Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.)

Zhai, Yufeng; Shen, Xiaoxia; Sun, Yipeng; Li, Qiao; Ma, Nan; Zhang, Xiaodan; Jia, Qiaojun; Liang, Zongsuo; Wang, Dekai

doi:10.1007/s00709-023-01855-5

Cited by 6 publications

(5 citation statements)

References 43 publications

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“…To explore the molecular mechanisms of auxin signal transduction, Aux/IAA and ARF genes have been identified and characterized in several plant species, including Arabidopsis thaliana [ 13 ], Malus [ 14 ], Zea mays [ 15 ], Coix lacryma-jobi [ 16 ], tomato [ 17 ], soybean [ 18 ], Vitis vinifera [ 19 ], Brassica rapa [ 20 ], Triticum aestivum [ 21 ], sorghum [ 22 ], Citrus sinensis [ 23 ] and Cucumis sativus [ 24 ]. Previous studies have found that the functions of Aux/IAA and ARF genes are relatively different in different plants [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

Effects of PmaIAA27 and PmaARF15 genes on drought stress tolerance in pinus massoniana

Li,

Quan

et al. 2023

BMC Plant Biol

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Background Auxin plays an important role in plant resistance to abiotic stress. The modulation of gene expression by Auxin response factors (ARFs) and the inhibition of auxin/indole-3-acetic acid (Aux/IAA) proteins play crucial regulatory roles in plant auxin signal transduction. However, whether the stress resistance of Masson pine (Pinus massoniana), as a representative pioneer species, is related to Aux/IAA and ARF genes has not been thoroughly studied and explored. Results The present study provides preliminary evidence for the regulatory role of the PmaIAA27 gene in abiotic stress response in Masson pine. We investigated the effects of drought and hormone treatments on Masson pine by examining the expression patterns of PmaIAA27 and PmaARF15 genes. Subsequently, we conducted gene cloning, functional testing using transgenic tobacco, and explored gene interactions. Exogenous auxin irrigation significantly downregulated the expression of PmaIAA27 while upregulating PmaARF15 in Masson pine seedlings. Moreover, transgenic tobacco with the PmaIAA27 gene exhibited a significant decrease in auxin content compared to control plants, accompanied by an increase in proline content - a known indicator of plant drought resistance. These findings suggest that overexpression of the PmaIAA27 gene may enhance drought resistance in Masson pine. To further investigate the interaction between PmaIAA27 and PmaARF15 genes, we performed bioinformatics analysis and yeast two-hybrid experiments which revealed interactions between PB1 structural region of PmaARF15 and PmaIAA27. Conclusion The present study provides new insights into the regulatory functions of Aux/IAA and ARF genes in Masson pine. Overexpression of PmaIAA gene may have negative effects on the growth of Masson pine, but may improve the drought resistance. Therefore, this study has great application prospects.

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Section: Introductionmentioning

confidence: 99%

Effects of PmaIAA27 and PmaARF15 genes on drought stress tolerance in pinus massoniana

Li,

Quan

et al. 2023

BMC Plant Biol

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“…Our findings showed that fragmental duplication events of SpapARFs and SpnpARFs were detected in both genomes, especially in Np-X, but no tandem duplication event occurred, suggesting that segmental duplication events are mainly promoting the expansion of the ARF gene family. Zhai et al (2023) also proposed that segmental duplication, rather than tandem duplications, contributed to the expansion of the ARF gene family in Coix lacryma-jobi . Additionally, the whole genome duplication may also contribute to this gene expansion in S. spontaneum due to the ploidy level of this plant species, which ranges from tetraploid (4x) to hexaploid (16x) ( Zhang et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, AcARF10 (homolog of ShARF04 ) was downregulated, but AcARF19a (homolog of ShARF07 ) and AcARF26a (homolog of ShARF17 ) were upregulated across all time points in A. chinensis against SA stress ( Su et al, 2021 ). In addition, transcript levels of ClARF5 (homolog of ShARF04 ), ClARF (homolog of ShARF07 ), and ClARF7 (homolog of ShARF17 ) were upregulated by SA application during all time points in C. lacryma-jobi ( Zhai et al, 2023 ). Taken together, these homologous ARF genes may act as positive or negative regulators against exogenous SA stress, depending on plant species.…”

