transcription factors (TFs) in a group of genes-of-interest (GOIs). EAT-UpTF utilizes genome-wide lists of TF-target genes generated by DNA affinity purification followed by sequencing (DAP-seq) or chromatin immunoprecipitation followed by sequencing (ChIP-seq). Unlike previous methods based on the two-step prediction of cis-motifs and DNA-element-binding TFs, our EAT-UpTF analysis enabled a one-step identification of enriched upstream TFs in a set of GOIs using lists of empirically determined TF-target genes. The tool is designed particularly for plant researches, due to the lack of analytic tools for upstream TF enrichment, and available at https://github.com/sangreashim/ EAT-UpTF and http://chromatindynamics.snu.ac.kr:8080/EatupTF.

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The bZIP53–IAA4 module inhibits adventitious root development in Populus

Cited by 34 publications

References 64 publications

Adventitious Rooting in Populus Species: Update and Perspectives

Adventitious Rooting in Populus Species: Update and Perspectives

Genome-wide analysis and expression profile of the bZIP gene family in poplar

EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes

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