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Shang C, Hou Q, Qiao G, Tian T, Wen X. CpSPL10-CpELF4 module involves in the negative regulation of flower bud differentiation in Chinese cherry. Int J Biol Macromol 2024; 280:135964. [PMID: 39322142 DOI: 10.1016/j.ijbiomac.2024.135964] [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: 08/07/2024] [Revised: 09/19/2024] [Accepted: 09/21/2024] [Indexed: 09/27/2024]
Abstract
SQUAMOSA promoter-binding protein-like (SPL) genes play a crucial role in regulating floral induction. Despite such importance, a comprehensive study of SPLs in Chinese cherry flower bud development has been absent. In this study, 32 CpSPL genes were identified. According to expression profiling, CpSPLs exhibited tissue-specific expression and distinct trends throughout flower bud differentiation. Specifically, CpSPL10 was greatly expressed at the beginning of the differentiation, and its role was further investigated. Its overexpression extended the vegetative growth of transgenic tobacco plants, delayed flowering by about 20 days. Moreover, the accumulation of NbELF4 (Early flowering 4) transcripts was enhanced due to the up-regulated levels of CpSPL10 in tobacco plants. ELF4 functions as a major element of the circadian clock; its high expression typically delays the transition from vegetative-to-reproductive growth. Further experiments revealed that CpSPL10 interacts with CpSPL9 or a transposase-derived transcription factor CpFRS5 (FAR1-RELATED SEQUENCE 5) and activates the expression of the downstream gene CpELF4. Notably, the GUS fusing reporter assay detected the activation of CpSPL10 and CpELF4 promoters in shoot apical meristems of transgenic Arabidopsis. These findings revealed the negative regulation of the CpSPL10-CpELF4 module in flower bud differentiation, providing references for supplementing the specific relationships among SPL, FRS, and ELF4.
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Affiliation(s)
- Chunqiong Shang
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, Guizhou Province, China; Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Tian Tian
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China.
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2
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Molinari MDC, Fuganti-Pagliarini R, Barbosa DDA, Marin SRR, Marin DR, Rech EL, Mertz-Henning LM, Nepomuceno AL. Flowering process in soybean under water deficit conditions: A review on genetic aspects. Genet Mol Biol 2021; 45:e20210016. [PMID: 34919115 PMCID: PMC8679260 DOI: 10.1590/1678-4685-gmb-2021-0016] [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] [Received: 01/24/2021] [Accepted: 09/30/2021] [Indexed: 11/22/2022] Open
Abstract
Soybean is a key crop in many countries, being used from human food to the animal industry due to its nutritional properties. Financially, the grain chain moves large sums of money into the economy of producing countries. However, like other agricultural commodities around the world, it can have its final yield seriously compromised by abiotic environmental stressors, like drought. As flowers imply in pods and in grains inside it to minimize damages caused by water restriction, researchers have focused on understanding flowering-process related genes and their interactions. Here a review dedicated to the soybean flowering process and gene network involved in it is presented, describing gene interactions and how genes act in this complex mechanism, also ruled by environmental triggers such as day-light and circadian cycle. The objective was to gather information and insights on the soybean flowering process, aiming to provide knowledge useful to assist in the development of drought-tolerant soybean lines, minimizing losses due to delays or anticipation of flowering and, consequently, restraining financial and productivity losses.
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Affiliation(s)
- Mayla Daiane Correa Molinari
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil.,Embrapa Soja, Londrina, PR, Brazil
| | | | - Daniel de Amorim Barbosa
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil.,Embrapa Soja, Londrina, PR, Brazil
| | | | | | - Elíbio Leopoldo Rech
- Embrapa Recursos Genéticos e Biotecnologia, Instituto Nacional de Ciência e Tecnologia em Biologia Sintética, Brasília, DF, Brazil
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Hao P, Wu A, Chen P, Wang H, Ma L, Wei H, Yu S. GhLUX1 and GhELF3 Are Two Components of the Circadian Clock That Regulate Flowering Time of Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2021; 12:691489. [PMID: 34434203 PMCID: PMC8380988 DOI: 10.3389/fpls.2021.691489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/20/2021] [Indexed: 05/30/2023]
Abstract
Photoperiod is an important external factor that regulates flowering time, the core mechanism of which lies in the circadian clock-controlled expression of FLOWERING LOCUS T (FT) and its upstream regulators. However, the roles of the circadian clock in regulating cotton flowering time are largely unknown. In this study, we cloned two circadian clock genes in cotton, GhLUX1 and GhELF3. The physicochemical and structural properties of their putative proteins could satisfy the prerequisites for the interaction between them, which was proved by yeast two-hybrid (Y2H) and Bimolecular Fluorescent Complimentary (BiFC) assays. Phylogenetic analysis of LUXs and ELF3s indicated that the origin of LUXs was earlier than that of ELF3s, but ELF3s were more divergent and might perform more diverse functions. GhLUX1, GhELF3, GhCOL1, and GhFT exhibited rhythmic expression and were differentially expressed in the early flowering and late-flowering cotton varieties under different photoperiod conditions. Both overexpression of GhLUX1 and overexpression of GhELF3 in Arabidopsis delayed flowering probably by changing the oscillation phases and amplitudes of the key genes in the photoperiodic flowering pathway. Both silencing of GhLUX1 and silencing of GhELF3 in cotton increased the expression of GhCOL1 and GhFT and resulted in early flowering. In summary, the circadian clock genes were involved in regulating cotton flowering time and could be the candidate targets for breeding early maturing cotton varieties.
