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Gao Y, Zhang Y, Ma C, Chen Y, Liu C, Wang Y, Wang S, Chen X. Editing the nuclear localization signals of E1 and E1Lb enables the production of tropical soybean in temperate growing regions. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2145-2156. [PMID: 38511622 PMCID: PMC11258983 DOI: 10.1111/pbi.14335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/05/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
Soybean is a typical short-day crop, and most commercial soybean cultivars are restricted to a relatively narrow range of latitudes due to photoperiod sensitivity. Photoperiod sensitivity hinders the utilization of soybean germplasms across geographical regions. When grown in temperate regions, tropical soybean responds to prolonged day length by increasing the vegetative growth phase and delaying flowering and maturity, which often pushes the harvest window past the first frost date. In this study, we used CRISPR/LbCas12a to edit a North American subtropical soybean cultivar named 06KG218440 that belongs to maturity group 5.5. By designing one gRNA to edit the nuclear localization signal (NLS) regions of both E1 and E1Lb, we created a series of new germplasms with shortened flowering time and time to maturity and determined their favourable latitudinal zone for cultivation. The novel partial function alleles successfully achieve yield and early maturity trade-offs and exhibit good agronomic traits and high yields in temperate regions. This work offers a straightforward editing strategy to modify subtropical and tropical soybean cultivars for temperate growing regions, a strategy that could be used to enrich genetic diversity in temperate breeding programmes and facilitate the introduction of important crop traits such as disease tolerance or high yield.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Yuguo Zhang
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Chuanyu Ma
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Yanhui Chen
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Chunxia Liu
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Seed Technology China Co., Ltd.YanglingChina
| | - Yanli Wang
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Songyuan Wang
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Xi Chen
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
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Wang X, Li Q, Zhu H, Song M, Zhang K, Ge W. Molecular mechanisms of miR172a and its target gene LbrTOE3 regulating maturation in Lilium. PLANTA 2023; 258:53. [PMID: 37515607 DOI: 10.1007/s00425-023-04208-x] [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: 04/27/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
MAIN CONCLUSION Lbr-miR172a could promote the growth phase transition and shorten maturation in Lilium, while LbrTOE3 inhibited this process and prolonged the growth period. Lilium is an ornamental flower with high economic value for both food and medicinal purposes. However, under natural conditions, Lilium bulbs take a long time and cost more to grow to commercial size. This research was conducted to shorten the maturation time by subjecting Lilium bulbs to alternating temperature treatment. To explore the molecular mechanism of the vegetative phase change (VPC) in Lilium after variable temperature treatment, the key module miR172a-TOE3 was selected based on a combined omics analysis. Gene cloning and transgene functional validation showed that overexpression of Lbr-mir172a promoted a phase change, while overexpression of LbrTOE3 inhibited this process. Subcellular localization and transcriptional activation assays indicated that LbrTOE3 was predominantly localized in the nucleus and showed transcriptional activity. In situ hybridization showed that LbrTOE3 expression was significantly downregulated after alternating temperature treatment. This study elucidates the molecular mechanisms of the phase transition of Lilium and provides a scientific basis for the phase transition in other plants.
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Affiliation(s)
- Xiaoshan Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Qing Li
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Haoran Zhu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Meiqi Song
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China.
| | - Wei Ge
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China.
