Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.)

View article
Plant Biology

Main article text

 

Introduction

Materials & Methods

Identification of peanut ARF gene family

Sequence analyses and the construction of evolutionary tree

Chromosomal distribution and tandem duplication analysis of AhARF genes

Expression patterns of AhARF genes in different tissues of Tifrunner

Proteins structure analysis of ARF6 sub-family

Transcriptomics analysis of four peanut varieties with different pod/seed sizes

Construction of GFP vector and subcellular localization of AhARF6-5 gene

Plant materials and hormone treatments

Quantitative reverse transcription polymerase chain reaction (qRT-PCR)

Results

Identification of peanut ARF gene family

Phylogenetic analysis of ARF genes

Chromosomal distribution and tandem duplication analysis of AhARF genes

Expression pattern analysis of AhARF genes in different tissues

AhARF6 protein properties and sequence analyses of ARF6 in peanut and other plants

Analysis of pod expression of the AhARF6 subfamily in four varieties and subcellular localisation of AhARF6-5 gene

Expression of AhARF6 genes in different tissues

Early responses of AhARF6 to exogenous NAA treatments

Discussion

Conclusions

Supplemental Information

Expression patterns of AhARF genes in different tissues.

The dates are from an expression atlas (Clevenger et al., 2016), Bar showed log2 (FPKM) colored blue to red. Information on 22 tissues has been provided in Additional file 2: Table S2. Fragments per Kilobase per Million mapped reads (FPKM) values of the AhARF genes are listed in Additional file 2: Table S6.

DOI: 10.7717/peerj.12319/supp-1

Expression analysis of AhARF6 sub-family genes in response to NAA treatment in peanut leaf.

qRT-PCR analysis of AhARF6 transcript levels was performed at the fifth leaf stage of plants treated with NAA for 0, 2, 4, 8, and 12 h. Values are means ± SD (n = 3). Different lowercase letters denote significant differences between the any two stages (P < 0.05, one-way ANOVA and Tukey’s test for multiple comparisons).

DOI: 10.7717/peerj.12319/supp-2

Expression analysis of AhARF6 sub-family genes in response to NAA treatment in peanut root.

qRT-PCR analysis of AhARF6 transcript levels was performed at the fifth leaf stage of plants treated with NAA for 0, 2, 4, 8, and 12 h. Values are means ± SD (n = 3). Different lowercase letters denote significant differences between the any two stages (P < 0.05, one-way ANOVA and Tukey’s test for multiple comparisons).

DOI: 10.7717/peerj.12319/supp-3

Information of AhARF genes.

DOI: 10.7717/peerj.12319/supp-4

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Peipei Li performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Qian Ma conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Chengxin Qu analyzed the data, prepared figures and/or tables, and approved the final draft.

Shuliang Zhu analyzed the data, prepared figures and/or tables, and approved the final draft.

Kunkun Zhao conceived and designed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Xingli Ma analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Zhongfeng Li analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Xingguo Zhang analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Fangping Gong conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Dongmei Yin conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw data are available in the Supplementary Tables.

Funding

This work was financially supported by grants from the National Natural Science Foundation of China (No. 31471525) for the design and execution of the study. Grants from Key program of NSFC-Henan United Fund (No. U1704232) and Key Scientific and Technological Project in Henan Province (No.161100111000; S2012–05-G03) for variety breeding and seed preservation. It was also funded through Innovation Scientists and Technicians Troop Construction Projects of Henan Province (No.2018JR0001) for data acquisition, data analysis and writing. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

4 Citations 1,445 Views 179 Downloads