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Kumar A, Mushtaq M, Kumar P, Sharma DP, Gahlaut V. Insights into flowering mechanisms in apple (Malus × domestica Borkh.) amidst climate change: An exploration of genetic and epigenetic factors. Biochim Biophys Acta Gen Subj 2024; 1868:130593. [PMID: 38408683 DOI: 10.1016/j.bbagen.2024.130593] [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: 07/20/2023] [Revised: 01/05/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Apple (Malus × domestica Borkh.) holds a prominent position among global temperate fruit crops, with flowering playing a crucial role in both production and breeding. This review delves into the intricate mechanisms governing apple flowering amidst the backdrop of climate change, acknowledging the profound influence of external and internal factors on biennial bearing, flower bud quality, and ultimately, fruit quality. Notably, the challenge faced in major apple production regions is not an inadequacy of flowers but an excess, leading to compromised fruit quality necessitating thinning practices. Climate change exacerbates these challenges, rendering apple trees more susceptible to crop failure due to unusual weather events, such as reduced winter snowfall, early spring cold weather, and hailstorms during flowering and fruit setting. Altered climatic conditions, exemplified by increased spring warming coupled with sub-freezing temperatures, negatively impact developing flower buds and decrease overall crop production. Furthermore, changing winter conditions affect chilling accumulation, disrupting flower development and synchronicity. Although the physiological perception of apple flowering has been reviewed in the past, the genetic, epigenetic, and multi-omics regulatory mechanisms governing floral induction and flowering are still rarely discussed in the case of apple flowering. This article comprehensively reviews the latest literature encompassing all aspects of apple flowering, aiming to broaden our understanding and address flowering challenges while also laying a solid foundation for future research in developing cultivars that are ideally adapted to climate change.
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Affiliation(s)
- Anshul Kumar
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India.
| | - Dharam Paul Sharma
- Department of Fruit Science, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India
| | - Vijay Gahlaut
- University Centre for Research & Development, Chandigarh University, Punjab 140413, India.
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Yuan X, Quan S, Liu J, Guo C, Zhang Z, Kang C, Niu J. Evolution of the PEBP gene family in Juglandaceae and their regulation of flowering pathway under the synergistic effect of JrCO and JrNF-Y proteins. Int J Biol Macromol 2022; 223:202-212. [PMID: 36347378 DOI: 10.1016/j.ijbiomac.2022.11.004] [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: 09/19/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Phosphatidyl ethanolamine-binding protein (PEBP) has a conserved PEBP domain and plays an important role in regulating the flowering time and growth of angiosperms. To understand the evolution of PEBP family genes in walnut family and the mechanism of regulating flowering in photoperiod pathway, 53 genes with PEBP domain were identified from 5 Juglandaceae plants. The PEBP gene family of Juglandaceae can be divided into four subgroups, FT-like, TFL-like, MFT-like and PEBP-like subgroups. These genes all show very high homology for motifs and gene structure in Juglandaceae. In addition, the results of gene replication and collinearity analysis showed that the evolution of PEBP genes was mainly purified and selected, and segmental repetition was the main driving force for the evolution of PEBP gene family in walnut family. We found that PEBP gene family played an important role in female flower bud differentiation, and most JrPEBP genes were highly expressed in leaf bud and female flower bud by qRT-PCR. In Arabidopsis, AtCO can not only directly bind to CORE2, but also interact with NF-Y complex to positively regulate the expression of AtFT gene. In this study, we proved that JrCO (the lineal homologue of AtCO) could not directly regulate the expression of JrFT gene, but could enhance the binding of JrNF-YB4/6 protein to the promoter of JrFT gene by forming a heteropolymer with NF-YB4/NF-YB6. We also confirmed that JrNF-YC1/3/7, JrNF-YB4/6 and JrCO can form a trimer structure similar to AtNF-YB-YC-CO of Arabidopsis, and then bind to the promoter of JrFT gene to promote the transcription of JrFT gene. In a word, through identification and analysis of PEBP gene family in Juglandaceae and study on the mechanism of photoperiod pathway regulating flowering in walnut, we have found that nuclear transcription factor NF-YB/YC plays a more important role in the trimer structure of NF-YB-YC-CO in walnut species. Our study has further perfected the flowering regulatory network of walnut species.
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Affiliation(s)
- Xing Yuan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Shaowen Quan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Jinming Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Caihua Guo
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Zhongrong Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Chao Kang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China.
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Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants. Semin Cell Dev Biol 2020; 109:20-30. [PMID: 32507412 DOI: 10.1016/j.semcdb.2020.05.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 01/01/2023]
Abstract
Plant growth and development, particularly the induction of flowering, are tightly controlled by key regulators in response to endogenous and environmental cues. The FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family of phosphatidylethanolamine-binding protein (PEBP) genes is central to plant development, especially the regulation of flowering time and plant architecture. FT, the long-sought florigen, promotes flowering and TFL1 represses flowering. The balance between FT and TFL1 modulates plant architecture by switching the meristem from indeterminate to determinate growth, or vice versa. Recent studies in a broad range of plant species demonstrated that, in addition to their roles in flowering time and plant architecture, FT/TFL1 family genes participate in diverse aspects of plant development, such as bamboo seed germination and potato tuber formation. In this review, we briefly summarize the evolution of the FT/TFL1 family and highlight recent findings on their conserved and divergent functions in different species.