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3
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Garg V, Reins J, Hackel A, Kühn C. Elucidation of the interactome of the sucrose transporter StSUT4: sucrose transport is connected to ethylene and calcium signalling. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7401-7416. [PMID: 36124639 PMCID: PMC9730799 DOI: 10.1093/jxb/erac378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Sucrose transporters of the SUT4 clade show dual targeting to both the plasma membrane as well as to the vacuole. Previous investigations revealed a role for the potato sucrose transporter StSUT4 in flowering, tuberization, shade avoidance response, and ethylene production. Down-regulation of StSUT4 expression leads to early flowering, tuberization under long days, far-red light insensitivity, and reduced diurnal ethylene production. Sucrose export from leaves was increased and a phase-shift of soluble sugar accumulation in source leaves was observed, arguing for StSUT4 to be involved in the entrainment of the circadian clock. Here, we show that StSUT4, whose transcripts are highly unstable and tightly controlled at the post-transcriptional level, connects components of the ethylene and calcium signalling pathway. Elucidation of the StSUT4 interactome using the split ubiquitin system helped to prove direct physical interaction between the sucrose transporter and the ethylene receptor ETR2, as well as with the calcium binding potato calmodulin-1 (PCM1) protein, and a calcium-load activated calcium channel. The impact of calcium ions on transport activity and dual targeting of the transporter was investigated in detail. For this purpose, a reliable esculin-based transport assay was established for SUT4-like transporters. Site-directed mutagenesis helped to identify a diacidic motif within the seventh transmembrane spanning domain that is essential for sucrose transport activity and targeting, but not required for calcium-dependent inhibition. A link between sucrose, calcium and ethylene signalling has been previously postulated with respect to pollen tube growth, shade avoidance response, or entrainment of the circadian clock. Here, we provide experimental evidence for the direct interconnection of these signalling pathways at the molecular level by direct physical interaction of the main players.
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Affiliation(s)
- Varsha Garg
- Humboldt-Universität zu Berlin, Institute of Biology, Department of Plant Physiology, Philippstr. 13 Building 12, 10115 Berlin, Germany
| | - Jana Reins
- Humboldt-Universität zu Berlin, Institute of Biology, Department of Plant Physiology, Philippstr. 13 Building 12, 10115 Berlin, Germany
| | - Aleksandra Hackel
- Humboldt-Universität zu Berlin, Institute of Biology, Department of Plant Physiology, Philippstr. 13 Building 12, 10115 Berlin, Germany
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Li C, Nong W, Zhao S, Lin X, Xie Y, Cheung MY, Xiao Z, Wong AYP, Chan TF, Hui JHL, Lam HM. Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. BMC Genomics 2022; 23:65. [PMID: 35057741 PMCID: PMC8780314 DOI: 10.1186/s12864-022-08308-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types of ncRNAs in the context of plant physiology, especially in response to salinity stress, are poorly understood. RESULTS Here, we challenged a cultivated soybean accession (C08) and a wild one (W05) with salt treatment and obtained their small RNA transcriptomes at six time points from both root and leaf tissues. In addition to thoroughly analyzing the differentially expressed miRNAs, we also documented the first case of miRNA arm-switching (miR166m), the swapping of dominant miRNA arm expression, in soybean in different tissues. Two arms of miR166m target different genes related to salinity stress (chloroplastic beta-amylase 1 targeted by miR166m-5p and calcium-dependent protein kinase 1 targeted by miR166m-3p), suggesting arm-switching of miR166m play roles in soybean in response to salinity stress. Furthermore, two pairs of miRNA:lncRNA interacting partners (miR166i-5p and lncRNA Gmax_MSTRG.35921.1; and miR394a-3p and lncRNA Gmax_MSTRG.18616.1) were also discovered in reaction to salinity stress. CONCLUSIONS This study demonstrates how ncRNA involves in salinity stress responses in soybean by miRNA arm switching and miRNA:lncRNA interactions. The behaviors of ncRNAs revealed in this study will shed new light on molecular regulatory mechanisms of stress responses in plants, and hence provide potential new strategies for crop improvement.
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Affiliation(s)
- Chade 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 Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Shancen Zhao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, P.R. China
| | - Xiao Lin
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yichun Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ming-Yan Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Zhixia Xiao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Annette Y P Wong
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. 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 Special Administrative Region, P.R. China.
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6
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Xing H, Li Y, Ren Y, Zhao Y, Wu X, Li HL. Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe). BMC Genomics 2022; 23:49. [PMID: 35021996 PMCID: PMC8756691 DOI: 10.1186/s12864-021-08273-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. RESULTS In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. CONCLUSION This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.
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Affiliation(s)
- Haitao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yuan Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
| | - Yun Ren
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Ying Zhao
- Research Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan, China
| | - Xiaoli Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
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7
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Lin X, Liu B, Weller JL, Abe J, Kong F. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:981-994. [PMID: 33090664 DOI: 10.1111/jipb.13021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean (Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.
