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Rolletschek H, Muszynska A, Schwender J, Radchuk V, Heinemann B, Hilo A, Plutenko I, Keil P, Ortleb S, Wagner S, Kalms L, Gündel A, Shi H, Fuchs J, Szymanski JJ, Braun HP, Borisjuk L. Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo. THE NEW PHYTOLOGIST 2024. [PMID: 39044722 DOI: 10.1111/nph.19990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024]
Abstract
The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear. Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling. Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response. The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation.
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Affiliation(s)
- Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Aleksandra Muszynska
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
- Amatera Biosciences, 4 rue Pierre Fontaine, Evry, 91000, France
| | - Jörg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Volodymyr Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Björn Heinemann
- Institut für Pflanzengenetik, Universität Hannover, Herrenhäuser Strasse, Hannover, 30419, Germany
| | - Alexander Hilo
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Iaroslav Plutenko
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Peter Keil
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Stefan Ortleb
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Steffen Wagner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Laura Kalms
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - André Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
- Department of Ecology, Environment and Plant Sciences, University of Stockholm, Stockholm, 10691, Sweden
| | - Hai Shi
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jörg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Jedrzej Jakub Szymanski
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich, D-52428, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Düsseldorf, 40225, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Universität Hannover, Herrenhäuser Strasse, Hannover, 30419, Germany
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
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Gazzarrini S, Song L. LAFL Factors in Seed Development and Phase Transitions. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:459-488. [PMID: 38657282 DOI: 10.1146/annurev-arplant-070623-111458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.
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Affiliation(s)
- Sonia Gazzarrini
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada;
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada;
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Klajn N, Kapczyńska K, Pasikowski P, Glazińska P, Kugiel H, Kęsy J, Wojciechowski W. Regulatory Effects of ABA and GA on the Expression of Conglutin Genes and LAFL Network Genes in Yellow Lupine ( Lupinus luteus L.) Seeds. Int J Mol Sci 2023; 24:12380. [PMID: 37569754 PMCID: PMC10418516 DOI: 10.3390/ijms241512380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
The maturation of seeds is a process of particular importance both for the plant itself by assuring the survival of the species and for the human population for nutritional and economic reasons. Controlling this process requires a strict coordination of many factors at different levels of the functioning of genetic and hormonal changes as well as cellular organization. One of the most important examples is the transcriptional activity of the LAFL gene regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2), as well as hormonal homeostasis-of abscisic acid (ABA) and gibberellins (GA) in particular. From the nutritional point of view, the key to seed development is the ability of seeds to accumulate large amounts of proteins with different structures and properties. The world's food deficit is mainly related to shortages of protein, and taking into consideration the environmental changes occurring on Earth, it is becoming necessary to search for a way to obtain large amounts of plant-derived protein while maintaining the diversity of its origin. Yellow lupin, whose storage proteins are conglutins, is one of the plant species native to Europe that accumulates large amounts of this nutrient in its seeds. In this article we have shown the key changes occurring in the developing seeds of the yellow-lupin cultivar Taper by means of modern molecular biology techniques, including RNA-seq, chromatographic techniques and quantitative PCR analysis. We identified regulatory genes fundamental to the seed-filling process, as well as genes encoding conglutins. We also investigated how exogenous application of ABA and GA3 affects the expression of LlLEC2, LlABI3, LlFUS3, and genes encoding β- and δ-conglutins and whether it results in the amount of accumulated seed storage proteins. The research shows that for each species, even related plants, very specific changes can be identified. Thus the analysis and possibility of using such an approach to improve and stabilize yields requires even more detailed and extended research.
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Affiliation(s)
- Natalia Klajn
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Katarzyna Kapczyńska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland;
| | - Paweł Pasikowski
- Life Sciences and Biotechnology Center, Łukasiewicz Research Network–PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland;
- Captor Therapeutics S.A., Duńska 11, 54-427 Wroclaw, Poland
| | - Paulina Glazińska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Hubert Kugiel
- LABcenter Life Agro Biotechnology Ltd., Gliniana 14, 97-300 Piotrków Trybunalski, Poland; (H.K.); (W.W.)
| | - Jacek Kęsy
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Waldemar Wojciechowski
- LABcenter Life Agro Biotechnology Ltd., Gliniana 14, 97-300 Piotrków Trybunalski, Poland; (H.K.); (W.W.)
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Liu D, Tan W, Wang H, Li W, Fu J, Li J, Zhou Y, Lin M, Xing W. Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms. BMC Genomics 2023; 24:413. [PMID: 37488485 PMCID: PMC10364417 DOI: 10.1186/s12864-023-09522-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Sugar beet (Beta vulgaris L.) is an economically essential sugar crop worldwide. Its agronomic traits are highly diverse and phenotypically plastic, influencing taproot yield and quality. The National Beet Medium-term Gene Bank in China maintains more than 1700 beet germplasms with diverse countries of origin. However, it lacks detailed genetic background associated with morphological variability and diversity. RESULTS Here, a comprehensive genome-wide association study (GWAS) of 13 agronomic traits was conducted in a panel of 977 sugar beet accessions. Almost all phenotypic traits exhibited wide genetic diversity and high coefficient of variation (CV). A total of 170,750 high-quality single-nucleotide polymorphisms (SNPs) were obtained using the genotyping-by-sequencing (GBS). Neighbour-joining phylogenetic analysis, principal component analysis, population structure and kinship showed no obvious relationships among these genotypes based on subgroups or regional sources. GWAS was carried out using a mixed linear model, and 159 significant associations were detected for these traits. Within the 25 kb linkage disequilibrium decay of the associated markers, NRT1/PTR FAMILY 6.3 (BVRB_5g097760); nudix hydrolase 15 (BVRB_8g182070) and TRANSPORT INHIBITOR RESPONSE 1 (BVRB_8g181550); transcription factor MYB77 (BVRB_2g023500); and ethylene-responsive transcription factor ERF014 (BVRB_1g000090) were predicted to be strongly associated with the taproot traits of root groove depth (RGD); root shape (RS); crown size (CS); and flesh colour (FC), respectively. For the aboveground traits, UDP-glycosyltransferase 79B6 (BVRB_9g223780) and NAC domain-containing protein 7 (BVRB_5g097990); F-box protein At1g10780 (BVRB_6g140760); phosphate transporter PHO1 (BVRB_3g048660); F-box protein CPR1 (BVRB_8g181140); and transcription factor MYB77 (BVRB_2g023500) and alcohol acyltransferase 9 (BVRB_2g023460) might be associated with the hypocotyl colour (HC); plant type (PT); petiole length (PL); cotyledon size (C); and fascicled leaf type (FLT) of sugar beet, respectively. AP-2 complex subunit mu (BVRB_5g106130), trihelix transcription factor ASIL2 (BVRB_2g041790) and late embryogenesis abundant protein 18 (BVRB_5g106150) might be involved in pollen quantity (PQ) variation. The candidate genes extensively participated in hormone response, nitrogen and phosphorus transportation, secondary metabolism, fertilization and embryo maturation. CONCLUSIONS The genetic basis of agronomical traits is complicated in heterozygous diploid sugar beet. The putative valuable genes found in this study will help further elucidate the molecular mechanism of each phenotypic trait for beet breeding.
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Affiliation(s)
- Dali Liu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wenbo Tan
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Hao Wang
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wangsheng Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jingjing Fu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jiajia Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Yuanhang Zhou
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Ming Lin
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Wang Xing
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China.
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China.
