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Gao X, Liu X, Zhang H, Cheng L, Wang X, Zhen C, Du H, Chen Y, Yu H, Zhu B, Xiao J. Genome-Wide Identification, Expression, and Interaction Analysis of the Auxin Response Factor and AUX/ IAA Gene Families in Vaccinium bracteatum. Int J Mol Sci 2024; 25:8385. [PMID: 39125955 PMCID: PMC11312502 DOI: 10.3390/ijms25158385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Auxin, a plant hormone, plays diverse roles in the modulation of plant growth and development. The transport and signal transduction of auxin are regulated by various factors involved in shaping plant morphology and responding to external environmental conditions. The auxin signal transduction is primarily governed by the following two gene families: the auxin response factor (ARF) and auxin/indole-3-acetic acid (AUX/IAA). However, a comprehensive genomic analysis involving the expression profiles, structures, and functional features of the ARF and AUX/IAA gene families in Vaccinium bracteatum has not been carried out to date. RESULTS Through the acquisition of genomic and expression data, coupled with an analysis using online tools, two gene family members were identified. This groundwork provides a distinguishing characterization of the chosen gene families in terms of expression, interaction, and response in the growth and development of plant fruits. In our genome-wide search of the VaARF and VaIAA genes in Vaccinium bracteatum, we identified 26 VaARF and 17 VaIAA genes. We analyzed the sequence and structural characteristics of these VaARF and VaIAA genes. We found that 26 VaARF and 17 VaIAA genes were divided into six subfamilies. Based on protein interaction predictions, VaIAA1 and VaIAA20 were designated core members of VaIAA gene families. Moreover, an analysis of expression patterns showed that 14 ARF genes and 12 IAA genes exhibited significantly varied expressions during fruit development. CONCLUSION Two key genes, namely, VaIAA1 and VaIAA20, belonging to a gene family, play a potentially crucial role in fruit development through 26 VaARF-IAAs. This study provides a valuable reference for investigating the molecular mechanism of fruit development and lays the foundation for further research on Vaccinium bracteatum.
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Affiliation(s)
- Xuan Gao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
| | - Xiaohui Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
| | - Hong Zhang
- Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (H.Z.); (X.W.); (Y.C.); (H.Y.)
| | - Li Cheng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
| | - Xingliang Wang
- Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (H.Z.); (X.W.); (Y.C.); (H.Y.)
| | - Cheng Zhen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
| | - Haijing Du
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
| | - Yufei Chen
- Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (H.Z.); (X.W.); (Y.C.); (H.Y.)
| | - Hongmei Yu
- Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (H.Z.); (X.W.); (Y.C.); (H.Y.)
| | - Bo Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
| | - Jiaxin Xiao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.G.); (X.L.); (L.C.); (C.Z.); (H.D.)
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Qi T, Yang W, Hassan MJ, Liu J, Yang Y, Zhou Q, Li H, Peng Y. Genome-wide identification of Aux/IAA gene family in white clover (Trifolium repens L.) and functional verification of TrIAA18 under different abiotic stress. BMC PLANT BIOLOGY 2024; 24:346. [PMID: 38684940 PMCID: PMC11057079 DOI: 10.1186/s12870-024-05034-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND White clover (Trifolium repens L.) is an excellent leguminous cool-season forage with a high protein content and strong nitrogen-fixing ability. Despite these advantages, its growth and development are markedly sensitive to environmental factors. Indole-3-acetic acid (IAA) is the major growth hormone in plants, regulating plant growth, development, and response to adversity. Nevertheless, the specific regulatory functions of Aux/IAA genes in response to abiotic stresses in white clover remain largely unexplored. RESULTS In this study, we identified 47 Aux/IAA genes in the white clover genome, which were categorized into five groups based on phylogenetic analysis. The TrIAAs promoter region co-existed with different cis-regulatory elements involved in developmental and hormonal regulation, and stress responses, which may be closely related to their diverse regulatory roles. Collinearity analysis showed that the amplification of the TrIAA gene family was mainly carried out by segmental duplication. White clover Aux/IAA genes showed different expression patterns in different tissues and under different stress treatments. In addition, we performed a yeast two-hybrid analysis to investigate the interaction between white clover Aux/IAA and ARF proteins. Heterologous expression indicated that TrIAA18 could enhance stress tolerance in both yeast and transgenic Arabidopsis thaliana. CONCLUSION These findings provide new scientific insights into the molecular mechanisms of growth hormone signaling in white clover and its functional characteristics in response to environmental stress.