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Affiliation(s)
- Xiaoya Lin
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510642, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510642, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510642, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
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8
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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9
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Garg V, Hackel A, Kühn C. Expression Level of Mature miR172 in Wild Type and StSUT4-Silenced Plants of Solanum tuberosum Is Sucrose-Dependent. Int J Mol Sci 2021; 22:ijms22031455. [PMID: 33535646 PMCID: PMC7867175 DOI: 10.3390/ijms22031455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/29/2022] Open
Abstract
In potato plants, the phloem-mobile miR172 is involved in the sugar-dependent transmission of flower and tuber inducing signal transduction pathways and a clear link between solute transport and the induction of flowering and tuberization was demonstrated. The sucrose transporter StSUT4 seems to play an important role in the photoperiod-dependent triggering of both developmental processes, flowering and tuberization, and the phenotype of StSUT4-inhibited potato plants is reminiscent to miR172 overexpressing plants. The first aim of this study was the determination of the level of miR172 in sink and source leaves of StSUT4-silenced as well as StSUT4-overexpressing plants in comparison to Solanum tuberosum ssp. Andigena wild type plants. The second aim was to investigate the effect of sugars on the level of miRNA172 in whole cut leaves, as well as in whole in vitro plantlets that were supplemented with exogenous sugars. Experiments clearly show a sucrose-dependent induction of the level of mature miR172 in short time as well as long time experiments. A sucrose-dependent accumulation of miR172 was also measured in mature leaves of StSUT4-silenced plants where sucrose export is delayed and sucrose accumulates at the end of the light period.
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10
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Li L, Li Q, Davis KE, Patterson C, Oo S, Liu W, Liu J, Wang G, Fontana JE, Thornburg TE, Pratt IS, Li F, Zhang Z, Zhou Y, Pan X, Zhang B. Response of Root Growth and Development to Nitrogen and Potassium Deficiency as well as microRNA-Mediated Mechanism in Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2021; 12:695234. [PMID: 34178008 PMCID: PMC8231928 DOI: 10.3389/fpls.2021.695234] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/17/2021] [Indexed: 05/13/2023]
Abstract
The mechanism of miRNA-mediated root growth and development in response to nutrient deficiency in peanut (Arachis hypogaea L.) is still unclear. In the present study, we found that both nitrogen (N) and potassium (K) deficiency resulted in a significant reduction in plant growth, as indicated by the significantly decreased dry weight of both shoot and root tissues under N or K deficiency. Both N and K deficiency significantly reduced the root length, root surface area, root volume, root vitality, and weakened root respiration, as indicated by the reduced O2 consuming rate. N deficiency significantly decreased primary root length and lateral root number, which might be associated with the upregulation of miR160, miR167, miR393, and miR396, and the downregulation of AFB3 and GRF. The primary and lateral root responses to K deficiency were opposite to that of the N deficiency condition. The upregulated miR156, miR390, NAC4, ARF2, and AFB3, and the downregulated miR160, miR164, miR393, and SPL10 may have contributed to the growth of primary roots and lateral roots under K deficiency. Overall, roots responded differently to the N or K deficiency stresses in peanuts, potentially due to the miRNA-mediated pathway and mechanism.
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Affiliation(s)
- Lijie Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Qian Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Kyle E. Davis
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Caitlin Patterson
- Department of Biology, East Carolina University, Greenville, NC, United States
- Elizabeth City State University, Elizabeth City, NC, United States
| | - Sando Oo
- Department of Biology, East Carolina University, Greenville, NC, United States
- Elizabeth City State University, Elizabeth City, NC, United States
| | - Wanying Liu
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jia Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Guo Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Julia Elise Fontana
- Department of Biology, East Carolina University, Greenville, NC, United States
| | | | - Isaac Seth Pratt
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Fei Li
- Peanut Research Institute, Luohe Academy of Agricultural Sciences, Luohe, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- Yanzhong Zhou,
| | - Yanzhong Zhou
- Peanut Research Institute, Luohe Academy of Agricultural Sciences, Luohe, China
- Yanzhong Zhou,
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
- Baohong Zhang,
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11
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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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12
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Brandoli C, Petri C, Egea-Cortines M, Weiss J. Gigantea: Uncovering New Functions in Flower Development. Genes (Basel) 2020; 11:genes11101142. [PMID: 32998354 PMCID: PMC7600796 DOI: 10.3390/genes11101142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO), as well as on the basis of interaction with miRNA. The complexity of the gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and volatile flower production.