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Mao H, Zhang W, Lv J, Yang J, Yang S, Jia B, Song J, Wu M, Pei W, Ma J, Zhang B, Zhang J, Wang L, Yu J. Overexpression of cotton Trihelix transcription factor GhGT-3b_A04 enhances resistance to Verticillium dahliae and affects plant growth in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2023; 283:153947. [PMID: 36898190 DOI: 10.1016/j.jplph.2023.153947] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/28/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Verticillium wilt is a soil-borne fungal disease that severely affects cotton fiber yield and quality. Herein, a cotton Trihelix family gene, GhGT-3b_A04, was strongly induced by the fungal pathogen Verticillium dahliae. Overexpression of the gene in Arabidopsis thaliana enhanced the plant's resistance to Verticillium wilt but inhibited the growth of rosette leaves. In addition, the primary root length, root hair number, and root hair length increased in GhGT-3b_A04-overexpressing plants. The density and length of trichomes on the rosette leaves also increased. GhGT-3b_A04 localized to the nucleus, and transcriptome analysis revealed that it induced gene expression for salicylic acid synthesis and signal transduction and activated gene expression for disease resistance. The gene expression for auxin signal transduction and trichome development was reduced in GhGT-3b_A04-overexpressing plants. Our results highlight important regulatory genes for Verticillium wilt resistance and cotton fiber quality improvement. The identification of GhGT-3b_A04 and other important regulatory genes can provide crucial reference information for future research on transgenic cotton breeding.
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Affiliation(s)
- Haoming Mao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Wenqing Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Junyuan Lv
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Jiaxiang Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Shuxian Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Bing Jia
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Jikun Song
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Man Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Wenfeng Pei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Jianjiang Ma
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Bingbing Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA.
| | - Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Jiwen Yu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Yang J, Tang Z, Yang W, Huang Q, Wang Y, Huang M, Wei H, Liu G, Lian B, Chen Y, Zhang J. Genome-wide characterization and identification of Trihelix transcription factors and expression profiling in response to abiotic stresses in Chinese Willow ( Salix matsudana Koidz). FRONTIERS IN PLANT SCIENCE 2023; 14:1125519. [PMID: 36938039 PMCID: PMC10020544 DOI: 10.3389/fpls.2023.1125519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Trihelix transcription factors (TTF) are a class of light-responsive proteins with a typical triple-helix structure (helix-loop-helix-loop-helix). Members of this gene family play an important role in plant growth and development, especially in various abiotic stress responses. Salix matsudana Koidz is an allotetraploid ornamental forest tree that is widely planted for its excellent resistance to stress, but no studies on its Trihelix gene family have been reported. In this study, the Trihelix gene family was analyzed at the genome-wide level in S. matsudana. A total of 78 S. matsudana Trihelix transcription factors (SmTTFs) were identified, distributed on 29 chromosomes, and classified into four subfamilies (GT-1, GT-2, SH4, SIP1) based on their structural features. The gene structures and conserved functional domains of these Trihelix genes are similar in the same subfamily and differ between subfamilies. The presence of multiple stress-responsive cis-elements on the promoter of the S. matsudana Trihelix gene suggests that the S. matsudana Trihelix gene may respond to abiotic stresses. Expression pattern analysis revealed that Trihelix genes have different functions during flooding stress, salt stress, drought stress and low temperature stress in S. matsudana. Given that SmTTF30, as a differentially expressed gene, has a faster response to flooding stress, we selected SmTTF30 for functional studies. Overexpression of SmTTF30 in Arabidopsis thaliana (Arabidopsis) enhances its tolerance to flooding stress. Under flooding stress, the leaf cell activity and peroxidase activity (POD) of the overexpression strain were significantly higher than the leaf cell activity and POD of the wild type, and the malondialdehyde (MDA) content was significantly lower than the MDA content of the wild type. Thus, these results suggest that SmTTF30 enhances plant flooding tolerance and plays a positive regulatory role in plant flooding tolerance.
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Affiliation(s)
- Jie Yang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
| | - Zhixuan Tang
- School of Life Sciences, Nantong University, Nantong, China
| | - Wuyue Yang
- School of Life Sciences, Nantong University, Nantong, China
| | - Qianhui Huang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yuqing Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Mengfan Huang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
| | - Hui Wei
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
| | - Guoyuan Liu
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
| | - Bolin Lian
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
| | - Yanhong Chen
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
| | - Jian Zhang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China
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Li Y, Hu Z, Dong Y, Xie Z. Overexpression of the cotton trihelix transcription factor GhGT23 in Arabidopsis mediates salt and drought stress tolerance by binding to GT and MYB promoter elements in stress-related genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1144650. [PMID: 36938019 PMCID: PMC10017854 DOI: 10.3389/fpls.2023.1144650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Cotton (Gossypium hirsutum L.) is the world's most economically valuable textile crop. However, cotton plants are often subjected to numerous abiotic stresses that can dramatically limit yield. Trihelix transcription factors (TTFs) play important roles in abiotic stress responses in many plant species, and efforts to better understand their roles in cotton abiotic stress responses are ongoing. In this study, a member of the cotton TTF family (GhGT23) was functionally characterized. This protein contains a SANT domain and is a member of the SIP subfamily of TTF proteins. GhGT23 was significantly (p < 0.05) and highly expressed in cotton fiber compared to relatively low expression in other tissues. A significant (p < 0.05) increase in GhGT23 expression occurred in cotton seedlings within 12 hours of drought, salt, and ABA exposure. The GhGT23 protein localized in the nucleus but exhibited no signs of transactivation activity. GhGT23 overexpression in Arabidopsis conferred enhanced drought and salt stress tolerance. The expression of stress-related genes was higher in transgenic Arabidopsis expressing GhGT23 than in wild-type plants subjected to salt stress. The results of electrophoretic mobility shift assay revealed that GhGT23 could bind to the GT cis-elements GT-1Box (Box II), GT2-Box, GT3-Box, GT-3a (Site1-type), GT-3b, and Box as well as the MYB cis-elements MBS1 and MRE4. Our results demonstrate that GhGT23 positively regulates salt and drought stress responses, possibly by enhancing the expression of stress-related genes.
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Affiliation(s)
- Yue Li
- College of Life Science, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Ziyao Hu
- College of Life Science, Xinjiang Agricultural University, Urumqi, China
| | - Yongmei Dong
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Zongming Xie
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
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Chen Y, Guo Y, Guan P, Wang Y, Wang X, Wang Z, Qin Z, Ma S, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Guo W, Peng H. A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. MOLECULAR PLANT 2023; 16:393-414. [PMID: 36575796 DOI: 10.1016/j.molp.2022.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/28/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Gene regulation is central to all aspects of organism growth, and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Panfeng Guan
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaobo Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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9
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Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing. Int J Mol Sci 2022; 23:ijms232012339. [PMID: 36293196 PMCID: PMC9604548 DOI: 10.3390/ijms232012339] [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: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of sequence complementarity and have recently emerged as critical regulators of seed germination. Here, we used the germinating embryos of two maize inbred lines with significant differences in seed storability to identify the miRNAs and target genes involved. We identified a total of 218 previously known and 448 novel miRNAs by miRNA sequencing and degradome analysis, of which 27 known and 11 newly predicted miRNAs are differentially expressed in two maize inbred lines, as measured by Gene Ontology (GO) enrichment analysis. We then combined transcriptome sequencing and real-time quantitative polymerase chain reaction (RT-PCR) to screen and confirm six pairs of differentially expressed miRNAs associated with seed storability, along with their negative regulatory target genes. The enrichment analysis suggested that the miRNAs/target gene mediation of seed storability occurs via the ethylene activation signaling pathway, hormone synthesis and signal transduction, as well as plant organ morphogenesis. Our results should help elucidate the mechanisms through which miRNAs are involved in seed storability in maize.