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Affiliation(s)
- Tiangang Qi
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weiqiang Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiefang Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujiao Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinyu Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Da Ros L, Bollina V, Soolanayakanahally R, Pahari S, Elferjani R, Kulkarni M, Vaid N, Risseuw E, Cram D, Pasha A, Esteban E, Konkin D, Provart N, Nambara E, Kagale S. Multi-omics atlas of combinatorial abiotic stress responses in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1118-1135. [PMID: 37248640 DOI: 10.1111/tpj.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/10/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Field-grown crops rarely experience growth conditions in which yield can be maximized. Environmental stresses occur in combination, with advancements in crop tolerance further complicated by its polygenic nature. Strategic targeting of causal genes is required to meet future crop production needs. Here, we employed a systems biology approach in wheat (Triticum aestivum L.) to investigate physio-metabolic adjustments and transcriptome reprogramming involved in acclimations to heat, drought, salinity and all combinations therein. A significant shift in magnitude and complexity of plant response was evident across stress scenarios based on the agronomic losses, increased proline concentrations and 8.7-fold increase in unique differentially expressed transcripts (DETs) observed under the triple stress condition. Transcriptome data from all stress treatments were assembled into an online, open access eFP browser for visualizing gene expression during abiotic stress. Weighted gene co-expression network analysis revealed 152 hub genes of which 32% contained the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) transcriptional repression motif. Cross-referencing against the 31 DETs common to all stress treatments isolated TaWRKY33 as a leading candidate for greater plant tolerance to combinatorial stresses. Integration of our findings with available literature on gene functional characterization allowed us to further suggest flexible gene combinations for future adaptive gene stacking in wheat. Our approach demonstrates the strength of robust multi-omics-based data resources for gene discovery in complex environmental conditions. Accessibility of such datasets will promote cross-validation of candidate genes across studies and aid in accelerating causal gene validation for crop resiliency.
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Affiliation(s)
- Letitia Da Ros
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Venkatesh Bollina
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Raed Elferjani
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Manoj Kulkarni
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Eddy Risseuw
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
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Lin JX, Ali A, Chu N, Fu HY, Huang MT, Mbuya SN, Gao SJ, Zhang HL. Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane. Front Microbiol 2023; 14:1257355. [PMID: 37744907 PMCID: PMC10513436 DOI: 10.3389/fmicb.2023.1257355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
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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Affiliation(s)
- Jia-Xin Lin
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Na Chu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua-Ying Fu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mei-Ting Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sylvain Ntambo Mbuya
- Faculté des Sciences Agronomiques, Département de production végétale, Laboratoire de Recherche en Biofortification, Defense et Valorisation des Cultures (BioDev), Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui-Li Zhang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
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Wang H, Zhai L, Wang S, Zheng B, Hu H, Li X, Bian S. Identification of R2R3-MYB family in blueberry and its potential involvement of anthocyanin biosynthesis in fruits. BMC Genomics 2023; 24:505. [PMID: 37648968 PMCID: PMC10466896 DOI: 10.1186/s12864-023-09605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Blueberries (Vaccinium corymbosum) are regarded as "superfoods" attributed to large amounts of anthocyanins, a group of flavonoid metabolites, which provide pigmentation in plant and beneficial effects for human health. MYB transcription factor is one of vital components in the regulation of plant secondary metabolism, which occupies a dominant position in the regulatory network of anthocyanin biosynthesis. However, the role of MYB family in blueberry responding to anthocyanin biosynthesis remains elusive. RESULTS In this study, we conducted a comprehensive analysis of VcMYBs in blueberry based on the genome data, including phylogenetic relationship, conserved motifs, identification of differentially expressed MYB genes during fruit development and their expression profiling, etc. A total of 437 unique MYB sequences with two SANT domains were identified in blueberry, which were divided into 3 phylogenetic trees. Noticeably, there are many trigenic and tetragenic VcMYBs pairs with more than 95% identity to each other. Meanwhile, the transcript accumulations of VcMYBs were surveyed underlying blueberry fruit development, and they showed diverse expression patterns, suggesting various functional roles in fruit ripening. More importantly, distinct transcript profiles between skin and pulp of ripe fruit were observed for several VcMYBs, such as VcMYB437, implying the potential roles in anthocyanin biosynthesis. CONCLUSIONS Totally, 437 VcMYBs were identified and characterized. Subsequently, their transcriptional patterns were explored during fruit development and fruit tissues (skin and pulp) closely related to anthocyanin biosynthesis. These genome-wide data and findings will contribute to demonstrating the functional roles of VcMYBs and their regulatory mechanisms for anthocyanins production and accumulation in blueberry in the future study.
