Genome-wide characterization and expression pattern of auxin response factor (ARF) gene family in soybean and common bean

Le, Bao; Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Le, Thu Nu Anh; Yang, Seung Hwan; Golokhvast, Kirill S.; Son., E.F. Nevins; Chung, Gyuhwa

doi:10.1007/s13258-016-0462-y

Cited by 16 publications

(9 citation statements)

References 47 publications

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“…Auxin plays a critical role in controlling plant growth and developmental and physiological processes, while IAA and ARF are key components in auxin signaling for regulating downstream reactions [4]. The numbers of IAA and ARF members are different among plants species; for example, there are 29 IAAs and 23 ARFs in Arabidopsis [6,20], 31 IAAs and 25 ARFs in rice [19,22], and 63 IAAs and 55 ARFs in soybean [27,34]. A total of 17 IAA and 24 ARF genes were reported in M. truncatula [32,33], while a total of 25 MtIAA and 40 MtARF genes were identified in this study based on the updated genome data.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Guo

2021

IJMS

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Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Guo

2021

IJMS

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“…Auxin response factors exert pivotal function in the regulation of plant growth and development through the auxin signaling pathway (Kepinski & Leyser, 2005; Li et al, 2016). Due to the significance of ARFs, genome-wide characterization of ARFs have been completed in many species such as model plants Arabidopsis (Hagen & Guilfoyle, 2002) and Solanum lycopersicum (Zouine et al, 2014), important crops such as soybean (Ha et al, 2013; Le et al, 2016) maize (Xing et al, 2011; Wang et al, 2012), fruit trees like citrus ( Citrus sinensis ) (Xie et al, 2015) apple ( Malus domestica ) (Luo et al, 2014), and so on. From embryogenesis to flowering, mutants in members of ARFs exhibit diverse phenotypes, which show their unique and redundant functions for plant development.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensisSonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission

Zhang¹,

Zeng²,

Chen³

et al. 2019

PeerJ

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Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.

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“…The results indicated that gene duplication was the main driving force for the expansion of the kiwifruit LPP family. In addition, major drivers of the evolution and expansion of gene families such as GmARF, GmHD-Zip, and GmMYB were segmental duplications (Du et al, 2012 ; Chen et al, 2014 ; Le et al, 2016 ). Our results demonstrated that all duplicated gene pairs possess Ka/Ks < 1. such as, the Ka/Ks < 1 had been reported SWEET genes family (Patil et al, 2015 ), GRAS genes family and Aux/IAA (Singh and Jain, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Identification and expression analysis of the lipid phosphate phosphatases gene family reveal their involvement in abiotic stress response in kiwifruit

Yang

Chen

et al. 2022

Front. Plant Sci.

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Lipid phosphate phosphatases (LPPs) are a key enzyme in the production and degradation of phosphatidic acid (PA), which plays an important role in plant growth, development, stress resistance and plant hormone response. Thus far, little is known about the LPP family genes in kiwifruit (Actinidia spp.). According to this study, 7 members in the AcLPP family were identified from the whole genome of kiwifruit, the subcellular localization predictions were mainly on the plasma membrane. Chromosomal localization analysis showed that the AcLPP genes were unevenly distributed on 5 chromosomes, it was determined to have undergone strong purifying selection pressure. There were 5 duplicate gene pairs and all underwent segmental duplication events. The LPP genes of kiwifruit were conserved when compared with other plants, especially in terms of evolutionary relationships, conserved motifs, protein sequences, and gene structures. Cis-regulatory elements mainly included hormone response elements and abiotic response elements. Functional annotation of GO revealed that AcLPP genes were closely related to phosphatase/hydrolase activity, phosphorus metabolism and dephosphorylation. AcLPP genes family were predicted to be targets of miRNA. Transcript level analysis revealed that the AcLPP family played diverse functions in different tissues and during growth, development, and postharvest storage stages. qPCR analysis showed that the members of AcLPP gene family might be regulated by ETH, ABA, GA3, and IAA hormone signals. The family members were regulated by the stress of salt stress, osmotic stress, cold stress, and heat stress. These results would provide a basis and reference for studying the agricultural characteristics of kiwifruit and improving its stress resistance.

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Genome-wide characterization and expression pattern of auxin response factor (ARF) gene family in soybean and common bean

Cited by 16 publications

References 47 publications

Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensisSonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission

Identification and expression analysis of the lipid phosphate phosphatases gene family reveal their involvement in abiotic stress response in kiwifruit

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