scholarly journals Characterization of cotton ARF factors and the role of GhARF2b in fiber development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiufang Zhang ◽  
Junfeng Cao ◽  
Chaochen Huang ◽  
Zishou Zheng ◽  
Xia Liu ◽  
...  

AbstractBackgroundCotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.ResultsHere, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cottonG. hirsutum, which has 73 ARF genes, and its putative extent parental diploidsG. arboreumandG. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that inG. hirsutum ARFgenes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate thatGhARF2b, a homolog of the ArabidopsisAtARF2, was preferentially expressed in developing ovules and fibers. Overexpression ofGhARF2bby a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.ConclusionOur results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

2020 ◽  
Author(s):  
Xiufang Zhang ◽  
Junfeng Cao ◽  
Chaochen Huang ◽  
Zishou Zheng ◽  
Xia Liu ◽  
...  

Abstract Background: Cotton fiber is a model system for studying plant cell development. At present, our understanding of cotton fiber development and the regulatory network is still primitive. Results: Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi of resulted in fewer but longer fiber. Conclusion: Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.


Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 128 ◽  
Author(s):  
Haron Salih ◽  
Shoupu He ◽  
Hongge Li ◽  
Zhen Peng ◽  
Xiongming Du

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.


Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2461
Author(s):  
Dongjie Yang ◽  
Yuanyuan Liu ◽  
Hailiang Cheng ◽  
Qiaolian Wang ◽  
Limin Lv ◽  
...  

Amino acid transporters (AATs) are a kind of membrane proteins that mediate the transport of amino acids across cell membranes in higher plants. The AAT proteins are involved in regulating plant cell growth and various developmental processes. However, the biological function of this gene family in cotton fiber development is not clear. In this study, 190, 190, 101, and 94 full-length AAT genes were identified from Gossypiumhirsutum, G. barbadense, G. arboreum, and G. raimondii. A total of 575 AAT genes from the four cotton species were divided into two subfamilies and 12 clades based on phylogenetic analysis. The AAT genes in the four cotton species were distributed on all the chromosomes. All GhAAT genes contain multiple exons, and each GhAAT protein has multiple conserved motifs. Transcriptional profiling and RT qPCR analysis showed that four GhATT genes tend to express specifically at the fiber initiation stage. Eight genes tend to express specifically at the fiber elongation and maturity stage, and four genes tend to express specifically at the fiber initiation and elongation stages. Our results provide a solid basis for further elucidating the biological function of AAT genes related to cotton fiber development and offer valuable genetic resources for crop improvement in the future.


2010 ◽  
Vol 57 (4) ◽  
pp. 462-468 ◽  
Author(s):  
Wenbin Liao ◽  
Juan Zhang ◽  
Nanfei Xu ◽  
Ming Peng

2012 ◽  
Vol 39 (9) ◽  
pp. 736 ◽  
Author(s):  
Hai Liu ◽  
Shenghua Jia ◽  
Defeng Shen ◽  
Jin Liu ◽  
Jie Li ◽  
...  

MicroRNA167 (miR167), as a conserved miRNA, has been implicated in auxin signalling by regulating the expression of certain auxin response factor (ARF) genes to determine the plant developmental process. Among the 10 MIR167 genes of rice, the precursor structures derived from MIR167a, MIR167b and MIR167c produce miR167 with high efficiency. To explore the biological function of miR167 in rice, four of its predicted target genes, OsARF6, OsARF12, OsARF17 and OsARF25, were identified in vivo. Although the expression levels of miR167 and its target OsARFs did not show an obvious negative correlation, the enhanced miR167 level in transgenic rice overexpressing miR167 resulted in a substantial decrease in mRNA levels of the four OsARF genes. Moreover, the transgenic rice plants were small in stature with remarkably reduced tiller number. These results suggest that miR167 is important for the appropriate expression of at least four OsARFs, which mediate the auxin response, to contribute to the normal growth and development of rice.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Senmiao FAN ◽  
Aiying LIU ◽  
Xianyan ZOU ◽  
Zhen ZHANG ◽  
Qun GE ◽  
...  