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10
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Huang Y, Zhou L, Hou C, Guo D. The dynamic proteome in Arabidopsis thaliana early embryogenesis. Development 2022; 149:276287. [DOI: 10.1242/dev.200715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The morphology of the flowering plant is established during early embryogenesis. In recent years, many studies have focused on transcriptional profiling in plant embryogenesis, but the dynamic landscape of the Arabidopsis thaliana proteome remains elusive. In this study, Arabidopsis embryos at 2/4-cell, 8-cell, 16-cell, 32-cell, globular and heart stages were collected for nanoproteomic analysis. In total, 5386 proteins were identified. Of these, 1051 proteins were universally identified in all developmental stages and a range of 27 to 2154 proteins was found to be stage specific. These proteins could be grouped into eight clusters according to their expression levels. Gene Ontology enrichment analysis showed that genes involved in ribosome biogenesis and auxin-activated signalling were enriched during early embryogenesis, indicating that active translation and auxin signalling are important events in Arabidopsis embryo development. Combining RNA-sequencing data with the proteomics analysis, the correlation between mRNA and protein was evaluated. An overall positive correlation was found between mRNA and protein. This work provides a comprehensive landscape of the Arabidopsis proteome in early embryogenesis. Some important proteins/transcription factors identified through network analysis may serve as potential targets for future investigation.
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Affiliation(s)
- Yingzhang Huang
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
| | - Limeng Zhou
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
| | - Chunhui Hou
- Southern University of Science and Technology 2 Department of Biology , , Shenzhen 518055 , China
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
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11
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Chen C, Du X. LEAFY COTYLEDONs: Connecting different stages of plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:916831. [PMID: 36119568 PMCID: PMC9470955 DOI: 10.3389/fpls.2022.916831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The life of higher plants progresses successively through embryonic, juvenile, adult, and reproductive stages. LEAFY COTYLEDON (LEC) transcription factors, first discovered in Arabidopsis thaliana several decades ago, play a key role in regulating plant embryonic development, seed maturation, and subsequent growth. Existing studies have demonstrated that LECs together with other transcription factors form a huge and complex regulatory network to regulate many aspects of plant growth and development and respond to environmental stresses. Here, we focus on the role that has received little attention about the LECs linking different developmental stages and generational cycles in plants. We summarize the current fragmented research progress on the LECs role and molecular mechanism in connecting embryonic and vegetative growth periods and the reproductive stage. Furthermore, the possibility of LECs controlling the maintenance and transition of plant growth stages through epigenetic modifications is discussed.
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12
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Joshi S, Paul P, Hartman JM, Perry SE. AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:861556. [PMID: 35419012 PMCID: PMC8996056 DOI: 10.3389/fpls.2022.861556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Plants have amazing regenerative properties with single somatic cells, or groups of cells able to give rise to fully formed plants. One means of regeneration is somatic embryogenesis, by which an embryonic structure is formed that "converts" into a plantlet. Somatic embryogenesis has been used as a model for zygotic processes that are buried within layers of maternal tissues. Understanding mechanisms of somatic embryo induction and development are important as a more accessible model for seed development. We rely on seed development not only for most of our caloric intake, but also as a delivery system for engineered crops to meet agricultural challenges. Regeneration of transformed cells is needed for this applied work as well as basic research to understand gene function. Here we focus on a MADS-domain transcription factor, AGAMOUS-Like15 (AGL15) that shows a positive correlation between accumulation levels and capacity for somatic embryogenesis. We relate AGL15 function to other transcription factors, hormones, and epigenetic modifiers involved in somatic embryo development.
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Affiliation(s)
- Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Priyanka Paul
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United States
| | - Jeanne M. Hartman
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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13
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Alves A, Confraria A, Lopes S, Costa B, Perdiguero P, Milhinhos A, Baena-González E, Correia S, Miguel CM. miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development. FRONTIERS IN PLANT SCIENCE 2022; 13:857611. [PMID: 35371172 PMCID: PMC8965291 DOI: 10.3389/fpls.2022.857611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of several plant developmental processes including embryogenesis. Most miRNA families are conserved across major groups of plant species, but their regulatory roles have been studied mainly in model species like Arabidopsis and other angiosperms. In gymnosperms, miRNA-dependent regulation has been less studied since functional approaches in these species are often difficult to establish. Given the fundamental roles of auxin signaling in somatic embryogenesis (SE) induction and embryo development, we investigated a previously predicted interaction between miR160 and a putative target encoding AUXIN RESPONSE FACTOR 18 in Pinus pinaster (PpARF18) embryonic tissues. Phylogenetic analysis of AUXIN RESPONSE FACTOR 18 (ARF18) from Pinus pinaster and Picea abies, used here as a model system of conifer embryogenesis, showed their close relatedness to AUXIN RESPONSE FACTOR (ARF) genes known to be targeted by miR160 in other species, including Arabidopsis ARF10 and ARF16. By using a luciferase (LUC) reporter system for miRNA activity in Arabidopsis protoplasts, we have confirmed that P. pinaster miR160 (ppi-miR160) interacts in vivo with PpARF18 target site. When the primary miR160 from P. pinaster was overexpressed in protoplasts under non-limiting levels of ARGONAUTE1, a significant increase of miR160 target cleavage activity was observed. In contrast, co-expression of the primary miRNA and the target mimic MIM160 led to a decrease of miR160 activity. Our results further support that this interaction is functional during consecutive stages of SE in the conifer model P. abies. Expression analyses conducted in five stages of development, from proembryogenic masses (PEMs) to the mature embryo, show that conifer ARF18 is negatively regulated by miR160 toward the fully developed mature embryo when miR160 reached its highest expression level. This study reports the first in vivo validation of a predicted target site of a conifer miRNA supporting the conservation of miR160 interaction with ARF targets in gymnosperms. The approach used here should be useful for future characterization of miRNA functions in conifer embryogenesis.
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Affiliation(s)
- Ana Alves
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Susana Lopes
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Bruno Costa
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Perdiguero
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), Madrid, Spain
| | - Ana Milhinhos
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Sandra Correia
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Célia M. Miguel
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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14
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Jin L, Chen M, Xiang M, Guo Z. RNAi-Based Antiviral Innate Immunity in Plants. Viruses 2022; 14:v14020432. [PMID: 35216025 PMCID: PMC8875485 DOI: 10.3390/v14020432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/13/2022] Open
Abstract
Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future.
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15
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A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population. PLoS Genet 2022; 18:e1010017. [PMID: 35108269 PMCID: PMC8843129 DOI: 10.1371/journal.pgen.1010017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/14/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program. Slash pine is an important source of original timber and resin production on commercial forest plantations. It is necessary to implement precise breeding strategies to improve timber quality and resin yield. However, little is known about the species’ molecular genetic basis. Using a transcriptome dataset with sequencing from 240 individuals in the slash pine population, we combined multiple approaches (based on gene variation, expression variation and co-expression network) to dissect the genetic structure for slash pine major breeding traits. We found that the research population could be divided into three genetic groups with a mean heterozygosity of 0.2246. We also found that six genes with important functions in slash pine resin synthesis and timber formation through association studies. Four new SNPs associatation with the average ring width were also discovered. Our results provide new insights into the molecular genetic basis of important traits in slash pine and provide a comprehensive method for association analyses of conifer tree species with large genome.
