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Li P, Zhao Z, Wang W, Wang T, Hu N, Wei Y, Sun Z, Chen Y, Li Y, Liu Q, Yang S, Gong J, Xiao X, Liu Y, Shi Y, Peng R, Lu Q, Yuan Y. Genome-wide analyses of member identification, expression pattern, and protein-protein interaction of EPF/EPFL gene family in Gossypium. BMC PLANT BIOLOGY 2024; 24:554. [PMID: 38877405 PMCID: PMC11177404 DOI: 10.1186/s12870-024-05262-7] [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: 07/31/2023] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Epidermal patterning factor / -like (EPF/EPFL) gene family encodes a class of cysteine-rich secretory peptides, which are widelyfound in terrestrial plants.Multiple studies has indicated that EPF/EPFLs might play significant roles in coordinating plant development and growth, especially as the morphogenesis processes of stoma, awn, stamen, and fruit skin. However, few research on EPF/EPFL gene family was reported in Gossypium. RESULTS We separately identified 20 G. raimondii, 24 G. arboreum, 44 G. hirsutum, and 44 G. barbadense EPF/EPFL genes in the 4 representative cotton species, which were divided into four clades together with 11 Arabidopsis thaliana, 13 Oryza sativa, and 17 Selaginella moellendorffii ones based on their evolutionary relationships. The similar gene structure and common motifs indicated the high conservation among the EPF/EPFL members, while the uneven distribution in chromosomes implied the variability during the long-term evolutionary process. Hundreds of collinearity relationships were identified from the pairwise comparisons of intraspecifc and interspecific genomes, which illustrated gene duplication might contribute to the expansion of cotton EPF/EPFL gene family. A total of 15 kinds of cis-regulatory elements were predicted in the promoter regions, and divided into three major categories relevant to the biological processes of development and growth, plant hormone response, and abiotic stress response. Having performing the expression pattern analyses with the basic of the published RNA-seq data, we found most of GhEPF/EPFL and GbEPF/EPFL genes presented the relatively low expression levels among the 9 tissues or organs, while showed more dramatically different responses to high/low temperature and salt or drought stresses. Combined with transcriptome data of developing ovules and fibers and quantitative Real-time PCR results (qRT-PCR) of 15 highly expressed GhEPF/EPFL genes, it could be deduced that the cotton EPF/EPFL genes were closely related with fiber development. Additionally, the networks of protein-protein interacting among EPF/EPFLs concentrated on the cores of GhEPF1 and GhEPF7, and thosefunctional enrichment analyses indicated that most of EPF/EPFLs participate in the GO (Gene Ontology) terms of stomatal development and plant epidermis development, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways of DNA or base excision repair. CONCLUSION Totally, 132 EPF/EPFL genes were identified for the first time in cotton, whose bioinformatic analyses of cis-regulatory elements and expression patterns combined with qRT-PCR experiments to prove the potential functions in the biological processes of plant growth and responding to abiotic stresses, specifically in the fiber development. These results not only provide comprehensive and valuable information for cotton EPF/EPFL gene family, but also lay solid foundation for screening candidate EPF/EPFL genes in further cotton breeding.
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Affiliation(s)
- Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Zilin Zhao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Wenkui Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Tao Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Nan Hu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Yangyang Wei
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Zhihao Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Yu Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Yanfang Li
- College of Agriculture, Tarim University, Alaer , Xinjiang, 843300, China
| | - Qiankun Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Shuhan Yang
- College of Agriculture, Tarim University, Alaer , Xinjiang, 843300, China
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Xianghui Xiao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Yuling Liu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Yuzhen Shi
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Renhai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China
| | - Quanwei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang , Henan, 455000, China.