Abstract Background Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTs has not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development. Results In this study, we have identified 131 GAUT genes in the genomes of four Gossypium species (G. raimondii, G. barbadense, G. hirsutum, and G. arboreum), and classified them as GAUT-A, GAUT-B and GAUT-C, which coding probable galacturonosyltransferases. Among them, the GAUT genes encode proteins GAUT1 to GAUT15. All GAUT proteins except for GAUT7 contain a conserved glycosyl transferase family 8 domain (H-DN-A-SVV-S-V-H-T-F). The conserved sequence of GAUT7 is PLN (phospholamban) 02769 domain. According to cis-elemet analysis, GAUT genes transcript levels may be regulated by hormones such as JA, GA, SA, ABA, Me-JA, and IAA. The evolution and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber strength were analyzed. Peak transcript level of GhGAUT genes have been observed before 15 DPA. In the six materials with high fiber strength, the transcription of GhGAUT genes were concentrated from 10 to 15 DPA; while the highest transcript levels in low fiber strength materials were detected between 5 and 10 DPA. These results lays the foundation for future research on gene function during cotton fiber development. Conclusions The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low strength fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high strength fiber is related to both elongation and thickening.


2016 ◽  
Author(s):  
Sizolwenkosi Mlotshwa ◽  
Gail J. Pruss ◽  
John L. Macarthur ◽  
Jason W. Reed ◽  
Vicki Vance

AbstractPlant viral suppressors of RNA silencing induce developmental defects similar to those caused by mutations in genes involved in the microRNA (miRNA) pathway. These abnormalities were originally thought to reflect a pleiotropic impact of silencing suppressors on miRNA control of plant development. However, subsequent work with the P1/HC-Pro potyviral suppressor of silencing showed that global impairment of the miRNA pathway was not responsible for the phenotypical anomalies. More recently, developmental defects caused by a P1/HC-Pro transgene under control of the 35S promoter were attributed to moderate upregulation of AUXIN RESPONSE FACTOR 8 (ARF8), a target of miR167. The key piece of evidence in that work was that the developmental defects in the 35S-pro:P1/HC-Pro transgenic Arabidopsis were greatly alleviated in the F1 progeny of a cross with plants carrying the arf8-6 mutation. Arf8-6 is a SALK line T-DNA insertion mutant, a class of mutations prone to inducing transcriptional silencing of transgenes expressed from the 35S promoter. Here we report a re-investigation of the role of ARF8 in P1/HC-Pro-mediated developmental defects. We characterized the progeny of a cross between our 35S-pro:P1/HC-Pro transgenic Arabidopsis line and the same arf8-6 T-DNA insertion mutant used in the earlier study. The T-DNA mutation had little effect in the F1 generation, but almost all arf8-6/P1/HC-Pro progeny had lost the P1/HC-Pro phenotype in the F2 generation. However, this loss of phenotype was not correlated with the number of functional copies of the ARF8 gene. Instead, it reflected transcriptional silencing of the 35S-pro:P1/HC-Pro transgene, as evidenced by a pronounced decrease in P1/HC-Pro mRNA2accompanied by the appearance of 35S promoter siRNAs. Furthermore, arf8-8, an independent loss-of-function point mutation, had no detectable effects on P1/HC-Pro phenotype in either the F1 or F2 generations. Together these data argue against the reported role of increased ARF8 expression in mediating developmental defects in P1/HC-Pro transgenic plants.Author SummaryRNA silencing is an important antiviral defense in plants that uses small RNA molecules to target the invading RNA. Plant viruses, however, have countered with proteins that suppress RNA silencing, and one of the best-studied plant viral suppressors of silencing is P1/HC-Pro. When the genetic model plant Arabidopsis thaliana is bioengineered to express P1/HC-Pro, the resulting plants display distinct developmental abnormalities. These abnormalities are thought to arise because P1/HC-Pro also interferes with the arm of RNA silencing that uses small RNAs called microRNAs (miRNAs) to regulate expression of the plant's own genes. Earlier work, however, showed that interference with all miRNAs in general could not be responsible for these developmental defects. More recently, it was reported that enhanced expression of a single miRNA-controlled gene, AUXIN RESPONSE FACTOR 8 (ARF8), underlies the developmental defects caused by P1/HC-Pro. However, using the same ARF8 mutation as that report, as well as a second, independent ARF8 loss-of function mutation, we now show that mis-regulation of ARF8 is not responsible for those defects. One or a few key miRNA-controlled factors might, in fact, underlie the developmental defects caused by P1/HC-Pro; however, our results show that ARF8 is not one of the key factors.


1986 ◽  
Vol 5 (1) ◽  
pp. 17-27 ◽  
Author(s):  
Vrinda S. Thaker ◽  
Sant Saroop ◽  
Pankaj P. Vaishnav ◽  
Yash Dev Singh

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