Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa

Abstract

Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13–17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18–20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

“…The ARF gene was initially identified to have 23 members in the model plant Arabidopsis and has since been identified in multiple species [ 5 ]. Rice has 25 ARF members [ 11 ], apple ( Malus domestica ) has 31 ARF members [ 55 ], silver birch ( Betula pendula ) has 17 members [ 56 ], birch ( Betula platyphylla ) has 15 members [ 57 ], Euscaphis konishii has 29 members [ 26 ], and Populus has 35 members [ 12 ]. However, the ARF gene has not yet been identified in Korean pine.…”

“…Similarly, in both Populus and Populus yunnanensis , which have 19 chromosomes, the ARF genes were distributed on 16 chromosomes, and the distribution of genes on different chromosomes was also uneven. Chromosome 1 was found to be the longest in both Populus and Populus yunnanensis , but it had fewer ARF genes [ 12 , 58 ]. The analysis indicated that ARF genes are distributed similarly on the chromosomes of woody plants, and the number of ARF genes on each chromosome is independent of chromosome length.…”

“…The proportion of PkorARF members lacking CTD domains in Korean pine (38.5%) is higher than that in other species, such as Arabidopsis (17.39%) [ 10 ], tomato ( Solanum lycopersicum ) (28.6%) [ 59 ], Brassica juncea var. tumida (22.6%) [ 60 ], and Populus (37.5%) [ 12 ]. However, the proportion of structural domains lacking in PkorARF (38.5%) is similar to that of PtrARF (37.5%), suggesting both variability in structure among different species and similarity in structure among closely related species.…”

“…With the advancement in genome sequencing, ARF genes have been identified in various species, including Arabidopsis ( Arabidopsis thaliana ) [ 10 ], rice ( Oryza sativa ) [ 11 ], Populus ( Populus trichocarpa ) [ 12 ], Soybean ( Glycine max ) [ 13 ], maize ( Zea mays ) [ 14 ]. The first ARF gene, AtARF1 , was initially discovered in the model plant Arabidopsis [ 10 ].…”

“…In addition, EkARF5.1 directly interacts with auxin response elements to regulate anthocyanin synthesis during fruit ripening in Euscaphis konishii [ 26 ]. In the case of Populus, the nuclear interaction between PtrARF23 and PtrIAA10, as well as PtrIAA28, is responsible for regulating wood formation [ 12 ]. The peu-miR160a-PeARF17.1/PeARF17.2 module is an important regulator involved in the development of the adventitious roots of poplar [ 27 ].…”