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Affiliation(s)
- Pengbo Hao
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, China
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4
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Tian M, Wu A, Zhang M, Zhang J, Wei H, Yang X, Ma L, Lu J, Fu X, Wang H, Yu S. Genome-Wide Identification of the Early Flowering 4 ( ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance. Front Genet 2021; 12:686852. [PMID: 34326861 PMCID: PMC8315153 DOI: 10.3389/fgene.2021.686852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock's regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.
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Affiliation(s)
- Miaomiao Tian
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xu Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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5
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Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore? Int J Mol Sci 2021; 22:ijms22094588. [PMID: 33925559 PMCID: PMC8123782 DOI: 10.3390/ijms22094588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.
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Fang X, Han Y, Liu M, Jiang J, Li X, Lian Q, Xie X, Huang Y, Ma Q, Nian H, Qi J, Yang C, Wang Y. Modulation of evening complex activity enables north-to-south adaptation of soybean. SCIENCE CHINA. LIFE SCIENCES 2021; 64:179-195. [PMID: 33230598 DOI: 10.1007/s11427-020-1832-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022]
Abstract
Soybean, a typical short-day crop, is sensitive to photoperiod, which is a major limiting factor defining its north-to-south cultivation range. The long-juvenile (LJ) trait is controlled primarily by the J locus which has been used for decades by soybean breeders to delay flowering and improve grain yield in tropical regions. The J gene encodes an ortholog of the Arabidopsis Evening Complex (EC) component EARLY FLOWERING 3 (ELF3). To identify modifiers of J, we conducted a forward genetic screen and isolated a mutant (eoj57) that in combination with j has longer flowering delay compared with j single mutant plants. Map-based cloning and genome re-sequencing identified eoj57 (designated as GmLUX2) as an ortholog of the Arabidopsis EC component LUX ARRHYTHMO (LUX). To validate that GmLUX2 is a modifier of J, we used trans-complementation and identified a natural variant allele with a similar phenotype. We also show that GmLUX2 physically interacts with GmELF3a/b and binds DNA, whereas the mutant and natural variant are attenuated in both activities. Transcriptome analysis shows that the GmLUX2-GmELF3a complex co-regulates the expression of several circadian clock-associated genes and directly represses E1 expression. These results provide mechanistic insight into how GmLUX2-GmELF3 controls flowering time via synergistic regulation of gene expression. These novel insights expand our understanding of the regulation of the EC complex, and facilitate the development of soybean varieties adapted for growth at lower latitudes.
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Affiliation(s)
- Xiaolong Fang
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yapeng Han
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Mengshi Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiacan Jiang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiang Li
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qichao Lian
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xianrong Xie
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yian Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qibin Ma
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Hai Nian
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Cunyi Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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7
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Li MW, Lam HM. The Modification of Circadian Clock Components in Soybean During Domestication and Improvement. Front Genet 2020; 11:571188. [PMID: 33193673 PMCID: PMC7554537 DOI: 10.3389/fgene.2020.571188] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/19/2020] [Indexed: 12/19/2022] Open
Abstract
Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.