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Xing L, Li Y, Qi S, Zhang C, Ma W, Zuo X, Liang J, Gao C, Jia P, Shah K, Zhang D, An N, Zhao C, Han M, Zhao J. Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation. PLANT & CELL PHYSIOLOGY 2019; 60:1702-1721. [PMID: 31077318 DOI: 10.1093/pcp/pcz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.
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Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Pen Jia
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Juan Zhao
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
- College of Mechanical and Electronic Engineering, Northwest A & F University, Yangling, Shaanxi, P. R. China
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Duan CG, Zhu JK, Cao X. Retrospective and perspective of plant epigenetics in China. J Genet Genomics 2018; 45:621-638. [PMID: 30455036 DOI: 10.1016/j.jgg.2018.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 01/21/2023]
Abstract
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
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Affiliation(s)
- Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Luo X, Gao Z, Wang Y, Chen Z, Zhang W, Huang J, Yu H, He Y. The NUCLEAR FACTOR-CONSTANS complex antagonizes Polycomb repression to de-repress FLOWERING LOCUS T expression in response to inductive long days in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:17-29. [PMID: 29667247 DOI: 10.1111/tpj.13926] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/27/2018] [Accepted: 03/26/2018] [Indexed: 05/07/2023]
Abstract
Many plants sense the seasonal cues, day length or photoperiod changes, to align the timing of the developmental transition to flowering with changing seasons for reproductive success. Inductive day lengths through the photoperiod pathway induce the expression of FLOWERING LOCUS T (FT) or FT relatives that encode a major mobile florigen to promote flowering. In Arabidopsis thaliana, under inductive long days the photoperiod pathway output CONSTANS (CO) accumulates toward the end of the day, and associates with the B and C subunits of Nuclear Factor Y (NF-Y) to form the NF-CO complex that acts to promote FT expression near dusk, whereas Polycomb group (PcG) proteins function to silence FT expression. How NF-CO acts to antagonize the function of PcG proteins to regulate FT expression remains unclear. Here, we show that the NF-CO complex bound to the proximal FT promoter, through chromatin looping, acts in concert with an NF-Y complex bound to a distal enhancer to reduce the levels of PcG proteins, including both Polycomb repressive complex 1 (PRC1) and PRC2 at the FT promoter, leading to a relieving of Polycomb silencing and thus FT de-repression near dusk. Thus, our study provides molecular insights on how the 'active' photoperiod pathway and the 'repressive' Polycomb silencing system interact to control temporal FT expression, conferring the long-day induction of flowering in Arabidopsis.
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Affiliation(s)
- Xiao Luo
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
| | - Zheng Gao
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yizhong Wang
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
| | - Zhijuan Chen
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenju Zhang
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jirong Huang
- Department of Biology, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Hao Yu
- Department of Biological Sciences & Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Yuehui He
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
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Moss SMA, Wang T, Voogd C, Brian LA, Wu R, Hellens RP, Allan AC, Putterill J, Varkonyi‐Gasic E. AcFT promotes kiwifruit in vitro flowering when overexpressed and Arabidopsis flowering when expressed in the vasculature under its own promoter. PLANT DIRECT 2018; 2:e00068. [PMID: 31245732 PMCID: PMC6508797 DOI: 10.1002/pld3.68] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 05/24/2023]
Abstract
Kiwifruit (Actinidia chinensis) has three FLOWERING LOCUS T (FT) genes, AcFT, AcFT1, and AcFT2, with differential expression and potentially divergent roles. AcFT was previously shown to be expressed in source leaves and induced in dormant buds by winter chilling. Here, we show that AcFT promotes flowering in A. chinensis, despite a short sequence insertion not present in other FT-like genes. A 3.5-kb AcFT promoter region contained all the regulatory elements required to mediate vascular expression in transgenic Arabidopsis thaliana (Arabidopsis). The promoter activation was initially confined to the veins in the distal end of the leaf, before extending to the veins in the base of the leaf, and was detected in inductive and noninductive photoperiods. The 3-kb and 2.7-kb promoter regions of AcFT1 and AcFT2, respectively, demonstrated different activation patterns in Arabidopsis, corresponding to differential expression in kiwifruit. Expression of AcFT cDNA from the AcFT promoter was capable to induce early flowering in transgenic Arabidopsis in noninductive photoperiods. Further, expression of AcFT cDNA fused to the green fluorescent protein was detected in the vasculature and was also capable to advance flowering in noninductive photoperiods. Taken together, these studies implicate AcFT in regulation of kiwifruit flowering time and as a candidate for kiwifruit florigen.
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Affiliation(s)
- Sarah M. A. Moss
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Present address:
The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Palmerston NorthPalmerston NorthNew Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Lara A. Brian
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
- Present address:
Centre for Tropical Crops and BiocommoditiesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Andrew C. Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Joanna Putterill
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Erika Varkonyi‐Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt AlbertAuckland Mail CentreAucklandNew Zealand
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