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Affiliation(s)
- Haiyang Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, China
| | - Shouwen Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Botian Zheng
- College of Plant Science, Jilin University, Changchun, China
| | - Honglu Hu
- College of Plant Science, Jilin University, Changchun, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, China.
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China.
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Wang D, Zuo J, Liu S, Wang W, Lu Q, Hao X, Fang Z, Liang T, Sun Y, Guo C, Zhao C, Tang Y. BRI1 EMS SUPPRESSOR1 genes regulate abiotic stress and anther development in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1219856. [PMID: 37621887 PMCID: PMC10446898 DOI: 10.3389/fpls.2023.1219856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023]
Abstract
BRI1 EMS SUPPRESSOR1 (BES1) family members are crucial downstream regulators that positively mediate brassinosteroid signaling, playing vital roles in the regulation of plant stress responses and anther development in Arabidopsis. Importantly, the expression profiles of wheat (Triticum aestivum L.) BES1 genes have not been analyzed comprehensively and systematically in response to abiotic stress or during anther development. In this study, we identified 23 BES1-like genes in common wheat, which were unevenly distributed on 17 out of 21 wheat chromosomes. Phylogenetic analysis clustered the BES1 genes into four major clades; moreover, TaBES1-3A2, TaBES1-3B2 and TaBES1-3D2 belonged to the same clade as Arabidopsis BES1/BZR1 HOMOLOG3 (BEH3) and BEH4, which participate in anther development. The expression levels of 23 wheat BES1 genes were assessed using real-time quantitative PCR under various abiotic stress conditions (drought, salt, heat, and cold), and we found that most TaBES1-like genes were downregulated under abiotic stress, particularly during drought stress. We therefore used drought-tolerant and drought-sensitive wheat cultivars to explore TaBES1 expression patterns under drought stress. TaBES1-3B2 and TaBES1-3D2 expression was high in drought-tolerant cultivars but substantially repressed in drought-sensitive cultivars, while TaBES1-6D presented an opposite pattern. Among genes preferentially expressed in anthers, TaBES1-3B2 and TaBES1-3D2 expression was substantially downregulated in thermosensitive genic male-sterile wheat lines compared to common wheat cultivar under sterile conditions, while we detected no obvious differences under fertile conditions. This result suggests that TaBES1-3B2 and TaBES1-3D2 might not only play roles in regulating drought tolerance, but also participate in low temperature-induced male sterility.