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Affiliation(s)
- Claudio Brandoli
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
| | - Cesar Petri
- Instituto de Hortofruticultura Subtropical y Mediterránea-UMA-CSIC, Departamento de Fruticultura Subtropical y Mediterránea, 29750 Algarrobo-costa, Málaga, Spain;
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
- Correspondence: ; Tel.: +34-868-071-078
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13
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Jeyaraj A, Elango T, Li X, Guo G. Utilization of microRNAs and their regulatory functions for improving biotic stress tolerance in tea plant [ Camellia sinensis (L.) O. Kuntze]. RNA Biol 2020; 17:1365-1382. [PMID: 32478595 DOI: 10.1080/15476286.2020.1774987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs play a central role in responses to biotic stressors through their interactions with their target mRNAs. Tea plant (Camellia sinensis L.), an important beverage crop, is vulnerable to tea geometrid and anthracnose disease that causes considerable crop loss and tea production worldwide. Sustainable production of tea in the current scenario to biotic factors is major challenges. To overcome the problem of biotic stresses, high-throughput sequencing (HTS) with bioinformatics analyses has been used as an effective approach for the identification of stress-responsive miRNAs and their regulatory functions in tea plant. These stress-responsive miRNAs can be utilized for miRNA-mediated gene silencing to enhance stress tolerance in tea plant. Therefore, this review summarizes the current understanding of miRNAs regulatory functions in tea plant responding to Ectropis oblique and Colletotrichum gloeosporioides attacks for future miRNA research. Also, it highlights the utilization of miRNA-mediated gene silencing strategies for developing biotic stress-tolerant tea plant.
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Affiliation(s)
- Anburaj Jeyaraj
- Tea Research Institute, Nanjing Agricultural University , Nanjing, China.,Department of Biotechnology, Karpagam Academy of Higher Education , Tamilnadu, India
| | - Tamilselvi Elango
- Tea Research Institute, Nanjing Agricultural University , Nanjing, China
| | - Xinghui Li
- Tea Research Institute, Nanjing Agricultural University , Nanjing, China
| | - Guiyi Guo
- Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University , Xinyang, P.R. China
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14
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Basso MF, Ferreira PCG, Kobayashi AK, Harmon FG, Nepomuceno AL, Molinari HBC, Grossi‐de‐Sa MF. MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1482-1500. [PMID: 30947398 PMCID: PMC6662102 DOI: 10.1111/pbi.13116] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/22/2019] [Accepted: 03/17/2019] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) modulate the abundance and spatial-temporal accumulation of target mRNAs and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding miRNAs (MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other miRNAs. Fine-tuning of MIR genes or miRNAs is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance. Current approaches for miRNA fine-tuning are based on the down- or up-regulation of MIR gene transcription and the use of genetic engineering tools to manipulate the final concentration of these miRNAs in the cytoplasm. Transgenesis, cisgenesis, intragenesis, artificial MIR genes, endogenous and artificial target mimicry, MIR genes editing using Meganucleases, ZNF proteins, TALENs and CRISPR/Cas9 or CRISPR/Cpf1, CRISPR/dCas9 or dCpf1, CRISPR13a, topical delivery of miRNAs and epigenetic memory have been successfully explored to MIR gene or miRNA modulation and improve agronomic traits in several model or crop plants. However, advantages and drawbacks of each of these new biotechnological tools (NBTs) are still not well understood. In this review, we provide a brief overview of the biogenesis and role of miRNAs in response to abiotic or biotic stresses, we present critically the main NBTs used for the manipulation of MIR genes and miRNAs, we show current efforts and findings with the MIR genes and miRNAs modulation in plants, and we summarize the advantages and drawbacks of these NBTs and provide some alternatives to overcome. Finally, challenges and future perspectives to miRNA modulating in important crops are also discussed.
