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Deng Q, Du P, Gangurde SS, Hong Y, Xiao Y, Hu D, Li H, Lu Q, Li S, Liu H, Wang R, Huang L, Wang W, Garg V, Liang X, Varshney RK, Chen X, Liu H. ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1848-1866. [PMID: 38391124 PMCID: PMC11182584 DOI: 10.1111/pbi.14306] [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: 08/30/2022] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.
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Affiliation(s)
- Quanqing Deng
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Sunil S. Gangurde
- International Crops Research Institute for the Semi‐Arid TropicHyderabadIndia
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Yuan Xiao
- School of Public HealthWannan Medical CollegeWuhuAnhui ProvinceChina
| | - Dongxiu Hu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Shaoxiong Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haiyan Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Runfeng Wang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Lu Huang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Wenyi Wang
- College of AgricultureSouth China Agricultural UniversityGuangzhouGuangdong ProvinceChina
| | - Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xuanqiang Liang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Rajeev K. Varshney
- College of AgricultureSouth China Agricultural UniversityGuangzhouGuangdong ProvinceChina
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
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Wang WN, Wei YT, Zhao ST, Yu FH, Wang JW, Gu CY, Liu XR, Sai N, Zhu JL, Wang QM, Bao QX, Mu XR, Liu YX, Loake GJ, Jiang JH, Meng LS. ABSCISIC ACID-INSENSITIVE 5-KIP-RELATED PROTEIN 1-SHOOT MERISTEMLESS modulates reproductive development of Arabidopsis. PLANT PHYSIOLOGY 2024; 195:2309-2322. [PMID: 38466216 DOI: 10.1093/plphys/kiae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/12/2024]
Abstract
Soil (or plant) water deficit accelerates plant reproduction. However, the underpinning molecular mechanisms remain unknown. By modulating cell division/number, ABSCISIC ACID-INSENSITIVE 5 (ABI5), a key bZIP (basic (region) leucine zippers) transcription factor, regulates both seed development and abiotic stress responses. The KIP-RELATED PROTEIN (KRP) cyclin-dependent kinases (CDKs) play an essential role in controlling cell division, and SHOOT MERISTEMLESS (STM) plays a key role in the specification of flower meristem identity. Here, our findings show that abscisic acid (ABA) signaling and/or metabolism in adjust reproductive outputs (such as rosette leaf number and open flower number) under water-deficient conditions in Arabidopsis (Arabidopsis thaliana) plants. Reproductive outputs increased under water-sufficient conditions but decreased under water-deficient conditions in the ABA signaling/metabolism mutants abscisic acid2-1 (aba2-1), aba2-11, abscisic acid insensitive3-1 (abi3-1), abi4-1, abi5-7, and abi5-8. Further, under water-deficient conditions, ABA induced-ABI5 directly bound to the promoter of KRP1, which encodes a CDK that plays an essential role in controlling cell division, and this binding subsequently activated KRP1 expression. In turn, KRP1 physically interacted with STM, which functions in the specification of flower meristem identity, promoting STM degradation. We further demonstrate that reproductive outputs are adjusted by the ABI5-KRP1-STM molecular module under water-deficient conditions. Together, our findings reveal the molecular mechanism by which ABA signaling and/or metabolism regulate reproductive development under water-deficient conditions. These findings provide insights that may help guide crop yield improvement under water deficiency.
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Affiliation(s)
- Wan-Ni Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Yu-Ting Wei
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Sheng-Ting Zhao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Fu-Huan Yu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Jing-Wen Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Cheng-Yue Gu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xin-Ran Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Na Sai
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Jin-Lei Zhu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Qi-Meng Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Qin-Xin Bao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xin-Rong Mu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Yu-Xin Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Gary J Loake
- Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University, Edinburgh University, Jiangsu Normal University, 101 Shanghai Road, Xuzhou 221116, China
- Institute of Molecular Plant Sciences, School of Biological Sciences, Edinburgh University, King's Buildings, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
- Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University, Edinburgh University, Jiangsu Normal University, 101 Shanghai Road, Xuzhou 221116, China
| | - Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
- Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University, Edinburgh University, Jiangsu Normal University, 101 Shanghai Road, Xuzhou 221116, China
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McCue KF, Mehlferber E, Reed R, Ortiz A, Ferrel J, Khanna R. Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite). PLANT DIRECT 2023; 7:e537. [PMID: 38044963 PMCID: PMC10690473 DOI: 10.1002/pld3.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/28/2023] [Accepted: 09/26/2023] [Indexed: 12/05/2023]
Abstract
A plant's growth and development are shaped by its genome and the capacity to negotiate its environment for access to light, water, and nutrients. There is a vital need to understand the interactions between the plant, its physical environment, and the fertilizers used in agriculture. In this study, a commercially available volcanic ash fertilizer, Azomite®, characterized as dacitic (rhyolitic) tuff breccia, was tested for its effect on promoting early seedling vigor. Early growth and photomorphogenesis processes are well studied in Arabidopsis. Seedling assays under different light conditions were used to dissect the underlying mechanisms involved. These assays are well established and can be translated to agriculturally important crop plants. The volcanic ash fertilizer was tested at different concentrations on seedlings grown on basic media lacking sucrose either in continuous darkness (Dc), continuous Red (Rc), Far-Red (FRc), or White Light (WLc). Micronutrients in the volcanic ash significantly increased seedling growth under Rc and WLc, but not under Dc and FRc, indicating that photosynthetically active radiation was required for the observed growth increase. Furthermore, red-light photoreceptor mutant, phyB-9, lacked the growth response, and higher amount of fertilizer reduced growth in all conditions tested. These data suggest that light triggers the ability of the seedling to utilize micronutrients in volcanic ash in a dose-dependent manner. The methods described here can be used to establish mechanisms of activity of various nutrient inputs and, coupled with whole-genome expression profiling, can lead to better insights into optimizing nutrient field applications to improve crop production.
