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Dong Y, Li S, Wu H, Gao Y, Feng Z, Zhao X, Shan L, Zhang Z, Ren H, Liu X. Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review. HORTICULTURE RESEARCH 2023; 10:uhad145. [PMID: 37691965 PMCID: PMC10483894 DOI: 10.1093/hr/uhad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023]
Abstract
Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.
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Affiliation(s)
- Yuming Dong
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Sen Li
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Haoying Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yiming Gao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongxuan Feng
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xi Zhao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Li Shan
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongren Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya Hainan 572000, China
| | - Xingwang Liu
- College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya Hainan 572000, China
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Aparna, Skarzyńska A, Pląder W, Pawełkowicz M. Impact of Climate Change on Regulation of Genes Involved in Sex Determination and Fruit Production in Cucumber. PLANTS (BASEL, SWITZERLAND) 2023; 12:2651. [PMID: 37514264 PMCID: PMC10385340 DOI: 10.3390/plants12142651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Environmental changes, both natural and anthropogenic, mainly related to rising temperatures and water scarcity, are clearly visible around the world. Climate change is important for crop production and is a major issue for the growth and productivity of cucumbers. Processes such as sex determination, flower morphogenesis and fruit development in cucumbers are highly sensitive to various forms of stress induced by climatic changes. It is noteworthy that many factors, including genetic factors, transcription factors, phytohormones and miRNAs, are crucial in regulating these processes and are themselves affected by climate change. Changes in the expression and activity of these factors have been observed as a consequence of climatic conditions. This review focuses primarily on exploring the effects of climate change and abiotic stresses, such as increasing temperature and drought, on the processes of sex determination, reproduction, and fruit development in cucumbers at the molecular level. In addition, it highlights the existing research gaps that need to be addressed in order to improve our understanding of the complex interactions between climate change and cucumber physiology. This, in turn, may lead to strategies to mitigate the adverse effects and enhance cucumber productivity in a changing climate.
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Affiliation(s)
- Aparna
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
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Luo H, Zhang H, Wang H. Advance in sex differentiation in cucumber. FRONTIERS IN PLANT SCIENCE 2023; 14:1186904. [PMID: 37265638 PMCID: PMC10231686 DOI: 10.3389/fpls.2023.1186904] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/20/2023] [Indexed: 06/03/2023]
Abstract
Cucumber belongs to the family Cucurbitaceae (melon genus) and is an annual herbaceous vegetable crop. Cucumber is an important cash crop that is grown all over the world. From morphology to cytology, from canonical genetics to molecular biology, researchers have performed much research on sex differentiation and its regulatory mechanism in cucumber, mainly in terms of cucumber sex determination genes, environmental conditions, and the effects of plant hormones, revealing its genetic basis to improve the number of female flowers in cucumber, thus greatly improving the yield of cucumber. This paper reviews the research progress of sex differentiation in cucumber in recent years, mainly focusing on sex-determining genes, environmental conditions, and the influence of phytohormones in cucumber, and provides a theoretical basis and technical support for the realization of high and stable yield cultivation and molecular breeding of cucumber crop traits.
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Affiliation(s)
- Haiyan Luo
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Hangzhou Lin’an District Agricultural and Rural Bureau, Hangzhou, China
| | - Huanchun Zhang
- Yantai Institute of Agricultural Sciences, Yantai, China
| | - Huasen Wang
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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Cao Q, Zhang H, Li T, He L, Zong J, Shan H, Huang L, Zhang Y, Liu H, Jiang J. Profiling miRNAs of Teleost Fish in Responses to Environmental Stress: A Review. BIOLOGY 2023; 12:biology12030388. [PMID: 36979079 PMCID: PMC10045198 DOI: 10.3390/biology12030388] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
miRNAs are a class of endogenous and evolutionarily conserved noncoding short RNA molecules that post-transcriptionally regulate gene expression through sequence-specific interactions with mRNAs and are capable of controlling gene expression by binding to miRNA targets and interfering with the final protein output. The miRNAs of teleost were firstly reported in zebrafish development, but there are recent studies on the characteristics and functions of miRNAs in fish, especially when compared with mammals. Environmental factors including salinity, oxygen concentration, temperature, feed, pH, environmental chemicals and seawater metal elements may affect the transcriptional and posttranscriptional regulators of miRNAs, contributing to nearly all biological processes. The survival of aquatic fish is constantly challenged by the changes in these environmental factors. Environmental factors can influence miRNA expression, the functions of miRNAs and their target mRNAs. Progress of available information is reported on the environmental effects of the identified miRNAs, miRNA targets and the use of miRNAs in fish.
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Affiliation(s)
- Quanquan Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- MARBEC, University Montpellier, CNRS, IFREMER, IRD, 34090 Montpellier, France
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Hailong Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lingjie He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiali Zong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongying Shan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lishi Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yupeng Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Haifeng Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
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Pawełkowicz ME, Skarzyńska A, Koter MD, Turek S, Pląder W. miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2022; 23:ijms23084317. [PMID: 35457133 PMCID: PMC9031375 DOI: 10.3390/ijms23084317] [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: 03/14/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA's target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants' somaclonal variation.
