Genome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in <i>Linum usitatissimum</i>
Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, <i>ARF</i> genes have not been investigated in flax (<i>Linum usitatissimum</i> L.), an important oilseed and fiber crop. In...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/13/11006 |
| Summary: | Auxin response factors (ARFs) are critical components of the auxin signaling pathway, and are involved in diverse plant biological processes. However, <i>ARF</i> genes have not been investigated in flax (<i>Linum usitatissimum</i> L.), an important oilseed and fiber crop. In this study, we comprehensively analyzed the <i>ARF</i> gene family and identified 33 <i>LuARF</i> genes unevenly distributed on the 13 chromosomes of Longya-10, an oil-use flax variety. Detailed analysis revealed wide variation among the ARF family members and predicted nuclear localization for all proteins. Nineteen LuARFs contained a complete ARF structure, including DBD, MR, and CTD, whereas the other fourteen lacked the CTD. Phylogenetic analysis grouped the LuARFs into four (I–V) clades. Combined with sequence analysis, the LuARFs from the same clade showed structural conservation, implying functional redundancy. Duplication analysis identified twenty-seven whole-genome-duplicated <i>LuARF</i> genes and four tandem-duplicated <i>LuARF</i> genes. These duplicated gene pairs’ K<sub>a</sub>/K<sub>s</sub> ratios suggested a strong purifying selection pressure on the <i>LuARF</i> genes. Collinearity analysis revealed that about half of the <i>LuARF</i> genes had homologs in other species, indicating a relatively conserved nature of the <i>ARFs</i>. The promoter analysis identified numerous hormone- and stress-related elements, and the qRT-PCR experiment revealed that all <i>LuARF</i> genes were responsive to phytohormone (IAA, GA3, and NAA) and stress (PEG, NaCl, cold, and heat) treatments. Finally, expression profiling of <i>LuARF</i> genes in different tissues by qRT-PCR indicated their specific functions in stem or capsule growth. Thus, our findings suggest the potential functions of <i>LuARFs</i> in flax growth and response to an exogenous stimulus, providing a basis for further functional studies on these genes. |
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| ISSN: | 1661-6596 1422-0067 |