Section: Discussionmentioning

confidence: 99%

“…AcARF1a and AcARF10 were negatively responsive to SA stress in kiwifruit ( Actinidia chinensis ) ( Su et al, 2021 ). Three ClARF genes ( ClARF4/8/12 ) were negatively regulated in response to abscisic acid (ABA) and SA treatments, while ClARF20 was positively regulated under Indole-3-acetic acid (IAA) and SA treatments ( Zhai et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Lin,

Ali,

Chu

et al. 2023

Front. Microbiol.

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Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 SpapARFs and 39 SpnpARFs were identified in two genomes of Saccharum spontaneum clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all ARF genes were clustered into four clades, which is identical to those ARF genes in maize (Zea mays) and sorghum (Sorghum bicolor). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The SpapARF and SpnpARF genes were unevenly distributed on chromosomes 1–8 and 1–10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in S. spontaneum. The post-transcriptional regulation of ARF genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative ShARF genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections and salicylic acid (SA) treatment. ShARF04 functioned as a positive regulator under Xa and Aaa stress, whereas it was a negative regulator under SA treatment. ShARF07/17 genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, ShARF22 was negatively modulated by Xa and Aaa stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane ARFs exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on ARF gene functions in sugarcane against diverse environmental stressors.

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“…It is worth highlighting that Job’s tears are considered the most closely related crop to sorghum [ 28 ]. The waterlogging-tolerant and humidity-induced disease-resistant traits observed in the Coix family, to which Job’s tears belong, are anticipated to contribute to the improvement in resistance breeding in maize and sorghum [ 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Spatial O2 Profile in Coix lacryma-jobi and Sorghum bicolor along the Gas Diffusion Pathway under Waterlogging Conditions

Tamaru,

Goto,

Sakagami

2023

Plants

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While internal aeration in plants is critical for adaptation to waterlogging, there is a gap in understanding the differences in oxygen diffusion gradients from shoots to roots between hypoxia-tolerant and -sensitive species. This study aims to elucidate the differences in tissue oxygen concentration at various locations on the shoot and root between a hypoxia-tolerant species and a -sensitive species using a microneedle sensor that allows for spatial oxygen profiling. Job’s tears, a hypoxia-tolerant species, and sorghum, a hypoxia-susceptible species, were tested. Plants aged 10 days were acclimated to a hypoxic agar solution for 12 days. Oxygen was profiled near the root tip, root base, root shoot junction, stem, and leaf. An anatomical analysis was also performed on the roots used for the O2 profile. The oxygen partial pressure (pO2) values at the root base and tip of sorghum were significantly lower than that of the root of Job’s tears. At the base of the root of Job’s tears, pO2 rapidly decreased from the root cortex to the surface, indicating a function to inhibit oxygen leakage. No significant differences in pO2 between the species were identified in the shoot part. The root cortex to stele ratio was significantly higher from the root tip to the base in Job’s tears compared to sorghum. The pO2 gradient began to differ greatly at the root shoot junction and root base longitudinally, and between the cortex and stele radially, between Job’s tears and sorghum. Differences in the root oxygen retention capacity and the cortex to stele ratio are considered to be related to differences in pO2.

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Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.)

Cited by 6 publications

References 43 publications

Effects of PmaIAA27 and PmaARF15 genes on drought stress tolerance in pinus massoniana

Effects of PmaIAA27 and PmaARF15 genes on drought stress tolerance in pinus massoniana

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Spatial O2 Profile in Coix lacryma-jobi and Sorghum bicolor along the Gas Diffusion Pathway under Waterlogging Conditions

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