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16
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Yang W, Hu J, Behera JR, Kilaru A, Yuan Y, Zhai Y, Xu Y, Xie L, Zhang Y, Zhang Q, Niu L. A Tree Peony Trihelix Transcription Factor PrASIL1 Represses Seed Oil Accumulation. FRONTIERS IN PLANT SCIENCE 2021; 12:796181. [PMID: 34956296 PMCID: PMC8702530 DOI: 10.3389/fpls.2021.796181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 05/31/2023]
Abstract
In many higher plants, seed oil accumulation is governed by complex multilevel regulatory networks including transcriptional regulation, which primarily affects fatty acid biosynthesis. Tree peony (Paeonia rockii), a perennial deciduous shrub endemic to China is notable for its seed oil that is abundant in unsaturated fatty acids. We discovered that a tree peony trihelix transcription factor, PrASIL1, localized in the nucleus, is expressed predominantly in developing seeds during maturation. Ectopic overexpression of PrASIL1 in Nicotiana benthamiana leaf tissue and Arabidopsis thaliana seeds significantly reduced total fatty acids and altered the fatty acid composition. These changes were in turn associated with the decreased expression of multitudinous genes involved in plastidial fatty acid synthesis and oil accumulation. Thus, we inferred that PrASIL1 is a critical transcription factor that represses oil accumulation by down-regulating numerous key genes during seed oil biosynthesis. In contrary, up-regulation of oil biosynthesis genes and a significant increase in total lipids and several major fatty acids were observed in PrASIL1-silenced tree peony leaves. Together, these results provide insights into the role of trihelix transcription factor PrASIL1 in controlling seed oil accumulation. PrASIL1 can be targeted potentially for oil enhancement in tree peony and other crops through gene manipulation.
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Affiliation(s)
- Weizong Yang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Jiayuan Hu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Jyoti R. Behera
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Yanping Yuan
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Yuhui Zhai
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Yanfeng Xu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Lihang Xie
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Qingyu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
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17
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Zhang L, Wu P, Li W, Feng T, Shockey J, Chen L, Zhang L, Lü S. Triacylglycerol biosynthesis in shaded seeds of tung tree (Vernicia fordii) is regulated in part by Homeodomain Leucine Zipper 21. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1735-1753. [PMID: 34643970 DOI: 10.1111/tpj.15540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Light quantity and quality affect many aspects of plant growth and development. However, few reports have addressed the molecular connections between seed oil accumulation and light conditions, especially dense shade. Shade-avoiding plants can redirect plant resources into extension growth at the expense of leaf and root expansion in an attempt to reach areas containing richer light. Here, we report that tung tree seed oil accumulation is suppressed by dense shade during the rapid oil accumulation phase. Transcriptome analysis confirmed that oil accumulation suppression due to dense shade was attributed to reduced expression of fatty acid and triacylglycerol biosynthesis-related genes. Through weighted gene co-expression network analysis, we identified 32 core transcription factors (TFs) specifically upregulated in densely shaded seeds during the rapid oil accumulation period. Among these, VfHB21, a class I homeodomain leucine zipper TF, was shown to suppress expression of FAD2 and FADX, two key genes related to α-eleostearic acid, by directly binding to HD-ZIP I/II motifs in their respective promoter regions. VfHB21 also binds to similar motifs in the promoters of VfWRI1 and VfDGAT2, two additional key seed lipid regulatory/biosynthetic genes. Functional conservation of HB21 during plant evolution was demonstrated by the fact that AtWRI1, AtSAD1, and AtFAD2 were downregulated in VfHB21-overexpressor lines of transgenic Arabidopsis, with concomitant seed oil reduction, and the fact that AtHB21 expression also was induced by shade. This study reveals some of the regulatory mechanisms that specifically control tung tree seed oil biosynthesis and more broadly regulate plant storage carbon partitioning in response to dense shade conditions.
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Affiliation(s)
- Lingling Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Pan Wu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Tao Feng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jay Shockey
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, USA
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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18
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Liu B, Sun G, Liu C, Liu S. LEAFY COTYLEDON 2: A Regulatory Factor of Plant Growth and Seed Development. Genes (Basel) 2021; 12:genes12121896. [PMID: 34946844 PMCID: PMC8701892 DOI: 10.3390/genes12121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors are key molecules in the regulation of gene expression in all organisms. The transcription factor LEAFY COTYLEDON 2 (LEC2), which belongs to the DNA-binding protein family, contains a B3 domain. The transcription factor is involved in the regulation of important plant biological processes such as embryogenesis, somatic embryo formation, seed storage protein synthesis, fatty acid metabolism, and other important biological processes. Recent studies have shown that LEC2 regulates the formation of lateral roots and influences the embryonic resetting of the parental vernalization state. The orthologs of LEC2 and their regulatory effects have also been identified in some crops; however, their regulatory mechanism requires further investigation. Here, we summarize the most recent findings concerning the effects of LEC2 on plant growth and seed development. In addition, we discuss the potential molecular mechanisms of the action of the LEC2 gene during plant development.
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19
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Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y. Structural basis of microRNA processing by Dicer-like 1. NATURE PLANTS 2021; 7:1389-1396. [PMID: 34593993 DOI: 10.1038/s41477-021-01000-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. In animals, pri-miRNAs are cleaved by Drosha to generate pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1). With a similar domain architecture as human Dicer, it is mysterious how DCL1 recognizes pri-miRNAs and performs two cleavages sequentially. Here, we report the single-particle cryo-electron microscopy structures of Arabidopsis DCL1 complexed with a pri-miRNA and a pre-miRNA, respectively, in cleavage-competent states. These structures uncover the plasticity of the PAZ domain, which is critical for the recognition of both pri-miRNA and pre-miRNA. These structures suggest that the helicase module serves as an engine that transfers the substrate between two sequential cleavage events. This study lays a foundation for dissecting the regulation mechanism of miRNA biogenesis in plants and provides insights into the dicing state of human Dicer.
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Affiliation(s)
- Xiaobin Wei
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Ke
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Aijia Wen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Gao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Feng
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases, Hangzhou, China.
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20
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Ruiz KA, Pelletier JM, Wang Y, Feng MJ, Behr JS, Ðào TQ, Li B, Kliebenstein D, Harada JJ, Jenik PD. A reevaluation of the role of the ASIL trihelix transcription factors as repressors of the seed maturation program. PLANT DIRECT 2021; 5:e345. [PMID: 34622120 PMCID: PMC8483069 DOI: 10.1002/pld3.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Developmental transitions are typically tightly controlled at the transcriptional level. Two of these transitions involve the induction of the embryo maturation program midway through seed development and its repression during the vegetative phase of plant growth. Very little is known about the factors responsible for this regulation during early embryogenesis, and only a couple of transcription factors have been characterized as repressors during the postgerminative phase. Arabidopsis 6b-INTERACTING PROTEIN-LIKE1 (ASIL1), a trihelix transcription factor, has been proposed to repress maturation both embryonically and postembryonically. Preliminary data also suggested that its closest paralog, ASIL2, might play a role as well. We used a transcriptomic approach, coupled with phenotypical observations, to test the hypothesis that ASIL1 and ASIL2 redundantly turn off maturation during both phases of growth. Our results indicate that, contrary to what was previously published, neither of the ASIL genes plays a role in the regulation of maturation, at any point during plant development. Analyses of gene ontology (GO)-enriched terms and published transcriptomic datasets suggest that these genes might be involved in responses during the vegetative phase to certain biotic and abiotic stresses.