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Affiliation(s)
- Dezhou Wang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Jinghong Zuo
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Shan Liu
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Weiwei Wang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Qing Lu
- Agriculture College, Yangtze University, Jingzhou, China
| | - Xiaocong Hao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Zhaofeng Fang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Ting Liang
- Agriculture College, Yangtze University, Jingzhou, China
| | - Yue Sun
- Agriculture College, Yangtze University, Jingzhou, China
| | - Chunman Guo
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Changping Zhao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
| | - Yimiao Tang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Hubei Collaborative Innovation Center for Grain Industry, Beijing, China
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Li H, Liu H, Hao C, Li T, Liu Y, Wang X, Yang Y, Zheng J, Zhang X. The auxin response factor TaARF15-A1 negatively regulates senescence in common wheat (Triticum aestivum L.). PLANT PHYSIOLOGY 2023; 191:1254-1271. [PMID: 36282536 PMCID: PMC9922429 DOI: 10.1093/plphys/kiac497] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 05/06/2023]
Abstract
Auxin plays an important role in regulating leaf senescence. Auxin response factors (ARFs) are crucial components of the auxin signaling pathway; however, their roles in leaf senescence in cereal crops are unknown. In this study, we identified TaARF15-A1 as a negative regulator of senescence in wheat (Triticum aestivum L.) by analyzing TaARF15-A1 overexpression (OE) and RNA interference lines and CRISPR/Cas9-based arf15 mutants. OE of TaARF15-A1 delayed senescence, whereas knockdown lines and knockout mutants showed accelerated leaf senescence and grain ripening. RNA-seq analysis revealed that TaARF15-A1 delays leaf senescence by negatively regulating senescence-promoting processes and positively modulating senescence-delaying genes including senescence-associated phytohormone biosynthesis and metabolism genes as well as transcription factors (TFs). We also demonstrated that TaARF15-A1 physically interacts with TaMYC2, a core jasmonic acid (JA) signaling TF that positively modulates wheat senescence. Furthermore, TaARF15-A1 suppressed the expression of TaNAM-1 (TaNAM-A1 and TaNAM-D1) via protein-protein interaction and competition with TaMYC2 for binding to its promoter to regulate senescence. Finally, we identified two haplotypes of TaARF15-A1 in global wheat collections. Association analysis revealed that TaARF15-A1-HapI has undergone strong selection during wheat breeding in China, likely owing to its earlier maturity. Thus, we identify TaARF15-A1 as a negative regulator of senescence in common wheat and present another perspective on the crosstalk between auxin and JA signaling pathways in regulating plant senescence.
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Affiliation(s)
- Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050000, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaolu Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yuxin Yang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yi SN, Mao JX, Zhang XY, Li XM, Zhang ZH, Li H. FveARF2 negatively regulates fruit ripening and quality in strawberry. FRONTIERS IN PLANT SCIENCE 2022; 13:1023739. [PMID: 36388474 PMCID: PMC9660248 DOI: 10.3389/fpls.2022.1023739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Auxin response factors (ARFs) are transcription factors that play important roles in plants. ARF2 is a member of the ARF family and participates in many plant growth and developmental processes. However, the role of ARF2 in strawberry fruit quality remains unclear. In this study, FveARF2 was isolated from the woodland strawberry 'Ruegen' using reverse transcription-polymerase chain reaction (RT-PCR), which showed that FveARF2 expression levels were higher in the stem than in other organs of the 'Ruegen' strawberry. Moreover, FaARF2 was higher in the white fruit stage of cultivated strawberry fruit than in other stage. Subcellular localization analysis showed that FveARF2 is located in the nucleus, while transcriptional activation assays showed that FveARF2 inhibited transcription in yeast. Silencing FveARF2 in cultivated strawberry fruit revealed earlier coloration and higher soluble solid, sugar, and anthocyanin content in the transgenic fruit than in the control fruit, overexpression of FveARF2 in strawberry fruit delayed ripening and lower soluble solid, sugar, and anthocyanin content compared to the control fruit. Gene expression analysis indicated that the transcription levels of the fruit ripening genes FaSUT1, FaOMT, and FaCHS increased in FveARF2-RNAi fruit and decreased in FveARF2-OE fruit, when compared with the control. Furthermore, yeast one-hybrid (Y1H) and GUS activity experiments showed that FveARF2 can directly bind to the AuxRE (TGTCTC) element in the FaSUT1, FaOMT, and FaCHS promoters in vitro and in vivo. Potassium ion supplementation improved the quality of strawberry fruit, while silencing FveARF2 increased potassium ion content in transgenic fruit. The Y1H and GUS activity experiments also confirmed that FveARF2 could directly bind to the promoter of FveKT12, a potassium transporter gene, and inhibited its expression. Taken together, we found that FveARF2 can negatively regulate strawberry fruit ripening and quality, which provides new insight for further study of the molecular mechanism of strawberry fruit ripening.
