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Lee J, Yeom SI. Global co-expression network for key factor selection on environmental stress RNA-seq dataset in Capsicum annuum. Sci Data 2023; 10:692. [PMID: 37828130 PMCID: PMC10570317 DOI: 10.1038/s41597-023-02592-3] [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: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Environmental stresses significantly affect plant growth, development, and productivity. Therefore, a deeper understanding of the underlying stress responses at the molecular level is needed. In this study, to identify critical genetic factors associated with environmental stress responses, the entire 737.3 Gb clean RNA-seq dataset across abiotic, biotic stress, and phytohormone conditions in Capsicum annuum was used to perform individual differentially expressed gene analysis and to construct gene co-expression networks for each stress condition. Subsequently, gene networks were reconstructed around transcription factors to identify critical factors involved in the stress responses, including the NLR gene family, previously implicated in resistance. The abiotic and biotic stress networks comprise 233 and 597 hubs respectively, with 10 and 89 NLRs. Each gene within the NLR groups in the network exhibited substantial expression to particular stresses. The integrated analysis strategy of the transcriptome network revealed potential key genes for complex environmental conditions. Together, this could provide important clues to uncover novel key factors using high-throughput transcriptome data in other species as well as plants.
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Affiliation(s)
- Junesung Lee
- Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Seon-In Yeom
- Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea.
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Li Y, Zhu J, Feng Y, Li Z, Ren Z, Liu N, Liu C, Hao J, Han Y. LsARF3 mediates thermally induced bolting through promoting the expression of LsCO in lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:958833. [PMID: 36160965 PMCID: PMC9498183 DOI: 10.3389/fpls.2022.958833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/09/2022] [Indexed: 06/16/2023]
Abstract
Lettuce (Lactuca sativa L.) is a leafy vegetable whose edible organs usually are leaf or stems, and thus high-temperature induced bolting followed by flower initiation is an undesirable trait in lettuce production. However, the molecular mechanism that controls lettuce bolting and flowering upon thermal treatments is largely unknown. Here, we identified a Lettuce auxin response factor 3 (LsARF3), the expression of which was enhanced by heat and auxin treatments. Interestingly, LsARF3 is preferentially expressed in stem apex, suggesting it might be associated with lettuce bolting. Transgenic lettuce overexpressing LsARF3 displayed early bolting and flowering, whereas knockout of LsARF3 dramatically delayed bolting and flowering in lettuce under normal or high temperature conditions. Furthermore, Exogenous application of IAA failed to rescue the late-bolting and -flowering phenotype of lsarf3 mutants. Several floral integrator genes including LsCO, LsFT, and LsLFY were co-expressed with LsARF3 in the overexpression and knockout lettuce plants. Yeast one-hybrid (Y1H) experiments suggested that LsARF3 could physically interact with the LsCO promoter, which was further confirmed by a dual luciferase assay in tobacco leaves. The results indicated that LsARF3 might directly modulate the expression of LsCO in lettuce. Therefore, these results demonstrate that LsARF3 could promote lettuce bolting in response to the high temperature by directly or indirectly activating the expression of floral genes such as LsCO, which provides new insights into lettuce bolting in the context of ARFs signaling and heat response.
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Affiliation(s)
- Yunfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiaqi Zhu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yixuan Feng
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zhenfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zheng Ren
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Ning Liu
- National Engineering Research Center for Vegetables, Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chaojie Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yingyan Han
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
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Hao J, Yang J, Liu X, Pan G, Li Y, Zhang X, Han Y, Fan S, Zhou Z. Molecular basis of high temperature-induced bolting in lettuce revealed by multi-omics analysis. BMC Genomics 2022; 23:580. [PMID: 35953780 PMCID: PMC9373282 DOI: 10.1186/s12864-022-08814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/31/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND High temperature induces early bolting in lettuce (Lactuca sativa L.), which affects both quality and production. However, the molecular mechanism underlying high temperature-induced bolting is still limited. RESULTS We performed systematical analysis of morphology, transcriptome, miRNAs and methylome in lettuce under high temperature treatment. Through a comparison of RNA-Seq data between the control and the high temperature treated lettuces at different time points totally identified 2944 up-regulated genes and 2203 down-regulated genes, which cover three floral pathways including photoperiod, age and gibberellin (GA) pathways. Genome wide analysis of miRNAs and methylome during high temperature treatment indicated miRNAs and DNA methylation might play a role controlling gene expression during high temperature-induced bolting. miRNA targets included some protein kinase family proteins, which potentially play crucial roles in this process. CONCLUSIONS Together, our results propose a possible regulation network involved in high temperature-induced bolting.
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Affiliation(s)
- Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Junwei Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaofeng Liu
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Gaoyang Pan
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yunfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Xiaolan Zhang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yingyan Han
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China.
| | - Shuangxi Fan
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China.
| | - Zhaoyang Zhou
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Wang Y, Li B, Li Y, Du W, Zhang Y, Han Y, Liu C, Fan S, Hao J. Application of exogenous auxin and gibberellin regulates the bolting of lettuce ( Lactuca sativa L.). Open Life Sci 2022; 17:438-446. [PMID: 35582624 PMCID: PMC9055172 DOI: 10.1515/biol-2022-0043] [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: 04/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/28/2023] Open
Abstract
Plant bolting is regulated and controlled by various internal and external factors. We aimed to provide an improved method for breeding to determine whether there is a synergism between hormones and to explore the regulatory effect of plant hormones on the bolting of leaf lettuce. Lettuce plants were sprayed with exogenous auxin and gibberellin separately or in combination. The specific bolting period was determined by the change in stem length and cytological observation. The dynamic changes in endogenous hormones and genes closely related to bolting were analyzed. Treatment with gibberellin alone and the combined application of auxin and gibberellin induced bolting on the fourth day, and treatment with auxin alone resulted in bolting on the eighth day. In the early bolting stage, the auxin contents in the stems of the treatment groups, especially the combined gibberellin and auxin group, were higher than those of the control group. After the application of exogenous auxin and gibberellin, we found that the expression of the ARF8 and GID1 genes was upregulated. Based on the results of our study, combined treatment with exogenous gibberellin and auxin was the best method to promote the bolting of leaf lettuce, and the ARF8 and GID1 genes are closely related to this process.