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Affiliation(s)
- Kevin A. Ruiz
- Department of BiologyFranklin & Marshall CollegeLancasterPAUSA
| | - Julie M. Pelletier
- Department of Plant Biology, College of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Yuchi Wang
- Department of BiologyFranklin & Marshall CollegeLancasterPAUSA
- Present address:
Chimera (Shanghai) Biotec Ltd.Shanghai CityChina
| | - Min Jun Feng
- Department of BiologyFranklin & Marshall CollegeLancasterPAUSA
- Present address:
Medical University of South CarolinaCharlestonSCUSA
| | - Jacqueline S. Behr
- Department of BiologyFranklin & Marshall CollegeLancasterPAUSA
- Present address:
Hoboken University Medical CenterHobokenNJUSA
| | - Thái Q. Ðào
- Department of BiologyFranklin & Marshall CollegeLancasterPAUSA
- Present address:
Department of Botany and Plant Biology, College of Agricultural SciencesOregon State UniversityCorvallisORUSA
| | - Baohua Li
- Department of Plant Sciences, College of Agricultural and Environmental SciencesUniversity of CaliforniaDavisCAUSA
- Present address:
College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Daniel Kliebenstein
- Department of Plant Sciences, College of Agricultural and Environmental SciencesUniversity of CaliforniaDavisCAUSA
| | - John J. Harada
- Department of Plant Biology, College of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Pablo D. Jenik
- Department of BiologyFranklin & Marshall CollegeLancasterPAUSA
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21
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Malovichko YV, Shikov AE, Nizhnikov AA, Antonets KS. Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications. Int J Mol Sci 2021; 22:ijms22179252. [PMID: 34502157 PMCID: PMC8430901 DOI: 10.3390/ijms22179252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
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22
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Tognacca RS, Botto JF. Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. PLANT COMMUNICATIONS 2021; 2:100169. [PMID: 34327318 PMCID: PMC8299061 DOI: 10.1016/j.xplc.2021.100169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.
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Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CP1428 Buenos Aires, Argentina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| | - Javier Francisco Botto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
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23
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Huang R, Liu M, Gong G, Wu P, Patra B, Yuan L, Qin H, Wang X, Wang G, Liao H, Gao L, Yang C, Li H, Zhang S. The Pumilio RNA-binding protein APUM24 regulates seed maturation by fine-tuning the BPM-WRI1 module in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1240-1259. [PMID: 33729679 DOI: 10.1111/jipb.13092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/15/2021] [Indexed: 05/25/2023]
Abstract
Pumilio RNA-binding proteins participate in messenger RNA (mRNA) degradation and translational repression, but their roles in plant development are largely unclear. Here, we show that Arabidopsis PUMILIO PROTEIN24 (APUM24), an atypical Pumilio-homology domain-containing protein, plays an important part in regulating seed maturation, a major stage of plant development. APUM24 is strongly expressed in maturing seeds. Reducing APUM24 expression resulted in abnormal seed maturation, wrinkled seeds, and lower seed oil contents, and APUM24 knockdown resulted in lower levels of WRINKLED 1 (WRI1), a key transcription factor controlling seed oil accumulation, and lower expression of WRI1 target genes. APUM24 reduces the mRNA stability of BTB/POZMATH (BPM) family genes, thus decreasing BPM protein levels. BPM is responsible for the 26S proteasome-mediated degradation of WRI1 and has important functions in plant growth and development. The 3' untranslated regions of BPM family genes contain putative Pumilio response elements (PREs), which are bound by APUM24. Reduced BPM or increased WRI1 expression rescued the deficient seed maturation of apum24-2 knockdown mutants, and APUM24 overexpression resulted in increased seed size and weight. Therefore, APUM24 is crucial to seed maturation through its action as a positive regulator fine-tuning the BPM-WRI1 module, making APUM24 a promising target for breeding strategies to increase crop yields.
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Affiliation(s)
- Ruihua Huang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Mengling Liu
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guanping Gong
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, 40546, USA
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, 40546, USA
| | - Hongting Qin
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiaoxu Wang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guohe Wang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimei Liao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lu Gao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hongqing Li
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shengchun Zhang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
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24
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Wu Y, Zheng L, Bing J, Liu H, Zhang G. Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination. Int J Mol Sci 2021; 22:ijms22105088. [PMID: 34065034 PMCID: PMC8151434 DOI: 10.3390/ijms22105088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/29/2022] Open
Abstract
Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in plant growth and abiotic stress responses. In our study, we found that the time of seed germination in AtENO2 mutation (eno2-) was earlier than that of wild type (WT) in Arabidopsis thaliana. Previous studies have shown that microRNAs (miRNAs) were vital in seed germination. After deep sequencing of small RNA, we found 590 differentially expressed miRNAs in total, of which 87 were significantly differentially expressed miRNAs. By predicting the target genes of miRNAs and analyzing the GO annotation, we have counted 18 genes related to seed germination, including ARF family, TIR1, INVC, RR19, TUDOR2, GA3OX2, PXMT1, and TGA1. MiR9736-z, miR5059-z, ath-miR167a-5p, ath-miR167b, ath-miR5665, ath-miR866-3p, miR10186-z, miR8165-z, ath-miR857, ath-miR399b, ath-miR399c-3p, miR399-y, miR163-z, ath-miR393a-5p, and ath-miR393b-5p are the key miRNAs regulating seed germination-related genes. Through KEGG enrichment analysis, we found that phytohormone signal transduction pathways were significantly enriched, and these miRNAs mentioned above also participate in the regulation of the genes in plant hormone signal transduction pathways, thus affecting the synthesis of plant hormones and further affecting the process of seed germination. This study laid the foundation for further exploration of the AtENO2 regulation for seed germination.
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25
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26
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Alves A, Cordeiro D, Correia S, Miguel C. Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:504. [PMID: 33803088 PMCID: PMC8001652 DOI: 10.3390/plants10030504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/25/2022]
Abstract
Small non-coding RNAs (sncRNAs) are molecules with important regulatory functions during development and environmental responses across all groups of terrestrial plants. In seed plants, the development of a mature embryo from the zygote follows a synchronized cell division sequence, and growth and differentiation events regulated by highly regulated gene expression. However, given the distinct features of the initial stages of embryogenesis in gymnosperms and angiosperms, it is relevant to investigate to what extent such differences emerge from differential regulation mediated by sncRNAs. Within these, the microRNAs (miRNAs) are the best characterized class, and while many miRNAs are conserved and significantly represented across angiosperms and other seed plants during embryogenesis, some miRNA families are specific to some plant lineages. Being a model to study zygotic embryogenesis and a relevant biotechnological tool, we systematized the current knowledge on the presence and characterization of miRNAs in somatic embryogenesis (SE) of seed plants, pinpointing the miRNAs that have been reported to be associated with SE in angiosperm and gymnosperm species. We start by conducting an overview of sncRNA expression profiles in the embryonic tissues of seed plants. We then highlight the miRNAs described as being involved in the different stages of the SE process, from its induction to the full maturation of the somatic embryos, adding references to zygotic embryogenesis when relevant, as a contribution towards a better understanding of miRNA-mediated regulation of SE.