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Affiliation(s)
- Shan-na Yi
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jian-xin Mao
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xin-yu Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Vegetable Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xiao-ming Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhi-hong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, China
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9
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Devate NB, Krishna H, Sunilkumar VP, Manjunath KK, Mishra CN, Jain N, Singh GP, Singh PK. Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study. Front Genet 2022; 13:1034947. [PMID: 36338980 PMCID: PMC9634069 DOI: 10.3389/fgene.2022.1034947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 09/10/2023] Open
Abstract
Wheat is the staple food crop of global importance for its grain nutrient quality. Grain iron and zinc content of the wheat grain is an important quantitatively inherited trait that is influenced by the environmental factors such as drought and heat stress. Phenotypic evaluation of 295 advanced breeding lines from the wheat stress breeding program of IARI was carried out under timely sown irrigated (IR), restricted irrigated, and late-sown conditions at New Delhi during the cropping season of 2020-21, and grain iron (GFeC) and zinc (GZnC) contents were estimated from both control and treatments. A statistically significant increase in GFeC and GZnC was observed under stress conditions compared to that of the control. Genotyping was carried out with the SNPs from the 35K Axiom Breeder's array, and marker-trait association was identified by GWAS analysis. Of the 23 MTAs identified, seven were linked with GFeC and sixteen were linked with GZnC. In silico analysis revealed a few important transcripts involved in various plant metabolism, growth, and development activities such as auxin response factor, root UVB sensitive proteins, potassium transporter, glycosyl transferase, COBRA, and F-box-like domain. The identified MTAs can be used for molecular breeding after validation and also for rapid development of micronutrient-rich varieties of wheat to mitigate hidden hunger.
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Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - V. P. Sunilkumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - C. N. Mishra
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. P. Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - P. K. Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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10
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Ma X, Zhao F, Su K, Lin H, Guo Y. Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq. BMC Genomics 2022; 23:551. [PMID: 35918639 PMCID: PMC9347155 DOI: 10.1186/s12864-022-08788-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022] Open
Abstract
Background In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have been reported based on the study of V. amurensis. In order to identify more candidate genes related to cold resistance in V. amurensis, QTL mapping and RNA-seq was conducted based on the hybrid population and different cold-resistance cultivars in this study. Results In this study, highly cold-resistant grape cultivar ‘Shuangyou’ (SY) which belongs to V. amurensis, and cold-sensitive cultivar ‘Red Globe’ (RG) which belongs to Vitis vinifera L. were used to identify cold resistance genes. Cold-resistance quantitative trait locus (QTL) mapping was performed based on genetic population construction through interspecific crossing of ‘Shuangyou’ and ‘Red Globe’. Additionally, transcriptome analysis was conducted for the dormant buds of these two cultivars at different periods. Based on transcriptome analysis and QTL mapping, many new structural genes and transcription factors which relate to V. amurensis cold resistance were discovered, including CORs (VaCOR413IM), GSTs (VaGST-APIC, VaGST-PARB, VaGSTF9 and VaGSTF13), ARFs (VaIAA27 and VaSAUR71), ERFs (VaAIL1), MYBs (VaMYBR2, VaMYBLL and VaMYB3R-1) and bHLHs (VaICE1 and VabHLH30). Conclusions This discovery of candidate cold-resistance genes will provide an important theoretical reference for grape cold-resistance mechanisms, research, and cold-resistant grape cultivar breeding in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08788-y.
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Affiliation(s)
- Xiaolele Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, 110866, People's Republic of China
| | - Fangyuan Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, 110866, People's Republic of China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China. .,College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, People's Republic of China. .,Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, 066004, People's Republic of China.
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, 110866, People's Republic of China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China. .,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, 110866, People's Republic of China.
