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Imani Asl E, Soorni A, Mehrabi R. Genome-wide characterization, functional analysis, and expression profiling of the Aux/IAA gene family in spinach. BMC Genomics 2024; 25:567. [PMID: 38840073 PMCID: PMC11155116 DOI: 10.1186/s12864-024-10467-z] [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: 01/14/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The auxin/indole-3-acetic acid (Aux/IAA) gene family is a crucial element of the auxin signaling pathway, significantly influencing plant growth and development. Hence, we conducted a comprehensive investigation of Aux/IAAs gene family using the Sp75 and Monoe-Viroflay genomes in spinach. RESULTS A total of 24 definitive Aux/IAA genes were identified, exhibiting diverse attributes in terms of amino acid length, molecular weight, and isoelectric points. This diversity underscores potential specific roles within the family, such as growth regulation and stress response. Structural analysis revealed significant variations in gene length and molecular weight. These variations indicate distinct roles within the Aux/IAA gene family. Chromosomal distribution analysis exhibited a dispersed pattern, with chromosomes 4 and 1 hosting the highest and lowest numbers of Aux/IAA genes, respectively. Phylogenetic analysis grouped the identified genes into distinct clades, revealing potential evolutionary relationships. Notably, the phylogenetic tree highlighted specific gene clusters suggesting shared genetic ancestry and potential functional synergies within spinach. Expression analysis under NAA treatment unveiled gene-specific and time-dependent responses, with certain genes exhibiting distinct temporal expression patterns. Specifically, SpoIAA5 displayed a substantial increase at 2 h post-NAA treatment, while SpoIAA7 and SpoIAA9 demonstrated continuous rises, peaking at the 4-hour time point. CONCLUSIONS These observations indicate a complex interplay of gene-specific and temporal regulation in response to auxin. Moreover, the comparison with other plant species emphasized both shared characteristics and unique features in Aux/IAA gene numbers, providing insights into the evolutionary dynamics of this gene family. This comprehensive characterization of Aux/IAA genes in spinach not only establishes the foundation for understanding their specific functions in spinach development but also provides a valuable resource for experimental validation and further exploration of their roles in the intricate network of auxin signaling pathways.
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Affiliation(s)
- Erfan Imani Asl
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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2
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Zhao S, Luo J, Tang M, Zhang C, Song M, Wu G, Yan X. Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line. Int J Mol Sci 2023; 25:174. [PMID: 38203344 PMCID: PMC10778984 DOI: 10.3390/ijms25010174] [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: 10/23/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.
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Affiliation(s)
- Shengbo Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junling Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Min Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Miaoying Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohong Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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3
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Jobert F, Yadav S, Robert S. Auxin as an architect of the pectin matrix. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6933-6949. [PMID: 37166384 PMCID: PMC10690733 DOI: 10.1093/jxb/erad174] [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: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.
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Affiliation(s)
- François Jobert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
- CRRBM, Université de Picardie Jules Verne, 80000, Amiens, France
| | - Sandeep Yadav
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Stéphanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
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4
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Wang J, Xue L, Zhang X, Hou Y, Zheng K, Fu D, Dong W. A New Function of MbIAA19 Identified to Modulate Malus Plants Dwarfing Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:3097. [PMID: 37687343 PMCID: PMC10490418 DOI: 10.3390/plants12173097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
The primary determinants of apple (Malus) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess the mechanisms underlying dwarfism in a mutant of Malus baccata. M. baccata dwarf mutant (Dwf) was previously obtained through natural mutation. It has considerably reduced plant height and internode length. A comparative transcriptome analysis of wild-type (WT) and Dwf mutant was performed to identify and annotate the differentially expressed genes responsible for the Dwf phenotype using RNA-seq and GO and KEGG pathway enrichment analyses. Multiple DEGs involved in hormone signaling pathways, particularly auxin signaling pathways, were identified. Moreover, the levels of endogenous indole-3-acetic acid (IAA) were lower in Dwf mutant than in WT. The Aux/IAA transcription factor gene MbIAA19 was downregulated in Dwf mutant due to a single nucleotide sequence change in its promoter. Genetic transformation assay demonstrated strong association between MbIAA19 and the dwarf phenotype. RNAi-IAA19 lines clearly exhibited reduced plant height, internode length, and endogenous IAA levels. Our study revealed that MbIAA19 plays a role in the regulation of dwarfism and endogenous IAA levels in M. baccata.
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Affiliation(s)
| | | | | | | | | | | | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (L.X.); (X.Z.); (Y.H.); (K.Z.); (D.F.)