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Affiliation(s)
- Man-Wah Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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8
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Wang Y, Yuan L, Su T, Wang Q, Gao Y, Zhang S, Jia Q, Yu G, Fu Y, Cheng Q, Liu B, Kong F, Zhang X, Song CP, Xu X, Xie Q. Light- and temperature-entrainable circadian clock in soybean development. PLANT, CELL & ENVIRONMENT 2020; 43:637-648. [PMID: 31724182 DOI: 10.1111/pce.13678] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/13/2019] [Accepted: 11/08/2019] [Indexed: 05/07/2023]
Abstract
In plants, the spatiotemporal expression of circadian oscillators provides adaptive advantages in diverse species. However, the molecular basis of circadian clock in soybean is not known. In this study, we used soybean hairy roots expression system to monitor endogenous circadian rhythms and the sensitivity of circadian clock to environmental stimuli. We discovered in experiments with constant light and temperature conditions that the promoters of clock genes GmLCLb2 and GmPRR9b1 drive a self-sustained, robust oscillation of about 24-h in soybean hairy roots. Moreover, we demonstrate that circadian clock is entrainable by ambient light/dark or temperature cycles. Specifically, we show that light and cold temperature pulses can induce phase shifts of circadian rhythm, and we found that the magnitude and direction of phase responses depends on the specific time of these two zeitgeber stimuli. We obtained a quadruple mutant lacking the soybean gene GmLCLa1, LCLa2, LCLb1, and LCLb2 using CRISPR, and found that loss-of-function of these four GmLCL orthologs leads to an extreme short-period circadian rhythm and late-flowering phenotype in transgenic soybean. Our study establishes that the morning-phased GmLCLs genes act constitutively to maintain circadian rhythmicity and demonstrates that their absence delays the transition from vegetative growth to reproductive development.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Tong Su
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ya Gao
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Siyuan Zhang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qian Jia
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Guolong Yu
- MOA Key Lab of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfu Fu
- MOA Key Lab of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qun Cheng
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiao Zhang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaodong Xu
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiguang Xie
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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9
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Li Y, Li D, Jiao Y, Schnable JC, Li Y, Li H, Chen H, Hong H, Zhang T, Liu B, Liu Z, You Q, Tian Y, Guo Y, Guan R, Zhang L, Chang R, Zhang Z, Reif J, Zhou X, Schnable PS, Qiu L. Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:389-401. [PMID: 31278885 PMCID: PMC6953199 DOI: 10.1111/pbi.13206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 05/22/2023]
Abstract
Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS® . Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait-associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub-populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.
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Affiliation(s)
- Ying‐hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Delin Li
- Data Biotech (Beijing) Co., Ltd.BeijingChina
- Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Yong‐qing Jiao
- Key Laboratory of Oil Crop Biology (MOA)Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina
| | - James C. Schnable
- Data Biotech (Beijing) Co., Ltd.BeijingChina
- Departmentof Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Data2Bio LLCAmesIAUSA
| | - Yan‐fei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui‐hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Huai‐zhu Chen
- Guangxi Academy of Agricultural SciencesNanningChina
| | - Hui‐long Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ting Zhang
- Data Biotech (Beijing) Co., Ltd.BeijingChina
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhang‐xiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Qing‐bo You
- Key Laboratory of Oil Crop Biology (MOA)Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Rong‐xia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Li‐juan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ru‐zhen Chang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhiwu Zhang
- Department of Crop and Soil SciencesWashington State UniversityPullmanWAUSA
| | - Jochen Reif
- Department of Breeding ResearchLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Xin‐an Zhou
- Key Laboratory of Oil Crop Biology (MOA)Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina
| | - Patrick S. Schnable
- Data Biotech (Beijing) Co., Ltd.BeijingChina
- Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Data2Bio LLCAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Li‐juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Lin K, Zhao H, Gan S, Li G. Arabidopsis ELF4-like proteins EFL1 and EFL3 influence flowering time. Gene 2019; 700:131-138. [PMID: 30917931 DOI: 10.1016/j.gene.2019.03.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 12/20/2022]
Abstract
The circadian clock synchronizes internal and external stimuli to ensure numerous biological processes occur at the optimal time. EARLY FLOWERING 4 (ELF4) is a key evening-phased component of the circadian clock and essential for photoperiod-dependent flowering time regulation in Arabidopsis thaliana. There are four homologous ELF4-like (EFL1-EFL4) genes in the Arabidopsis genome but their functions are unknown. Protein sequence alignment and phylogenetic analysis showed that these four EFL proteins contained an evolutionarily conserved domain, DUF1313, of unknown function. To investigate the physical roles of these genes in Arabidopsis, we overexpressed the four homologous EFL genes in the elf4 mutant background. Under both long-day (LD) and short-day (SD) conditions, overexpression of EFL1 not only completely rescued the early flowering phenotype of the elf4 mutant, but also delayed flowering. Overexpression of EFL2, however, failed to rescue this phenotype and overexpression of EFL3 partially rescued the early flowering phenotype. The transcription levels of the key flowering time regulation genes CONSTANS (CO) and FLOWERING LOCUS T (FT) were significantly decreased in the EFL1- and EFL3-overexpressing transgenic lines in a dose-dependent manner, compared with the elf4 mutant. These results suggest that EFL1 and EFL3 are involved in flowering time regulation in Arabidopsis.
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Affiliation(s)
- Ke Lin
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China; Department of Biology Science and Technology, Taishan University, Tai'an 271000, Shandong, China
| | - Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Shuo Gan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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