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11
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Hajibarat Z, Saidi A. Senescence-associated proteins and nitrogen remobilization in grain filling under drought stress condition. J Genet Eng Biotechnol 2022; 20:101. [PMID: 35819732 PMCID: PMC9276853 DOI: 10.1186/s43141-022-00378-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022]
Abstract
Background Plants use escape strategies including premature senescence and leaf reduction to cope in response to drought stress, which in turn reduces plant leaves and photosynthesis. This strategy allows the new generation (seeds) to survive under drought but, plants experience more yield loss during stress condition. The amount of damage caused by drought stress is compensated by the expression of genes involved in regulating leaf aging. Leaf senescence alters the expression of thousands of genes and ultimately affecting grain protein content, grain yield, and nitrogen utilization efficiency. Also, under drought stress, nitrogen in the soil will not become as much available and causes the beginning and acceleration of the senescence process of leaves. The main body of the abstract This review identified proteins signaling and functional proteins involved in senescence. Further, transcription factors and cell wall degradation enzymes (proteases) related to senescence during drought stress were surveyed. We discuss the regulatory pathways of genes as a result of the degradation of proteins during senescence process. Senescence is strongly influenced by plant hormones and environmental factors including the availability of nitrogen. During maturity or drought stress, reduced nitrogen uptake can cause nitrogen to be remobilized from leaves and stems to seeds, eventually leading to leaf senescence. Under these conditions, genes involved in chloroplast degradation and proteases show increased expression. The functional (proteases) and regulatory proteins such as protein kinases and phosphatases as well as transcription factors (AP2/ERF, NAC, WRKY, MYB, and bZIP) are involved in leaf senescence and drought stress. Short conclusion In this review, senescence-associated proteins involved in leaf senescence and regulatory and functional proteins in response to drought stress during grain filling were surveyed. The present study predicts on the role of nitrogen transporters, transcription factors and regulatory genes involved in the late stages of plant growth with the aim of understanding their mechanisms of action during grain filling stage. For a better understanding, the relevant evidence for the balance between grain filling and protein breakdown during grain filling in cereals is presented.
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Affiliation(s)
- Zohreh Hajibarat
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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12
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Genetic Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.). Life (Basel) 2022; 12:life12050700. [PMID: 35629367 PMCID: PMC9147279 DOI: 10.3390/life12050700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first domesticated crop and is the most popular cereal crop in the world. Because of a lack of systematic research on cold signaling pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway under cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic processes and elements. This review also highlights possible strategies for improving cold tolerance in wheat.
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13
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Verma S, Negi NP, Pareek S, Mudgal G, Kumar D. Auxin response factors in plant adaptation to drought and salinity stress. PHYSIOLOGIA PLANTARUM 2022; 174:e13714. [PMID: 35560231 DOI: 10.1111/ppl.13714] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Salinity and drought stresses affect plant growth worldwide and limit crop production. Auxin is crucial in regulating plants' salinity and drought stress adaptative response. As a chemical messenger, auxin influences gene expression through a family of functionally distinct transcription factors, the DNA-binding AUXIN RESPONSE FACTORS (ARFs). Various studies have revealed the important roles of ARFs in regulating drought and salinity stress responses in plants. Different ARFs regulate soluble sugar content, promote root development, and maintain chlorophyll content under drought and saline stress conditions to help plants adapt to these stresses. The functional characterization of ARFs pertaining to the regulation of drought and salinity stress responses is still in its infancy. Interestingly, the small RNA-mediated post-transcriptional regulation of ARF expression has been shown to influence plant responses to both stresses. The current knowledge on the diverse roles of ARFs in conferring specificity to auxin-mediated drought and salinity stress responses has not been reviewed to date. In this review, we summarize the recent research concerning the role of ARFs in response to drought and salinity stresses: gene expression patterns, functional characterization, and post-transcriptional regulation under drought and salinity stresses. We have also reviewed the modulation of ARF expression by other molecular regulators in the context of drought and salt stress signaling.