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Zhang K, He S, Sui Y, Gao Q, Jia S, Lu X, Jia L. Genome-Wide Characterization of HSP90 Gene Family in Cucumber and Their Potential Roles in Response to Abiotic and Biotic Stresses. Front Genet 2021; 12:584886. [PMID: 33613633 PMCID: PMC7889589 DOI: 10.3389/fgene.2021.584886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/14/2021] [Indexed: 11/29/2022] Open
Abstract
Heat shock protein 90 (HSP90) possesses critical functions in plant developmental control and defense reactions. The HSP90 gene family has been studied in various plant species. However, the HSP90 gene family in cucumber has not been characterized in detail. In this study, a total of six HSP90 genes were identified from the cucumber genome, which were distributed to five chromosomes. Phylogenetic analysis divided the cucumber HSP90 genes into two groups. The structural characteristics of cucumber HSP90 members in the same group were similar but varied among different groups. Synteny analysis showed that only one cucumber HSP90 gene, Csa1G569290, was conservative, which was not collinear with any HSP90 gene in Arabidopsis and rice. The other five cucumber HSP90 genes were collinear with five Arabidopsis HSP90 genes and six rice HSP90 genes. Only one pair of paralogous genes in the cucumber HSP90 gene family, namely one pair of tandem duplication genes (Csa1G569270/Csa1G569290), was detected. The promoter analysis showed that the promoters of cucumber HSP90 genes contained hormone, stress, and development-related cis-elements. Tissue-specific expression analysis revealed that only one cucumber HSP90 gene Csa3G183950 was highly expressed in tendril but low or not expressed in other tissues, while the other five HSP90 genes were expressed in all tissues. Furthermore, the expression levels of cucumber HSP90 genes were differentially induced by temperature and photoperiod, gibberellin (GA), downy mildew, and powdery mildew stimuli. Two cucumber HSP90 genes, Csa1G569270 and Csa1G569290, were both differentially expressed in response to abiotic and biotic stresses, which means that these two HSP90 genes play important roles in the process of cucumber growth and development. These findings improve our understanding of cucumber HSP90 family genes and provide preliminary information for further studies of cucumber HSP90 gene functions in plant growth and development.
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Affiliation(s)
- Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shuaishuai He
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yihu Sui
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Qinghai Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shuangshuang Jia
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Li Jia
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
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Martínez C, Jamilena M. To be a male or a female flower, a question of ethylene in cucurbits. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101981. [PMID: 33517096 DOI: 10.1016/j.pbi.2020.101981] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/20/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Within the Cucurbitaceae family, most of its species develop unisexual female and male flowers, either on the same plant (monoecy) or on different plants (dioecy). As in other plant families, these two sex morphotypes have evolved from hermaphrodite species; however, many evolutionary events have occurred in cucurbits allowing easy conversion from dioecy to monoecy and vice versa. The variability in sex morphotypes is higher in the domesticated species of the family, which together with recent advances in genomics, make cucurbits an ideal model to study the genetic and molecular mechanisms that control sex determination in plants. Conventional studies demonstrated that ethylene was the master regulator of sex determination in cucurbits, although some cultivated species may respond differently to ethylene action. In this article, we survey the new advances in hormonal and genetic control of sex determination in cucurbit species, control which establishes the ethylene biosynthesis and signaling genes as being those that determine the floral meristem towards a male, female or hermaphrodite flower. The interactions between these genes are integrated into a model that explains the occurrence and distribution of unisexal and hermaphrodite flowers within the different sex morphotypes. We underline the significance of this scientific progress with regard to breeding programs for agronomically-important sex-associated traits.
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Affiliation(s)
- Cecilia Martínez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, 04120 Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, 04120 Almería, Spain.
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Xu R, Li S, Guo S, Zhao Q, Abramson MJ, Li S, Guo Y. Environmental temperature and human epigenetic modifications: A systematic review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113840. [PMID: 31884209 DOI: 10.1016/j.envpol.2019.113840] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/26/2019] [Accepted: 12/16/2019] [Indexed: 05/28/2023]
Abstract
The knowledge about the effects of environmental temperature on human epigenome is a potential key to understand the health impacts of temperature and to guide acclimation under climate change. We performed a systematic review on the epidemiological studies that have evaluated the association between environmental temperature and human epigenetic modifications. We identified seven original articles on this topic published between 2009 and 2019, including six cohort studies and one cross-sectional study. They focused on DNA methylation in elderly people (blood sample) or infants (placenta sample), with sample size ranging from 306 to 1798. These studies were conducted in relatively low temperature setting (median/mean temperature: 0.8-13 °C), and linear models were used to evaluate temperature-DNA methylation association over short period (≤28 days). It has been reported that short-term ambient temperature could affect global human DNA methylation. A total of 15 candidate genes (ICAM-1, CRAT, F3, TLR-2, iNOS, ZKSCAN4, ZNF227, ZNF595, ZNF597, ZNF668, CACNA1H, AIRE, MYEOV2, NKX1-2 and CCDC15) with methylation status associated with ambient temperature have been identified. DNA methylation on ZKSCAN4, ICAM-1 partly mediated the effect of short-term cold temperature on high blood pressure and ICAM-1 protein (related to cardiovascular events), respectively. In summary, epidemiological evidence about the impacts of environment temperature on human epigenetics remains scarce and limited to short-term linear effect of cold temperature on DNA methylation in elderly people and infants. More studies are needed to broaden our understanding of temperature related epigenetic changes, especially under a changing climate.
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Affiliation(s)
- Rongbin Xu
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Shuaijun Guo
- Centre for Community Child Health, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Qi Zhao
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Michael J Abramson
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Shanshan Li
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Yuming Guo
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia.
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