| | - Youlu Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
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Yang X, Wang J, Mao X, Li C, Li L, Xue Y, He L, Jing R. A Locus Controlling Leaf Rolling Degree in Wheat under Drought Stress Identified by Bulked Segregant Analysis. PLANTS 2022; 11:plants11162076. [PMID: 36015380 PMCID: PMC9414355 DOI: 10.3390/plants11162076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
Drought stress frequently occurs, which seriously restricts the production of wheat (Triticum aestivum L.). Leaf rolling is a typical physiological phenomenon of plants during drought stress. To understand the genetic mechanism of wheat leaf rolling, we constructed an F2 segregating population by crossing the slight-rolling wheat cultivar “Aikang 58” (AK58) with the serious-rolling wheat cultivar ″Zhongmai 36″ (ZM36). A combination of bulked segregant analysis (BSA) with Wheat 660K SNP Array was used to identify molecular markers linked to leaf rolling degree. A major locus for leaf rolling degree under drought stress was detected on chromosome 7A. We named this locus LEAF ROLLING DEGREE 1 (LERD1), which was ultimately mapped to a region between 717.82 and 720.18 Mb. Twenty-one genes were predicted in this region, among which the basic helix-loop-helix (bHLH) transcription factor TraesCS7A01G543300 was considered to be the most likely candidate gene for LERD1. The TraesCS7A01G543300 is highly homologous to the Arabidopsis ICE1 family proteins ICE/SCREAM, SCREAM2 and bHLH093, which control stomatal initiation and development. Two nucleotide variation sites were detected in the promoter region of TraesCS7A01G543300 between the two wheat cultivars. Gene expression assays indicated that TraesCS7A01G543300 was higher expressed in AK58 seedlings than that of ZM36. This research discovered a candidate gene related to wheat leaf rolling under drought stress, which may be helpful for understanding the leaf rolling mechanism and molecular breeding in wheat.
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Affiliation(s)
- Xi Yang
- College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghong Xue
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liheng He
- College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China
- Correspondence: (L.H.); (R.J.)
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (L.H.); (R.J.)
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Wei H, Jing Y, Zhang L, Kong D. Phytohormones and their crosstalk in regulating stomatal development and patterning. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2356-2370. [PMID: 33512461 DOI: 10.1093/jxb/erab034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Phytohormones play important roles in regulating various aspects of plant growth and development as well as in biotic and abiotic stress responses. Stomata are openings on the surface of land plants that control gas exchange with the environment. Accumulating evidence shows that various phytohormones, including abscisic acid, jasmonic acid, brassinosteroids, auxin, cytokinin, ethylene, and gibberellic acid, play many roles in the regulation of stomatal development and patterning, and that the cotyledons/leaves and hypocotyls/stems of Arabidopsis exhibit differential responsiveness to phytohormones. In this review, we first discuss the shared regulatory mechanisms controlling stomatal development and patterning in Arabidopsis cotyledons and hypocotyls and those that are distinct. We then summarize current knowledge of how distinct hormonal signaling circuits are integrated into the core stomatal development pathways and how different phytohormones crosstalk to tailor stomatal density and spacing patterns. Knowledge obtained from Arabidopsis may pave the way for future research to elucidate the effects of phytohormones in regulating stomatal development and patterning in cereal grasses for the purpose of increasing crop adaptive responses.
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Affiliation(s)
- Hongbin Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yifeng Jing
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Lei Zhang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Dexin Kong
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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Xu K, Guo L, Ye H. A naturally optimized mass transfer process: The stomatal transpiration of plant leaves. JOURNAL OF PLANT PHYSIOLOGY 2019; 234-235:138-144. [PMID: 30798115 DOI: 10.1016/j.jplph.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 02/09/2019] [Accepted: 02/09/2019] [Indexed: 06/09/2023]
Abstract
Stomatal transpiration of leaves is a dominant pathway of plant physiological water loss. The leaf transpiration rate when stomata are fully open is commonly at the same level as the evaporation rate of a wet surface of the same area as that of the leaf area, although the cumulative area of the stomatal pores is typically less than 3% of the leaf area. To elucidate the highly efficient diffusion of the stomatal array from the perspective of mass transfer theory, stomatal distribution characteristics of various kinds of leaves were obtained with optical microscope, and steady diffusions of water vapor from isolated zero-depth circular stomata, elliptical stomata, and distributed stomatal arrays without airflow parallel to the surface were simulated with the finite element method. It was found that the long perimeter of the elliptical stomata and the specific distribution characteristics of the stomatal array are the dominant reasons for the highly efficient diffusion of the stomatal array on the leaves. Furthermore, the simulation results reveal that extremal transpiration rates exist for the stomatal arrays with different distribution characteristics. It was found that the transpiration rates of the vegetation tend to approach the extremal values for flourishing development in the process of natural optimization.
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Affiliation(s)
- Kai Xu
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Liang Guo
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Hong Ye
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
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