1
|
Zhang F, Ma J, Liu Y, Fang J, Wei S, Xie R, Han P, Zhao X, Bo S, Lu Z. A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways. Life (Basel) 2024; 14:141. [PMID: 38255756 PMCID: PMC10820167 DOI: 10.3390/life14010141] [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: 11/27/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The MYB transcription factor family can regulate biological processes such as ABA signal transduction to cope with drought stress, but its evolutionary mechanism and the diverse pathways of response to drought stress in different species are rarely reported. In this study, a total of 4791 MYB family members were identified in 908,757 amino acid sequences from 12 model plants or crops using bioinformatics methods. It was observed that the number of MYB family members had a linear relationship with the chromosome ploidy of species. A phylogenetic analysis showed that the MYB family members evolved in subfamily clusters. In response to drought stress, the pathways of MYB transcription factor families exhibited species-specific diversity, with closely related species demonstrating a higher resemblance. This study provides abundant references for drought resistance research and the breeding of wheat, soybean, and other plants.
Collapse
Affiliation(s)
- Fan Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Jie Ma
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Ying Liu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Jing Fang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Shuli Wei
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Pingan Han
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot 010110, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| |
Collapse
|
2
|
Expression analysis of plant intracellular Ras-group related leucine-rich repeat proteins (PIRLs) in Arabidopsis thaliana. Biochem Biophys Rep 2022; 30:101241. [PMID: 35280522 PMCID: PMC8904235 DOI: 10.1016/j.bbrep.2022.101241] [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: 11/02/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Arabidopsis thaliana contains a family of nine genes known as plant intracellular Ras-group related leucine-rich repeat (LRR) proteins (PIRLs). These are structurally similar to animals and fungal LRR proteins and play important roles in developmental pathways. However, to date, no detailed tissue-specific expression analysis of these PIRLs has been performed. Therefore, in this study, we generated promoter:GUS transgenic plants for the nine A. thaliana PIRL genes and identified their expression patterns in seedlings and floral organs at different developmental stages. Most PIRL members showed expression in the root apical region and in the vascular tissue of primary and lateral roots. Shoot apex-specific expression was recorded for PIRL1 and PIRL8. Furthermore, PIRL1, PIRL3, PIRL5, PIRL6, and PIRL7 showed distinct expression patterns in flowers, especially in pollen and anthers. In addition, co-expression network analysis identified cases where PIRLs were co-expressed with other genes known to have specific functions related to growth and development. Taken together, the tissue-specific expression patterns of PIRL genes improve our understanding of the functions of this gene family in plant growth and development. PIRL constituting gene family in A. thaliana is widely distributed among plants. PIRL1, 2, 3, and 6 were strongly expressed in anther and/or pollen, consistent with their function in pollen development. PIRL7 was distinctively expressed in pollen and pollen tube, suggesting its role in pollen function.
Collapse
|
3
|
Moin M, Bakshi A, Madhav MS, Kirti PB. Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice. Brief Funct Genomics 2018; 17:339-351. [PMID: 29579147 DOI: 10.1093/bfgp/ely010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.
Collapse
Affiliation(s)
- Mazahar Moin
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| |
Collapse
|
4
|
The Arabidopsis Plant Intracellular Ras-group LRR (PIRL) Family and the Value of Reverse Genetic Analysis for Identifying Genes that Function in Gametophyte Development. PLANTS 2013; 2:507-20. [PMID: 27137390 PMCID: PMC4844374 DOI: 10.3390/plants2030507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/02/2013] [Accepted: 07/24/2013] [Indexed: 12/31/2022]
Abstract
Arabidopsis thaliana has proven a powerful system for developmental genetics, but identification of gametophytic genes with developmental mutants can be complicated by factors such as gametophyte-lethality, functional redundancy, or poor penetrance. These issues are exemplified by the Plant Intracellular Ras-group LRR (PIRL) genes, a family of nine genes encoding a class of leucine-rich repeat proteins structurally related to animal and fungal LRR proteins involved in developmental signaling. Previous analysis of T-DNA insertion mutants showed that two of these genes, PIRL1 and PIRL9, have an essential function in pollen formation but are functionally redundant. Here, we present evidence implicating three more PIRLs in gametophyte development. Scanning electron microscopy revealed that disruption of either PIRL2 or PIRL3 results in a low frequency of pollen morphological abnormalities. In addition, molecular analysis of putative pirl6 insertion mutants indicated that knockout alleles of this gene are not represented in current Arabidopsis mutant populations, suggesting gametophyte lethality may hinder mutant recovery. Consistent with this, available microarray and RNA-seq data have documented strongest PIRL6 expression in developing pollen. Taken together, these results now implicate five PIRLs in gametophyte development. Systematic reverse genetic analysis of this novel LRR family has therefore identified gametophytically active genes that otherwise would likely be missed by forward genetic screens.
Collapse
|
5
|
Le Provost G, Sulmon C, Frigerio JM, Bodénès C, Kremer A, Plomion C. Role of waterlogging-responsive genes in shaping interspecific differentiation between two sympatric oak species. TREE PHYSIOLOGY 2012; 32:119-34. [PMID: 22170438 DOI: 10.1093/treephys/tpr123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pedunculate (Quercus robur L.) and sessile oak (Quercus petreae Matt. Liebl.) are closely related species with a widely sympatric distribution in Europe. These two oak species are also known to display different ecological features, particularly related to their adaptation to soil waterlogging. Pedunculate oak grows in humid areas and can withstand high moisture content of the soil, whereas sessile oak requires drier soil with better drainage. The main goal of this study was to explore the role of gene expression contributing to differences in terms of waterlogging tolerance between these two species. We implemented a series of experiments aimed at evaluating whether differentially expressed genes between species are associated with their ecological preferences and underlie adaptive genetic divergence. Rooted cuttings of both species were grown in hydroponic conditions and subjected to gradual root hypoxia. White roots were sampled after 6, 12, 24 and 48 h. Real-time polymerase chain reaction (qPCR) was first used to monitor the expression of 10 known waterlogging-responsive genes, to identify discriminating sampling time points along the kinetics of hypoxia. Secondly, four subtractive suppressive hybridization libraries (sessile vs. pedunculate, pedunculate vs. sessile for early and late responses) were generated to isolate differentially expressed genes between species. A total of 2160 high-quality expressed sequence tags were obtained and annotated, and a subset of 45 genes were selected for qPCR analysis in a second independent factorial experimental design applying two stress durations per two species. Significant differences of gene expression between pedunculate and sessile oaks were detected, suggesting species-specific molecular strategies to respond to hypoxia. This study revealed that the ability of pedunculate oak to maintain glycolysis and fermentation under hypoxic conditions may help explain its tolerance to waterlogging.
Collapse
|