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Affiliation(s)
- Ana Alves
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal;
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Daniela Cordeiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.C.); (S.C.)
| | - Sandra Correia
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.C.); (S.C.)
| | - Célia Miguel
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal;
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
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27
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Liu X, Zhang D, Zhang J, Chen Y, Liu X, Fan C, Wang RRC, Hou Y, Hu Z. Overexpression of the Transcription Factor AtLEC1 Significantly Improved the Lipid Content of Chlorella ellipsoidea. Front Bioeng Biotechnol 2021; 9:626162. [PMID: 33681161 PMCID: PMC7925920 DOI: 10.3389/fbioe.2021.626162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
Microalgae are considered to be a highly promising source for the production of biodiesel. However, the regulatory mechanism governing lipid biosynthesis has not been fully elucidated to date, and the improvement of lipid accumulation in microalgae is essential for the effective production of biodiesel. In this study, LEAFY COTYLEDON1 (LEC1) from Arabidopsis thaliana, a transcription factor (TF) that affects lipid content, was transferred into Chlorella ellipsoidea. Compared with wild-type (WT) strains, the total fatty acid content and total lipid content of AtLEC1 transgenic strains were significantly increased by 24.20–32.65 and 22.14–29.91%, respectively, under mixotrophic culture conditions and increased by 24.4–28.87 and 21.69–30.45%, respectively, under autotrophic conditions, while the protein content of the transgenic strains was significantly decreased by 18.23–21.44 and 12.28–18.66%, respectively, under mixotrophic and autotrophic conditions. Fortunately, the lipid and protein content variation did not affect the growth rate and biomass of transgenic strains under the two culture conditions. According to the transcriptomic data, the expression of 924 genes was significantly changed in the transgenic strain (LEC1-1). Of the 924 genes, 360 were upregulated, and 564 were downregulated. Based on qRT-PCR results, the expression profiles of key genes in the lipid synthesis pathway, such as ACCase, GPDH, PDAT1, and DGAT1, were significantly changed. By comparing the differentially expressed genes (DEGs) regulated by AtLEC1 in C. ellipsoidea and Arabidopsis, we observed that approximately 59% (95/160) of the genes related to lipid metabolism were upregulated in AtLEC1 transgenic Chlorella. Our research provides a means of increasing lipid content by introducing exogenous TF and presents a possible mechanism of AtLEC1 regulation of lipid accumulation in C. ellipsoidea.
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Affiliation(s)
- Xiao Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,Analysis and Test Center, Guangzhou Higher Education Mega Center, Guangdong University of Technology, Guangzhou, China
| | - Jianhui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiuli Liu
- Inner Mongolia Academy of Agriculture and Animal Husbandry, Huhhot, China
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Richard R-C Wang
- United States Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT, United States
| | - Yongyue Hou
- Inner Mongolia Academy of Agriculture and Animal Husbandry, Huhhot, China
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
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28
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Dhaka N, Sharma R. MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey! Crit Rev Biotechnol 2021; 41:594-608. [PMID: 33682533 DOI: 10.1080/07388551.2021.1873238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.
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Affiliation(s)
- Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Haryana, India.,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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29
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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30
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Armenta-Medina A, Gillmor CS, Gao P, Mora-Macias J, Kochian LV, Xiang D, Datla R. Developmental and genomic architecture of plant embryogenesis: from model plant to crops. PLANT COMMUNICATIONS 2021; 2:100136. [PMID: 33511346 PMCID: PMC7816075 DOI: 10.1016/j.xplc.2020.100136] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 05/08/2023]
Abstract
Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that, through cell division and cell identity specification in early embryogenesis, establishes the major cell lineages and tissues of the adult plant. The subsequent morphogenesis phase produces the full-sized embryo, while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination, ensuring continuation of the plant life cycle. In this review on embryogenesis, we compare the model eudicot Arabidopsis thaliana with monocot crops, focusing on genome activation, paternal and maternal regulation of early zygote development, and key organizers of patterning, such as auxin and WOX transcription factors. While the early stages of embryo development are apparently conserved among plant species, embryo maturation programs have diversified between eudicots and monocots. This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation, and also assures seed germination in different environmental conditions. This review describes the most important features of embryonic development in plants, and the scope and applications of genomics in plant embryo studies.
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Affiliation(s)
- Alma Armenta-Medina
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Javier Mora-Macias
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Daoquan Xiang
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
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31
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Rolletschek H, Muszynska A, Borisjuk L. The process of seed maturation is influenced by mechanical constraints. THE NEW PHYTOLOGIST 2021; 229:19-23. [PMID: 32735708 DOI: 10.1111/nph.16815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland-Gatersleben, 06466, Germany
| | - Aleksandra Muszynska
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland-Gatersleben, 06466, Germany
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland-Gatersleben, 06466, Germany
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32
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Liu X, Zhang H, Ma L, Wang Z, Wang K. Genome-Wide Identification and Expression Profiling Analysis of the Trihelix Gene Family Under Abiotic Stresses in Medicago truncatula. Genes (Basel) 2020; 11:genes11111389. [PMID: 33238556 PMCID: PMC7709032 DOI: 10.3390/genes11111389] [Citation(s) in RCA: 4] [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: 10/23/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
The trihelix transcription factor (GT) family is widely involved in regulating plant growth and development, and most importantly, responding to various abiotic stresses. Our study first reported the genome-wide identification and analysis of GT family genes in Medicago truncatula. Overall, 38 trihelix genes were identified in the M. truncatula genome and were classified into five subfamilies (GT-1, GT-2, SH4, GTγ and SIP1). We systematically analyzed the phylogenetic relationship, chromosomal distribution, tandem and segmental duplication events, gene structures and conserved motifs of MtGTs. Syntenic analysis revealed that trihelix family genes in M. truncatula had the most collinearity relationship with those in soybean followed by alfalfa, but very little collinearity with those in the maize and rice. Additionally, tissue-specific expression analysis of trihelix family genes suggested that they played various roles in the growth and development of specific tissues in M. truncatula. Moreover, the expression of some MtGT genes, such as MtGT19, MtGT20, MtGT22, and MtGT33, was dramatically induced by drought, salt, and ABA treatments, illustrating their vital roles in response to abiotic stresses. These findings are helpful for improving the comprehensive understanding of trihelix family; additionally, the study provides candidate genes for achieving the genetic improvement of stress resistance in legumes.
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Affiliation(s)
- Xiqiang Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (H.Z.); (Z.W.)
| | - Han Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (H.Z.); (Z.W.)
| | - Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Zan Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (H.Z.); (Z.W.)
| | - Kun Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (H.Z.); (Z.W.)
- Correspondence: ; Tel.: +86-010-6273-3338
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33
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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34
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Almeida FA, Passamani LZ, Santa-Catarina C, Mooney BP, Thelen JJ, Silveira V. Label-Free Quantitative Phosphoproteomics Reveals Signaling Dynamics Involved in Embryogenic Competence Acquisition in Sugarcane. J Proteome Res 2020; 19:4145-4157. [PMID: 32964716 DOI: 10.1021/acs.jproteome.0c00652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, a label-free quantitative phosphoproteomic analysis was performed to identify and quantify signaling events related to the acquisition of embryogenic competence in sugarcane. Embryogenic and nonembryogenic calli were compared at the multiplication phase, resulting in the identification of 163 phosphoproteins unique to embryogenic calli, 9 unique to nonembryogenic calli, and 51 upregulated and 40 downregulated in embryogenic calli compared to nonembryogenic calli. Data are available via ProteomeXchange with identifier PXD018054. Motif-x analysis revealed the enrichment of [xxxpSPxxx], [RxxpSxxx], and [xxxpSDxxx] motifs, which are predicted phosphorylation sites for several kinases related to stress responses. The embryogenic-related phosphoproteins (those unique and upregulated in embryogenic calli) identified in the present study are related to abscisic acid-induced signaling and abiotic stress response; they include OSK3, ABF1, LEAs, and RD29Bs. On the other hand, the nonembryogenic-related phosphoproteins EDR1 and PP2Ac-2 are negative regulators of abscisic acid signaling, suggesting a relationship between phosphoproteins involved in the abscisic acid and stress responses in the acquisition of embryogenic competence. Moreover, embryogenic-related phosphoproteins associated with epigenetic modifications, such as HDA6, HDA19, and TOPLESS, and with RNA metabolism, including AGO1, DEAH5, SCL30, UB2C, and SR45, were identified to play potential roles in embryogenic competence. These results reveal novel phosphorylation sites for several proteins and identify potential candidate biomarkers for the acquisition of embryogenic competence in sugarcane.