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Affiliation(s)
| | | | | | - Frank G. Harmon
- Plant Gene Expression CenterUSDA‐ARSAlbanyCAUSA
- Department of Plant and Microbial BiologyUC BerkeleyBerkeleyCAUSA
| | | | | | - Maria Fatima Grossi‐de‐Sa
- Embrapa Genetic Resources and BiotechnologyBrasíliaDFBrazil
- Post‐Graduation Program in Genomic Sciences and BiotechnologyCatholic University of BrasíliaBrasíliaDFBrazil
- Post‐Graduation Program in BiotechnologyPotiguar University (UNP)NatalRNBrazil
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15
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Guo X, Niu J, Cao X. Heterologous Expression of Salvia miltiorrhiza MicroRNA408 Enhances Tolerance to Salt Stress in Nicotiana benthamiana. Int J Mol Sci 2018; 19:E3985. [PMID: 30544912 PMCID: PMC6321395 DOI: 10.3390/ijms19123985] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate the expression of target genes post-transcriptionally; they are known to play major roles in development and responses to abiotic stress. MicroRNA408 (miR408) is a conserved small RNA in plants; it was reported that miR408 genes were involved in abiotic stress in Arabidopsis. However, miR408 in Salvia miltiorrhiza has been rarely investigated. In this study, we cloned Sm-MIR408, the miR408 precursor sequence, and its promoter sequence from S. miltiorrhiza and the role in tolerance to salt stress is described. The effects of salt stress on miR408 expression were studied by using β-glucuronidase (GUS) staining. Our data indicated that transgenic tobacco overexpressing Sm-MIR408 promoted seed germination and reduced the accumulation of reactive oxygen species under salt stress. Transcript levels of antioxidative genes, i.e., NbSOD, NbPOD, and NbCAT, and their enzyme activities increased in salinity-stressed transgenic tobacco plants, suggesting a better antioxidant system to cope the oxidative damage caused by salinity stress. Taken together, these findings indicated that miR408 functions in positive responses to salt tolerance in tobacco.
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Affiliation(s)
- Xiaorong Guo
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shanxi Normal University, Xi'an 710062, China.
| | - Junfeng Niu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shanxi Normal University, Xi'an 710062, China.
| | - Xiaoyan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shanxi Normal University, Xi'an 710062, China.
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16
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Tong W, Yu J, Hou Y, Li F, Zhou Q, Wei C, Bennetzen JL. Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). PLANTA 2018; 248:1417-1429. [PMID: 30128600 DOI: 10.1007/s00425-018-2983-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Circular RNA (circRNA) discovery, expression patterns and experimental validation in developing tea leaves indicates its correlation with circRNA-parental genes and potential roles in ceRNA interaction network. Circular RNAs (circRNAs) have recently emerged as a novel class of abundant endogenous stable RNAs produced by circularization with regulatory potential. However, identification of circRNAs in plants, especially in non-model plants with large genomes, is challenging. In this study, we undertook a systematic identification of circRNAs from different stage tissues of tea plant (Camellia sinensis) leaf development using rRNA-depleted circular RNA-seq. By combining two state-of-the-art detecting tools, we characterized 3174 circRNAs, of which 342 were shared by each approach, and thus considered high-confidence circRNAs. A few predicted circRNAs were randomly chosen, and 20 out of 24 were experimental confirmed by PCR and Sanger sequencing. Similar in other plants, tissue-specific expression was also observed for many C. sinensis circRNAs. In addition, we found that circRNA abundances were positively correlated with the mRNA transcript abundances of their parental genes. qRT-PCR validated the differential expression patterns of circRNAs between leaf bud and young leaf, which also indicated the low expression abundance of circRNAs compared to the standard mRNAs from the parental genes. We predicted the circRNA-microRNA interaction networks, and 54 of the differentially expressed circRNAs were found to have potential tea plant miRNA binding sites. The gene sets encoding circRNAs were significantly enriched in chloroplasts related GO terms and photosynthesis/metabolites biosynthesis related KEGG pathways, suggesting the candidate roles of circRNAs in photosynthetic machinery and metabolites biosynthesis during leaf development.