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Affiliation(s)
- Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Solan, India
| | - Neelam Prabha Negi
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Shalini Pareek
- School of Life Sciences, Jaipur National University, Jaipur, Rajasthan, India
| | - Gaurav Mudgal
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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14
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Li X, Zhang X, Shi T, Chen M, Jia C, Wang J, Hou Z, Han J, Bian S. Identification of ARF family in blueberry and its potential involvement of fruit development and pH stress response. BMC Genomics 2022; 23:329. [PMID: 35477362 PMCID: PMC9047364 DOI: 10.1186/s12864-022-08556-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background Auxin responsive factor (ARF) family is one of core components in auxin signalling pathway, which governs diverse developmental processes and stress responses. Blueberry is an economically important berry-bearing crop and prefers to acidic soil. However, the understandings of ARF family has not yet been reported in blueberry. Results In the present study, 60 ARF genes (VcARF) were identified in blueberry, and they showed diverse gene structures and motif compositions among the groups and similar within each group in the phylogenetic tree. Noticeably, 9 digenic, 5 trigenic and 6 tetragenic VcARF pairs exhibited more than 95% identity to each other. Computational analysis indicated that 23 VcARFs harbored the miRNA responsive element (MRE) of miR160 or miR167 like other plant ARF genes. Interestingly, the MRE of miR156d/h-3p was observed in the 5’UTR of 3 VcARFs, suggesting a potentially novel post-transcriptional control. Furthermore, the transcript accumulations of VcARFs were investigated during fruit development, and three categories of transcript profiles were observed, implying different functional roles. Meanwhile, the expressions of VcARFs to different pH conditions (pH4.5 and pH6.5) were surveyed in pH-sensitive and tolerant blueberry species, and a number of VcARFs showed different transcript accumulations. More importantly, distinct transcriptional response to pH stress (pH6.5) were observed for several VcARFs (such as VcARF6s and VcARF19-3/19–4) between pH-sensitive and tolerant species, suggesting their potential roles in adaption to pH stress. Conclusions Sixty VcARF genes were identified and characterized, and their transcript profiles were surveyed during fruit development and in response to pH stress. These findings will contribute to future research for eliciting the functional roles of VcARFs and regulatory mechanisms, especially fruit development and adaption to pH stress. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08556-y.
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Affiliation(s)
- Xuyan Li
- College of Plant Science, Jilin University, Changchun, China
| | - Xiaoyi Zhang
- College of Plant Science, Jilin University, Changchun, China
| | - Tianran Shi
- College of Plant Science, Jilin University, Changchun, China
| | - Min Chen
- College of Plant Science, Jilin University, Changchun, China
| | - Chengguo Jia
- College of Plant Science, Jilin University, Changchun, China
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Zhixia Hou
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Research & Development Center of Blueberry, Beijing, 100083, China
| | - Junyou Han
- College of Plant Science, Jilin University, Changchun, China.
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China.
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15
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Sun L, Yang Y, Pan H, Zhu J, Zhu M, Xu T, Li Z, Dong T. Molecular Characterization and Target Prediction of Candidate miRNAs Related to Abiotic Stress Responses and/or Storage Root Development in Sweet Potato. Genes (Basel) 2022; 13:110. [PMID: 35052451 PMCID: PMC8774570 DOI: 10.3390/genes13010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 02/01/2023] Open
Abstract
Sweet potato is a tuberous root crop with strong environmental stress resistance. It is beneficial to study its storage root formation and stress responses to identify sweet potato stress- and storage-root-thickening-related regulators. Here, six conserved miRNAs (miR156g, miR157d, miR158a-3p, miR161.1, miR167d and miR397a) and six novel miRNAs (novel 104, novel 120, novel 140, novel 214, novel 359 and novel 522) were isolated and characterized in sweet potato. Tissue-specific expression patterns suggested that miR156g, miR157d, miR158a-3p, miR167d, novel 359 and novel 522 exhibited high expression in fibrous roots or storage roots and were all upregulated in response to storage-root-related hormones (indole acetic acid, IAA; zeaxanthin, ZT; abscisic acid, ABA; and gibberellin, GAs). The expression of miR156g, miR158a-3p, miR167d, novel 120 and novel 214 was induced or reduced dramatically by salt, dehydration and cold or heat stresses. Moreover, these miRNAs were all upregulated by ABA, a crucial hormone modulator in regulating abiotic stresses. Additionally, the potential targets of the twelve miRNAs were predicted and analyzed. Above all, these results indicated that these miRNAs might play roles in storage root development and/or stress responses in sweet potato as well as provided valuable information for the further investigation of the roles of miRNA in storage root development and stress responses.