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Affiliation(s)
- Felipe A Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Lucas Z Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, CBB-UENF, Campos dos Goytacazes 28013-602, Rio de Janeiro, Brazil
| | - Brian P Mooney
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211 Columbia, Missouri, United States
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211 Columbia, Missouri, United States
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
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35
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Liu J, Guo X, Zhai T, Shu A, Zhao L, Liu Z, Zhang S. Genome-wide identification and characterization of microRNAs responding to ABA and GA in maize embryos during seed germination. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:949-957. [PMID: 32526094 DOI: 10.1111/plb.13142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are an important class of non-coding small RNAs that regulate the expression of target genes through mRNA cleavage or translational inhibition. Previous studies have revealed their roles in regulating seed dormancy and germination in model plants such as Arabidopsis thaliana, rice (Oryza sativa) and maize (Zea mays). However, the miRNA response to exogenous gibberellic acid (GA) and abscisic acid (ABA) during seed germination in maize has yet to be explored. In this study, small RNA libraries were generated and sequenced from maize embryos treated with GA, ABA or double-distilled water as control. A total of 247 miRNAs (104 known and 143 novel) were identified, of which 45 known and 53 novel miRNAs were differentially expressed in embryos in the different treatment groups. In total, 74 (37 up-regulated and 37 down-regulated) and 55 (23 up-regulated and 32 down-regulated) miRNAs were expressed in response to GA and to ABA, respectively, and a total of 18 known and 38 novel miRNAs displayed differential expression between the GA- and ABA-treated groups. Using bioinformatics tools, we predicted the target genes of the differentially expressed miRNAs. Using GO enrichment and KEGG pathway analysis of these targets, we showed that miRNAs differentially expressed in our samples affect genes encoding proteins involved in the peroxisome, ribosome and plant hormonal signalling pathways. Our results indicate that miRNA-mediated gene expression influences the GA and ABA signalling pathways during seed germination.
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Affiliation(s)
- J Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - X Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - T Zhai
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - A Shu
- Rice Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - L Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Z Liu
- Institute of Soil and Fertilizer & Resource and Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - S Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
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36
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Liu J, Sun L, Chen Y, Wei L, Hao Y, Yu Z, Wang Z, Zhang H, Zhang X, Li M, Wang H, Xiao J, Wang X. The Regulatory Network of CMPG1-V in Wheat- Blumeria graminis f. sp. tritici Interaction Revealed by Temporal Profiling Using RNA-Seq. Int J Mol Sci 2020; 21:ijms21175967. [PMID: 32825128 PMCID: PMC7504233 DOI: 10.3390/ijms21175967] [Citation(s) in RCA: 4] [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: 07/16/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Wheat powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici (Bgt), is a prevalent fungal disease. The diploid wheat relative Haynaldia villosa (H. villosa) showed broad-spectrum resistance (BSR) to Pm. A previous study reported an E3 ligase gene, CMPG1-V from H. villosa, showing BSR to Pm. To elucidate the regulatory network mediated by CMPG1-V, in this study, gene expression profiling of CMPG1-V transgenic plant (CMPG1-VOE) and its receptor Yangmai 158 was analyzed and compared after Bgt inoculation at four infection stages. GO and KEGG analysis revealed obvious reprogramming of SA and ABA signaling, starch/sucrose metabolism, and photosynthesis in CMPG1-VOE, compared with those in Yangmai 158. Transcripts of SA synthesis genes SARD1 and UGT, signaling factors TGA and PRs, and SnRKs in ABA signaling were specifically upregulated in CMPG1-VOE rather than Yangmai 158. Transcripts of LHCII in photosynthesis, GLUC and TPP in starch/sucrose metabolism were also induced distinctly in CMPG1-VOE. WGCNA analysis showed crucial regulatory candidates of CMPG1-V, involving serine/threonine-protein kinase in phosphorylation, glucosyltransferase in flavonoid biosynthesis, defense factor WRKYs, and peroxidase in oxidative stress. Our results facilitate the deciphering of the resistant regulatory network of CMPG1-V and the identification of key candidates which might be employed in breeding programs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Xiue Wang
- Correspondence: ; Tel.: +86-25-8439-5308
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37
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Tian R, Wang F, Zheng Q, Niza VMAGE, Downie AB, Perry SE. Direct and indirect targets of the arabidopsis seed transcription factor ABSCISIC ACID INSENSITIVE3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1679-1694. [PMID: 32445409 DOI: 10.1111/tpj.14854] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/09/2020] [Accepted: 05/15/2020] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor in the B3 domain family. ABI3, along with B3 domain transcription factors LEAFY COTYLEDON2 (LEC2) and FUSCA3 (FUS3), and LEC1, a subunit of the CCAAT box-binding complex, form the so-called LAFL network to control various aspects of seed development and maturation. ABI3 also contributes to the abscisic acid (ABA) response. We report on chromatin immunoprecipitation-tiling array experiments to map binding sites for ABI3 globally. We also assessed transcriptomes in response to ABI3 by comparing developing abi3-5 and wild-type seeds and combined this information to ascertain direct and indirect responsive ABI3 target genes. ABI3 can induce and repress its transcription of target genes directly and some intriguing differences exist in cis motifs between these groups of genes. Directly regulated targets reflect the role of ABI3 in seed maturation, desiccation tolerance, entry into a quiescent state and longevity. Interestingly, ABI3 directly represses a gene encoding a microRNA (MIR160B) that targets AUXIN RESPONSE FACTOR (ARF)10 and ARF16 that are involved in establishment of dormancy. In addition, ABI3, like FUS3, regulates genes encoding MIR156 but while FUS3 only induces genes encoding this product, ABI3 induces these genes during the early stages of seed development, but represses these genes during late development. The interplay between ABI3, the other LAFL genes, and the VP1/ABI3-LIKE (VAL) genes, which are involved in the transition to seedling development are examined and reveal complex interactions controlling development.
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Affiliation(s)
- Ran Tian
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Fangfang Wang
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Qiaolin Zheng
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Venus M A G E Niza
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - A Bruce Downie
- UK Seed Biology Group, Department of Horticulture, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Sharyn E Perry
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
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38
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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39
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Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
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40
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Wu J, Mohamed D, Dowhanik S, Petrella R, Gregis V, Li J, Wu L, Gazzarrini S. Spatiotemporal Restriction of FUSCA3 Expression by Class I BPCs Promotes Ovule Development and Coordinates Embryo and Endosperm Growth. THE PLANT CELL 2020; 32:1886-1904. [PMID: 32265266 PMCID: PMC7268797 DOI: 10.1105/tpc.19.00764] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/10/2020] [Accepted: 04/03/2020] [Indexed: 05/06/2023]
Abstract
Spatiotemporal regulation of gene expression is critical for proper developmental timing in plants and animals. The transcription factor FUSCA3 (FUS3) regulates developmental phase transitions by acting as a link between hormonal pathways in Arabidopsis (Arabidopsis thaliana). However, the mechanisms governing its spatiotemporal expression pattern are poorly understood. Here, we show that FUS3 is repressed in the ovule integuments and seed endosperm. FUS3 repression requires class I BASIC PENTACYSTEINE (BPC) proteins, which directly bind GA/CT cis-elements in FUS3 and restrict its expression pattern. During vegetative and reproductive development, FUS3 derepression in bpc1-1 bpc2 (bpc1/2) double mutant or misexpression in ProML1:FUS3 lines causes dwarf plants carrying defective flowers and aborted ovules. After fertilization, ectopic FUS3 expression in bpc1/2 endosperm or ProML1:FUS3 endosperm and endothelium increases endosperm nuclei proliferation and seed size, causing delayed or arrested embryo development. These phenotypes are rescued in bpc1/2 fus3-3 Finally, class I BPCs interact with FIS-PRC2 (FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex2), which represses FUS3 in the endosperm during early seed development. We propose that BPC1 and 2 promote the transition from reproductive to seed development by repressing FUS3 in ovule integuments. After fertilization, BPC1 and 2 and FIS-PRC2 repress FUS3 in the endosperm to coordinate early endosperm and embryo growth.
