. 2023 Apr 13;24(1):199.

doi: 10.1186/s12864-023-09263-y.

Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale

Can Si^{1

2}, Danqi Zeng^{1

2

3}, Jaime A Teixeira da Silva⁴, Shengxiang Qiu^{1

2}, Jun Duan^{1

2}, Song Bai⁵, Chunmei He^{6

7}

Affiliations

¹ Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
² South China National Botanical Garden, Guangzhou, 510650, China.
³ University of the Chinese Academy of Sciences, Beijing, 100049, China.
⁴ , Miki-Cho, Kagawa-Ken, Japan.
⁵ Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China. baisong@gdaas.cn.
⁶ Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. hechunmei2012@scbg.ac.cn.
⁷ South China National Botanical Garden, Guangzhou, 510650, China. hechunmei2012@scbg.ac.cn.

PMID: 37055721
PMCID: PMC10099678
DOI: 10.1186/s12864-023-09263-y

Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale

Can Si et al. BMC Genomics. 2023.

. 2023 Apr 13;24(1):199.

doi: 10.1186/s12864-023-09263-y.

Authors

Can Si^{1

2}, Danqi Zeng^{1

2

3}, Jaime A Teixeira da Silva⁴, Shengxiang Qiu^{1

2}, Jun Duan^{1

2}, Song Bai⁵, Chunmei He^{6

7}

Affiliations

¹ Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
² South China National Botanical Garden, Guangzhou, 510650, China.
³ University of the Chinese Academy of Sciences, Beijing, 100049, China.
⁴ , Miki-Cho, Kagawa-Ken, Japan.
⁵ Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China. baisong@gdaas.cn.
⁶ Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. hechunmei2012@scbg.ac.cn.
⁷ South China National Botanical Garden, Guangzhou, 510650, China. hechunmei2012@scbg.ac.cn.

PMID: 37055721
PMCID: PMC10099678
DOI: 10.1186/s12864-023-09263-y

Abstract

Background: The auxin indole-3-acetic acid (IAA) is a vital phytohormone that influences plant growth and development. Our previous work showed that IAA content decreased during flower development in the medicinally important orchid Dendrobium officinale, while Aux/IAA genes were downregulated. However, little information about auxin-responsive genes and their roles in D. officinale flower development exists.

Results: This study validated 14 DoIAA and 26 DoARF early auxin-responsive genes in the D. officinale genome. A phylogenetic analysis classified the DoIAA genes into two subgroups. An analysis of cis-regulatory elements indicated that they were related by phytohormones and abiotic stresses. Gene expression profiles were tissue-specific. Most DoIAA genes (except for DoIAA7) were sensitive to IAA (10 μmol/L) and were downregulated during flower development. Four DoIAA proteins (DoIAA1, DoIAA6, DoIAA10 and DoIAA13) were mainly localized in the nucleus. A yeast two-hybrid assay showed that these four DoIAA proteins interacted with three DoARF proteins (DoARF2, DoARF17, DoARF23).

Conclusions: The structure and molecular functions of early auxin-responsive genes in D. officinale were investigated. The DoIAA-DoARF interaction may play an important role in flower development via the auxin signaling pathway.

Keywords: ARF genes; Aux/IAA genes; Cis-regulatory element; Dendrobium officinale; Flower development.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1**
Phylogenetic tree of Aux/IAA proteins from *Dendrobium officinale*, *Arabidopsis thaliana* and *Oryza sativa*. A Phylogenetic tree of the predicted Aux/IAA proteins from *D. officinale*. B Phylogenetic relationship of Aux/IAA proteins among the three plant species. Red circles, *D. officinale*; luminous green squares, *O. sativa*; pink triangles, *A. thaliana*

**Fig. 2**
Multiple alignment of 14 Aux/IAA proteins from *Dendrobium officinale*. Conserved domains I, II, III, IV are underlined. Bipartite NLS (between domains I and II), as well as NLS in domain IV, are indicated with a line above them

**Fig. 3**
Expression patterns of 14 *DoIAA* genes in different organs of *Dendrobium officinale*. A Different organs of *D. officinale*. B Transcript profiles of *DoIAA* genes in eight organs of *D. officinale*. Red and blue indicate high and low expression levels, respectively. Wr, white part of roots; Gr, green part of roots; St, stems; Fb, flower buds; Co, column; Le, leaves; Li, lip; Se, sepals

**Fig. 4**
Expression patterns of 14 *DoIAA* genes at three flower development stages of *Dendrobium officinale*. A Three flower development stages. S1 indicates early flower buds, S2 indicates middle-stage flower buds, and S3 indicates fully-opened flowers. B Transcript profiles of *DoIAA* genes and the correlation coefficient with IAA content at the three flower developmental stages. Red represents a high transcript level and a positive correlation whereas blue represents a low transcript level and a negative correlation. Four genes (*DoIAA1*, 6, 10, 13), indicated within red boxes, were used for the subcellular localization and yeast two-hybrid analysis

**Fig. 5**
Expression patterns of 14 *DoIAA* genes in the IAA treatment. Error bars represent the mean ± standard deviation (SD) of three biological replicates (n = 3). * and ** indicate significant differences at p < 0.05 and p < 0.01, respectively (DMRT)

**Fig. 6**
Subcellular localization of YFP, DoIAA1-YFP, DoIAA6-YFP, DoIAA10-YFP and DoIAA13-YFP with nucleus localization marker NLS mCherry. Bars = 5 μm

**Fig. 7**
Analysis of the interaction between Aux/IAA and ARF proteins using a yeast two-hybrid assay. DoARF2, 17 and 23 were cloned into the pGADT7 vector; DoIAA1, 6, 10 and 13 were cloned into the pGBKT7 vector. All recombinants were transformed into yeast strain AH109 and plated on the following double or quadruple selection media: SD/-Leu/-Trp, SD/-Leu/-Trp/-His/-Ade and SD/-Leu/-Trp/-His/-Ade + X-α-gal. An empty vector was used as the control

**Fig. 8**
A proposed model of the Aux/IAA-ARF module in the mediation of auxin-signaling during *Dendrobium officinale* flower development

See this image and copyright information in PMC

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Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale

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Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale

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Affiliations

Abstract

Conflict of interest statement

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