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Affiliation(s)
- Kent F. McCue
- Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research UnitUSDAAlbanyCaliforniaUSA
| | - Elijah Mehlferber
- Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Robert Reed
- Biotechnology Education & Specialized Training (BEST) Internship Program, i‐Cultiver, Inc., in collaboration with Contra Costa Community CollegeSan PabloCaliforniaUSA
| | - Alexis Ortiz
- Biotechnology Education & Specialized Training (BEST) Internship Program, i‐Cultiver, Inc., in collaboration with Contra Costa Community CollegeSan PabloCaliforniaUSA
| | - Jon Ferrel
- Azomite Mineral Products, Inc.NephiUtahUSA
- i‐Cultiver, Inc.MantecaCaliforniaUSA
| | - Rajnish Khanna
- i‐Cultiver, Inc.MantecaCaliforniaUSA
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
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Bao QX, Mu XR, Tong C, Li C, Tao WZ, Zhao ST, Liu YX, Wang WN, Wei YT, Yu FH, Wang JW, Sun ZL, Fan BL, Sun J, Wang C, Loake G, Meng LS. Sugar status in preexisting leaves determines systemic stomatal development within newly developing leaves. Proc Natl Acad Sci U S A 2023; 120:e2302854120. [PMID: 37276396 PMCID: PMC10268241 DOI: 10.1073/pnas.2302854120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/11/2023] [Indexed: 06/07/2023] Open
Abstract
Stomata are pores found in the epidermis of stems or leaves that modulate both plant gas exchange and water/nutrient uptake. The development and function of plant stomata are regulated by a diverse range of environmental cues. However, how carbohydrate status in preexisting leaves might determine systemic stomatal formation within newly developing leaves has remained obscure. The glucose (Glc) sensor HEXOKINASE1 (HXK1) has been reported to decrease the stability of an ethylene/Glc signaling transcriptional regulator, EIN3 (ETHYLENE INSENSITIVE3). EIN3 in turn directly represses the expression of SUC2 (sucrose transporter 2), encoding a master transporter of sucrose (Suc). Further, KIN10, a nuclear regulator involved in energy homeostasis, has been reported to repress the transcription factor SPCH (SPEECHLESS), a master regulator of stomatal development. Here, we demonstrate that the Glc status of preexisting leaves determines systemic stomatal development within newly developing leaves by the HXK1-¦EIN3-¦SUC2 module. Further, increasing Glc levels in preexisting leaves results in a HXK1-dependent decrease of EIN3 and increase of SUC2, triggering the perception, amplification and relay of HXK1-dependent Glc signaling and thereby triggering Suc transport from mature to newly developing leaves. The HXK1-¦EIN3-¦SUC2 molecular module thereby drives systemic Suc transport from preexisting leaves to newly developing leaves. Subsequently, increasing Suc levels within newly developing leaves promotes stomatal formation through the established KIN10⟶ SPCH module. Our findings thus show how a carbohydrate signal in preexisting leaves is sensed, amplified and relayed to determine the extent of systemic stomatal development within newly developing leaves.
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Affiliation(s)
- Qin-Xin Bao
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Xin-Rong Mu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Chen Tong
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Cong Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, People’s Republic of China
| | - Wen-Zhe Tao
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Sheng-Ting Zhao
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Yu-xin Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Wan-Ni Wang
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Yu-ting Wei
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Fu-Huan Yu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Jing-wen Wang
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Zhi-Lan Sun
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Bing-Ling Fan
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Jia Sun
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
| | - Chen Wang
- School of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu210095, People’s Republic of China
| | - Gary J. Loake
- Jiangsu Normal University–Edinburgh University, Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
- Institute of Molecular Plant Sciences, School of Biological Sciences, Edinburgh University, EdinburghEH9 3BF, United Kingdom
| | - Lai-Sheng Meng
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu221116, People’s Republic of China
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Yin CC, Huang YH, Zhang X, Zhou Y, Chen SY, Zhang JS. Ethylene-mediated regulation of coleoptile elongation in rice seedlings. PLANT, CELL & ENVIRONMENT 2023; 46:1060-1074. [PMID: 36397123 DOI: 10.1111/pce.14492] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Rice is an important food crop in the world and the study of its growth and plasticity has a profound influence on sustainable development. Ethylene modulates multiple agronomic traits of rice as well as abiotic and biotic stresses during its lifecycle. It has diverse roles, depending on the organs, developmental stages and environmental conditions. Compared to Arabidopsis (Arabidopsis thaliana), rice ethylene signalling pathway has its own unique features due to its special semiaquatic living environment and distinct plant structure. Ethylene signalling and responses are part of an intricate network in crosstalk with internal and external factors. This review will summarize the current progress in the mechanisms of ethylene-regulated coleoptile growth in rice, with a special focus on ethylene signaling and interaction with other hormones. Insights into these molecular mechanisms may shed light on ethylene biology and should be beneficial for the genetic improvement of rice and other crops.
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Affiliation(s)
- Cui-Cui Yin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Yi-Hua Huang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Xun Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Zhou
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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