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Affiliation(s)
- Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jie Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Qiying Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Henan Key Laboratory of Tea Plant Biology, College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
| | - Jeffrey L Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
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17
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Shivaraj SM, Jain A, Singh A. Highly preserved roles of Brassica MIR172 in polyploid Brassicas: ectopic expression of variants of Brassica MIR172 accelerates floral transition. Mol Genet Genomics 2018; 293:1121-1138. [PMID: 29752548 DOI: 10.1007/s00438-018-1444-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/03/2018] [Indexed: 12/21/2022]
Abstract
Functional characterization of regulatory genes governing flowering time is a research priority for breeding earliness in crop Brassicas. Highly polyploid genomes of Brassicas pose challenges in unraveling homeolog gene function. In Arabidopsis, five MIR172 paralogs control flowering time and floral organ identity by down-regulating AP2 and AP2-like genes. The impact of homeolog diversification on MIR172 loci, however, needs to be examined in morphologically diverse Brassicas. Herein, we analyze fractionation status and phylogeny of MIR172 and target AP2 from Brassicas and compare functionality of MIR172 variants representing distinct sub-genomes and progenitor genomes. Copy number analysis revealed higher retention of MIR172 loci relative to AP2 in diploid and amphi-diploid Brassica species. Dendrogram of 87 MIR172 sequences from Brassicaceae showed five major clusters corresponding to MIR172a-MIR172e which further separated into sub-genome and progenitor genome specific clades. Similar groupings were observed in the phylogeny of 11 Brassica AP2 and AP2-like genes. Over-expression of a pair of natural variants for each of MIR172b, MIR172d and MIR172e representing sub-genomes, progenitor genomes and species of Brassicas displayed floral acceleration in all transgenic lines indicating a strong selection pressure on MIR172. All gain-of-function lines, except 35S::MIR172e and 35S::MIR172e' displayed floral organ defects implying altered target spectrum of MIR172e relative to MIR172b and MIR172d. Expression of MIR172e caused marginal earliness in flowering time in B. juncea. In conclusion, this study demonstrates tightly preserved role of homeologs and natural variants of MIR172 family in mediating flowering in Brassicas and suggests their deployment for introgression of early flowering trait.
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Affiliation(s)
- S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India
- Département de Phytologie-Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, QC, Canada
| | - Aditi Jain
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India.
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18
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Cao D, Takeshima R, Zhao C, Liu B, Jun A, Kong F. Molecular mechanisms of flowering under long days and stem growth habit in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1873-1884. [PMID: 28338712 DOI: 10.1093/jxb/erw394] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Precise timing of flowering is critical to crop adaptation and productivity in a given environment. A number of classical E genes controlling flowering time and maturity have been identified in soybean [Glycine max (L.) Merr.]. The public availability of the soybean genome sequence has accelerated the identification of orthologues of Arabidopsis flowering genes and their functional analysis, and has allowed notable progress towards understanding the molecular mechanisms of flowering in soybean. Great progress has been made particularly in identifying genes and modules that inhibit flowering in long-day conditions, because a reduced or absent inhibition of flowering by long daylengths is an essential trait for soybean, a short-day (SD) plant, to expand its adaptability toward higher latitude environments. In contrast, the molecular mechanism of floral induction by SDs remains elusive in soybean. Here we present an update on recent work on molecular mechanisms of flowering under long days and of stem growth habit, outlining the progress in the identification of genes responsible, the interplay between photoperiod and age-dependent miRNA-mediated modules, and the conservation and divergence in photoperiodic flowering and stem growth habit in soybean relative to other legumes, Arabidopsis, and rice (Oryza sativa L.).
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Affiliation(s)
- Dong Cao
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Ryoma Takeshima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Chen Zhao
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Abe Jun
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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