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Affiliation(s)
- Li Sun
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
| | - Yiyu Yang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
| | - Hong Pan
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Jiahao Zhu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China; (H.P.); (T.X.)
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221008, China; (L.S.); (Y.Y.); (J.Z.); (M.Z.)
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16
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Jin L, Yarra R, Zhou L, Cao H. The auxin response factor (ARF) gene family in Oil palm (Elaeis guineensis Jacq.): Genome-wide identification and their expression profiling under abiotic stresses. PROTOPLASMA 2022; 259:47-60. [PMID: 33792785 DOI: 10.1007/s00709-021-01639-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Auxin response factors (ARFs) play vital role in controlling growth and developmental processes of plants via regulating the auxin signaling pathways. However, the identification and functional roles of ARFs in oil palm plants remain elusive. Here, we identified a total of 23 ARF (EgARF) genes in oil palm through a genome-wide identification approach. The EgARF gene structure analysis revealed the presence of intron-rich ARF gene family in genome of oil palm. Further analysis demonstrated the uneven distribution of 23EgARFs on 16 chromosomes of oil palm. Phylogenetic analysis clustered all the EgARFs into four groups. Twenty-one EgARFs contained BDD, ARF, and CTD domains, whereas EgARF5 and EgARF7 lacked the CTD domain. The evolution of ARF genes in oil palm genome has been expanded by segmental duplication events. The cis-acting regulatory elements of EgARF gene family were predominantly associated with the stress and hormone responses. Expression profiling data demonstrated the constitutive and tissue-specific expression of EgARF genes in various tissues of oil palm. Real-time PCR analysis of 19 EgARF genes expression levels under cold, drought, and salt stress conditions proved their prominent role under abiotic stress responses. Altogether, our study provides a basis for studying the molecular and functional roles of ARF genes in oil palm.
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Affiliation(s)
- Longfei Jin
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China.
| | | | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China
| | - Hongxing Cao
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China
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17
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Hou Q, Qiu Z, Wen Z, Zhang H, Li Z, Hong Y, Qiao G, Wen X. Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L. Int J Mol Sci 2021; 22:11968. [PMID: 34769398 PMCID: PMC8584427 DOI: 10.3390/ijms222111968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhilang Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Huimin Zhang
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Zhengchun Li
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
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18
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Taagen E, Tanaka J, Gul A, Sorrells ME. Positional-based cloning 'fail-safe' approach is overpowered by wheat chromosome structural variation. THE PLANT GENOME 2021; 14:e20106. [PMID: 34197040 DOI: 10.1002/tpg2.20106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
Positional-based cloning is a foundational method for understanding the genes and gene networks that control valuable agronomic traits such as grain yield components. In this study, we sought to positionally clone the causal genetic variant of a 1000-grain weight (TGW) quantitative trait loci (QTL) on wheat (Triticum aestivum L.) chromosome arm 5AL. We developed heterogenous inbred families (HIFs) (>5,000 plants) for enhanced genotypic resolution and fine-mapped the QTL to a 10-Mbp region. The transcriptome of developing grains from positive and negative control HIF haplotypes revealed presence-absence chromosome arm 5AS structural variation and unexpectedly no differential expression of genes within the chromosome arm 5AL candidate region. Evaluation of genomic, transcriptomic, and phenotypic data, and predicted function of genes, identified that the 5AL QTL was the result of strong linkage disequilibrium (LD) with chromosome arm 5AS presence or absence (HIF r2 = 0.91). Structural variation is common in wheat, and our results highlight that the redundant polyploid genome's masking of such variation is a significant barrier to positional cloning. We propose recommendations for more efficient and robust detection of structural variation, including transitioning from a single nucleotide polymorphism (SNP) to a haplotype-based approach to identify positional cloning targets. We also present nine candidate genes for grain yield components based on chromosome arm 5AS presence or absence, which may unveil hidden variation of homoeolog dosage-dependent genes across the group five chromosome short arms. Taken together, our discovery demonstrates the phenotypic resiliency of polyploid genomic structural variation and highlights a considerable challenge to routine positional cloning in wheat.
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Affiliation(s)
- Ella Taagen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - James Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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