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Affiliation(s)
- Yubo Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Bingyan Li
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Yunfeng Li
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Wei Du
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Yueting Zhang
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Yingyan Han
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Chaojie Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Shuangxi Fan
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, P.R. China
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Rosental L, Still DW, You Y, Hayes RJ, Simko I. Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3319-3337. [PMID: 34196730 DOI: 10.1007/s00122-021-03898-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study, the effects of photoperiod and ambient temperature on bolting and flowering regulation were studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI 251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 h) and long (16 h) days and low (20 °C) and high (35 °C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2), and two candidate genes were identified by fine mapping, homology, and gene expression studies. In short days and high temperature conditions, qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8, and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences and were used to design a genetic marker which may be used to identify the late bolting trait.
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Affiliation(s)
- Leah Rosental
- Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - David W Still
- Agriculture Research Institute, California State University, Cal Poly Pomona, Pomona, CA, USA
- Department of Plant Sciences, Cal Poly Pomona, Pomona, CA, USA
| | - Youngsook You
- Department of Plant Sciences, Cal Poly Pomona, Pomona, CA, USA
| | - Ryan J Hayes
- Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA
- Agricultural Research Service, Forage Seed and Cereal Research Unit, U.S. Department of Agriculture, Corvallis, OR, USA
| | - Ivan Simko
- Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA.
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Han R, Truco MJ, Lavelle DO, Michelmore RW. A Composite Analysis of Flowering Time Regulation in Lettuce. FRONTIERS IN PLANT SCIENCE 2021; 12:632708. [PMID: 33763095 PMCID: PMC7982828 DOI: 10.3389/fpls.2021.632708] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/16/2021] [Indexed: 05/08/2023]
Abstract
Plants undergo profound physiological changes when transitioning from vegetative to reproductive growth. These changes affect crop production, as in the case of leafy vegetables. Lettuce is one of the most valuable leafy vegetable crops in the world. Past genetic studies have identified multiple quantitative trait loci (QTLs) that affect the timing of the floral transition in lettuce. Extensive functional molecular studies in the model organism Arabidopsis provide the opportunity to transfer knowledge to lettuce to explore the mechanisms through which genetic variations translate into changes in flowering time. In this review, we integrated results from past genetic and molecular studies for flowering time in lettuce with orthology and functional inference from Arabidopsis. This summarizes the basis for all known genetic variation underlying the phenotypic diversity of flowering time in lettuce and how the genetics of flowering time in lettuce projects onto the established pathways controlling flowering time in plants. This comprehensive overview reveals patterns across experiments as well as areas in need of further study. Our review also represents a resource for developing cultivars with delayed flowering time.
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Affiliation(s)
- Rongkui Han
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Maria José Truco
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
| | - Dean O. Lavelle
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
| | - Richard W. Michelmore
- The Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- *Correspondence: Richard W. Michelmore,
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Genome-Wide Identification of WRKY Transcription Factors in the Asteranae. PLANTS 2019; 8:plants8100393. [PMID: 31581604 PMCID: PMC6843914 DOI: 10.3390/plants8100393] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/27/2019] [Accepted: 09/29/2019] [Indexed: 02/07/2023]
Abstract
The WRKY transcription factors family, which participates in many physiological processes in plants, constitutes one of the largest transcription factor families. The Asterales and the Apiales are two orders of flowering plants in the superorder Asteranae. Among the members of the Asterales, globe artichoke (Cynara cardunculus var. scolymus L.), sunflower (Helianthus annuus L.), and lettuce (Lactuca sativa L.) are important economic crops worldwide. Within the Apiales, ginseng (Panax ginseng C. A. Meyer) and Panax notoginseng (Burk.) F.H. Chen are important medicinal plants, while carrot (Daucus carota subsp. carota L.) has significant economic value. Research involving genome-wide identification of WRKY transcription factors in the Asterales and the Apiales has been limited. In this study, 490 WRKY genes, 244 from three species of the Apiales and 246 from three species of the Asterales, were identified and categorized into three groups. Within each group, WRKY motif characteristics and gene structures were similar. WRKY gene promoter sequences contained light responsive elements, core regulatory elements, and 12 abiotic stress cis-acting elements. WRKY genes were evenly distributed on each chromosome. Evidence of segmental and tandem duplication events was found in all six species in the Asterales and the Apiales, with segmental duplication inferred to play a major role in WRKY gene evolution. Among the six species, we uncovered 54 syntenic gene pairs between globe artichoke and lettuce. The six species are thus relatively closely related, consistent with their traditional taxonomic placement in the Asterales. This study, based on traditional species classifications, was the first to identify WRKY transcription factors in six species from the Asteranae. Our results lay a foundation for further understanding of the role of WRKY transcription factors in species evolution and functional differentiation.
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Liu X, Lv S, Liu R, Fan S, Liu C, Liu R, Han Y. Correction: Transcriptomic analysis reveals the roles of gibberellin-regulated genes and transcription factors in regulating bolting in lettuce (Lactuca sativa L.). PLoS One 2019; 14:e0221609. [PMID: 31461498 PMCID: PMC6713346 DOI: 10.1371/journal.pone.0221609] [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] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0191518.].
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