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5
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Starosta E, Szwarc J, Niemann J, Szewczyk K, Weigt D. Brassica napus Haploid and Double Haploid Production and Its Latest Applications. Curr Issues Mol Biol 2023; 45:4431-4450. [PMID: 37232751 DOI: 10.3390/cimb45050282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Rapeseed is one of the most important oil crops in the world. Increasing demand for oil and limited agronomic capabilities of present-day rapeseed result in the need for rapid development of new, superior cultivars. Double haploid (DH) technology is a fast and convenient approach in plant breeding as well as genetic research. Brassica napus is considered a model species for DH production based on microspore embryogenesis; however, the molecular mechanisms underlying microspore reprogramming are still vague. It is known that morphological changes are accompanied by gene and protein expression patterns, alongside carbohydrate and lipid metabolism. Novel, more efficient methods for DH rapeseed production have been reported. This review covers new findings and advances in Brassica napus DH production as well as the latest reports related to agronomically important traits in molecular studies employing the double haploid rapeseed lines.
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Affiliation(s)
- Ewa Starosta
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Justyna Szwarc
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Katarzyna Szewczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
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6
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Qin S, Fu S, Yang Y, Sun Q, Wang J, Dong Y, Gu X, Wang T, Xie X, Mo X, Jiang H, Yu Y, Yan J, Chu J, Zheng B, He Y. Comparative Microscopic, Transcriptome and IAA Content Analyses Reveal the Stem Growth Variations in Two Cultivars Ilex verticillata. PLANTS (BASEL, SWITZERLAND) 2023; 12:1941. [PMID: 37653858 PMCID: PMC10220661 DOI: 10.3390/plants12101941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 09/02/2023]
Abstract
Ilex verticillata is not only an excellent ornamental tree species for courtyards, but it is also a popular bonsai tree. 'Oosterwijk' and 'Red sprite' are two varieties of Ilex verticillata. The former has a long stem with few branches, while the latter has a short stem. In order to explain the stem growth differences between the two cultivars 'Oosterwijk' and 'Red sprite', determination of the microstructure, transcriptome sequence and IAA content was carried out. The results showed that the xylem thickness, vessel area and vessel number of 'Oosterwijk' were larger than in 'Red sprite'. In addition, our analysis revealed that the differentially expressed genes which were enriched in phenylpropanoid biosynthesis; phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis in the black and tan modules of the two varieties. We found that AST, HCT and bHLH 94 may be key genes in the formation of shoot difference. Moreover, we found that the IAA content and auxin-related DEGs GH3.6, GH3, ATRP5, IAA27, SAUR36-like, GH3.6-like and AIP 10A5-like may play important roles in the formation of shoot differences. In summary, these results indicated that stem growth variations of 'Oosterwijk' and 'Red sprite' were associated with DEGs related to phenylpropanoid biosynthesis, phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis, as well as auxin content and DEGs related to the auxin signaling pathway.
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Affiliation(s)
- Sini Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Siyi Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Ying Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Qiumin Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Jingqi Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Yanling Dong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Xinyi Gu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Tao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Xiaoting Xie
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China;
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou 310058, China;
| | - Youxiang Yu
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Jijun Yan
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (J.Y.); (J.C.)
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (J.Y.); (J.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (S.Q.); (S.F.); (Y.Y.); (Q.S.); (J.W.); (Y.D.); (X.G.); (T.W.); (X.X.); (B.Z.)
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions, Zhejiang A&F University, Hangzhou 311300, China
- National Forestry and Grassland Administration (NFGA) Research Center for Ilex, Hangzhou 311300, China
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Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie ( Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development. Int J Mol Sci 2022; 23:ijms232315117. [PMID: 36499437 PMCID: PMC9736067 DOI: 10.3390/ijms232315117] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.
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Gao Y, Yuan Y, Zhang X, Song H, Yang Q, Yang P, Gao X, Gao J, Feng B. Conuping BSA-Seq and RNA-Seq Reveal the Molecular Pathway and Genes Associated with the Plant Height of Foxtail Millet (Setaria italica). Int J Mol Sci 2022; 23:ijms231911824. [PMID: 36233125 PMCID: PMC9569614 DOI: 10.3390/ijms231911824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Foxtail millet (Setaria italica) plays an important role in C4 crop research and agricultural development in arid areas due to its short growth period, drought tolerance, and barren tolerance. Exploration of the dwarfing mechanism and the dwarf genes of foxtail millet can provide a reference for dwarf breeding and dwarf research of other C4 crops. In this study, genetic analysis was performed using phenotypic data, candidate genes were screened by bulk segregant analysis sequencing (BSA-Seq); differentially expressed genes and metabolic pathways in different strains of high samples were analyzed by RNA sequencing (RNA-Seq). The association analysis of BSA-Seq and RNA-Seq further narrowed the candidate range. As a result, a total of three quantitative trait loci (QTLs) and nine candidate genes related to plant height were obtained on chromosomes I and IX. Based on the functional prediction of the candidate genes, we propose a hypothetical mechanism for the formation of millet dwarfing, in which, metabolism and MAPK signaling play important roles in the formation of foxtail millet plant height.
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Affiliation(s)
- Yongbin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
- Dexing Township Agro-Pastoral Comprehensive Service Center, Nyingchi 860700, China
| | - Yuhao Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Xiongying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Hui Song
- Anyang Academy of Agricultural Sciences, Anyang 455099, China
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Pu Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Jinfeng Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Yangling 712100, China
- Correspondence:
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