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. 2022 May 10;23(10):5309.
doi: 10.3390/ijms23105309.

Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology

Lu Luo  1   2 , Qian Wan  3 , Zipeng Yu  1 , Kun Zhang  2 , Xiurong Zhang  2 , Suqing Zhu  2 , Yongshan Wan  2 , Zhaojun Ding  1 , Fengzhen Liu  2
Affiliations

Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology

Lu Luo et al. Int J Mol Sci. .

Abstract

Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.

Keywords: auxin response factor; expression; genome-wide identification; peanut; root morphology.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study or in the collection, analyses, or interpretation of the data.

Figures

Figure 1
Figure 1
Chromosome distribution of ARFs in cultivar (A) and wild (B) peanuts. Chromosomes belong to the A sub-genome of A. hypogaea (Arahy.02–10) and their homologues from A. duranensis are colored in yellow, while the chromosomes that belong to the B sub-genome of A. hypogaea (Arahy.12–20) and their homologues from A. ipaensis are colored in green. Chromosomes that do not contain ARFs and ARFs located on the scaffold are not shown.
Figure 2
Figure 2
Phylogenetic tree, cis-elements, and gene structure analysis of ARFs in wild and cultivar peanuts. Gene structures are shown in the outer cycle, and cis-elements are shown in the cycle inside the gene names. The red, green, and blue dots represent AhARFs, AdARFs, and AiARFs, respectively.
Figure 3
Figure 3
Duplication derived ARFs in wild and cultivar peanuts. (A) The orthologous genes (black lines), paralogous genes (red), and tandem repeat (blue) in cultivar peanut. (B) The Ks value distribution of the duplicated orthologous genes between the wild and cultivar peanut.
Figure 4
Figure 4
Heatmap illustration of tissue expression patterns of AhARFs based on FPKM values. The log2 transformation of FPKM values and visualization were performed by TBtools. Scalebar on top right indicates the levels of gene expression.
Figure 5
Figure 5
Genome-wide prediction of ARF-binding elements. (A) Definition of DR5 and IR8 elements. N indicates A, C, G, or T. (B) Number of DR5, IR8, and AuxRE in peanut genomes. (C) GO analysis of genes carrying DR5, IR8, or AuxRE in their promoters, and only the GO terms of those containing at least 40 genes are shown here.
Figure 6
Figure 6
Root morphology and their correlation with AhARF expression levels in peanut germplasms. (A) Root morphology of peanut germplasms. JK, Jinkins Jumbo; 41165, Meiyinxuan 41165; SX64, Shixuan 64; JH27, Juhua 27; FH2, Fenghua 2; EH3, Ehua 3; SH11, Shanhua 11; ZH12, Zhonghua 12. (B) Total root length, root surface area, root mean diameter, and root tip number of peanut germplasms. Lower case letters (a, b, c, d) indicate statistically significant differences between cultivars. (C) Relative expression levels of AhARFs in peanut roots. (D) Pearson’s correlation analysis between root morphology and expression of AhARFs. R2, Pearson’s correlation coefficient.
Figure 7
Figure 7
Subcellular localization analysis of AhARFs in N. benthamiana leaves.
See this image and copyright information in PMC

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