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Affiliation(s)
- Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China
- Department of Biological Sciences, University of Toronto Scarborough, Ontario M1C 1A4, Canada
| | - Deka Mohamed
- Department of Biological Sciences, University of Toronto Scarborough, Ontario M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3G5, Canada
| | - Sebastian Dowhanik
- Department of Biological Sciences, University of Toronto Scarborough, Ontario M1C 1A4, Canada
| | - Rosanna Petrella
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- Department of Biological Sciences, University of Toronto Scarborough, Ontario M1C 1A4, Canada
- Chongqing Key Laboratory of Economic Plant Biotechnology, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing 402160, China
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, Ontario M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3G5, Canada
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41
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Malovichko YV, Shtark OY, Vasileva EN, Nizhnikov AA, Antonets KS. Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea ( Pisum sativum L.). Cells 2020; 9:E779. [PMID: 32210065 PMCID: PMC7140803 DOI: 10.3390/cells9030779] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 02/07/2023] Open
Abstract
The garden pea (Pisum sativum L.) is a legume crop of immense economic value. Extensive breeding has led to the emergence of numerous pea varieties, of which some are distinguished by accelerated development in various stages of ontogenesis. One such trait is rapid seed maturation, which, despite novel insights into the genetic control of seed development in legumes, remains poorly studied. This article presents an attempt to dissect mechanisms of early maturation in the pea line Sprint-2 by means of whole transcriptome RNA sequencing in two developmental stages. By using a de novo assembly approach, we have obtained a reference transcriptome of 25,756 non-redundant entries expressed in pea seeds at either 10 or 20 days after pollination. Differential expression in Sprint-2 seeds has affected 13,056 transcripts. A comparison of the two pea lines with a common maturation rate demonstrates that while at 10 days after pollination, Sprint-2 seeds show development retardation linked to intensive photosynthesis, morphogenesis, and cell division, and those at 20 days show a rapid onset of desiccation marked by the cessation of translation and cell anabolism and accumulation of dehydration-protective and -storage moieties. Further inspection of certain transcript functional categories, including the chromatin constituent, transcription regulation, protein turnover, and hormonal regulation, has revealed transcriptomic trends unique to specific stages and cultivars. Among other remarkable features, Sprint-2 demonstrated an enhanced expression of transposable element-associated open reading frames and an altered expression of major maturation regulators and DNA methyltransferase genes. To the best of our knowledge, this is the first comparative transcriptomic study in which the issue of the seed maturation rate is addressed.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Ekaterina N. Vasileva
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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42
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Xu X, Chen X, Chen Y, Zhang Q, Su L, Chen X, Chen Y, Zhang Z, Lin Y, Lai Z. Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour. Sci Rep 2020; 10:4626. [PMID: 32170163 PMCID: PMC7069941 DOI: 10.1038/s41598-020-60946-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/07/2020] [Indexed: 11/09/2022] Open
Abstract
miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.
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Affiliation(s)
- Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qinglin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liyao Su
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Plotnikova A, Kellner MJ, Schon MA, Mosiolek M, Nodine MD. MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis. THE PLANT CELL 2019; 31:2929-2946. [PMID: 31562217 PMCID: PMC6925019 DOI: 10.1105/tpc.19.00395] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/16/2019] [Accepted: 09/25/2019] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis (Arabidopsis thaliana), we developed or applied high-throughput sequencing-based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts, including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have profound effects on embryonic gene expression programs. Moreover, we demonstrated that the miRNA-mediated repression of six transcription factors are individually required for proper division patterns of various embryonic cell lineages. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and they provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.
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Affiliation(s)
- Alexandra Plotnikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Max J Kellner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael A Schon
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael D Nodine
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW. Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus. THE PLANT CELL 2019; 31:2370-2385. [PMID: 31439805 DOI: 10.1101/334581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/22/2019] [Accepted: 08/12/2019] [Indexed: 05/28/2023]
Abstract
Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.
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Affiliation(s)
- Charlotte Miller
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rachel Wells
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Neil McKenzie
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Trick
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Joshua Ball
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Abdelhak Fatihi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Thierry Chardot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Loic Lepiniec
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW. Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus. THE PLANT CELL 2019; 31:2370-2385. [PMID: 31439805 PMCID: PMC6790077 DOI: 10.1105/tpc.18.00577] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/22/2019] [Accepted: 08/12/2019] [Indexed: 05/23/2023]
Abstract
Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.
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Affiliation(s)
- Charlotte Miller
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rachel Wells
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Neil McKenzie
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Trick
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Joshua Ball
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Abdelhak Fatihi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Thierry Chardot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Loic Lepiniec
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Institut National de la Recherche Agronomique Versailles, route de Saint-Cyr, 78000 Versailles, France
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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46
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In-silico identification and analysis of miRNAs from germinating seeds in Paris polyphylla var. yunnanensis by deep sequencing. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00348-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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47
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Ma Z, Liu M, Sun W, Huang L, Wu Q, Bu T, Li C, Chen H. Genome-wide identification and expression analysis of the trihelix transcription factor family in tartary buckwheat (Fagopyrum tataricum). BMC PLANT BIOLOGY 2019; 19:344. [PMID: 31390980 PMCID: PMC6686422 DOI: 10.1186/s12870-019-1957-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND In the study, the trihelix family, also referred to as GT factors, is one of the transcription factor families. Trihelix genes play roles in the light response, seed maturation, leaf development, abiotic and biological stress and other biological activities. However, the trihelix family in tartary buckwheat (Fagopyrum tataricum), an important usable medicinal crop, has not yet been thoroughly studied. The genome of tartary buckwheat has recently been reported and provides a theoretical basis for our research on the characteristics and expression of trihelix genes in tartary buckwheat based at the whole level. RESULTS In the present study, a total of 31 FtTH genes were identified based on the buckwheat genome. They were named from FtTH1 to FtTH31 and grouped into 5 groups (GT-1, GT-2, SH4, GTγ and SIP1). FtTH genes are not evenly distributed on the chromosomes, and we found segmental duplication events of FtTH genes on tartary buckwheat chromosomes. According to the results of gene and motif composition, FtTH located in the same group contained analogous intron/exon organizations and motif organizations. qRT-PCR showed that FtTH family members have multiple expression patterns in stems, roots, leaves, fruits, and flowers and during fruit development. CONCLUSIONS Through our study, we identified 31 FtTH genes in tartary buckwheat and synthetically further analyzed the evolution and expression pattern of FtTH proteins. The structure and motif organizations of most genes are conserved in each subfamily, suggesting that they may be functionally conserved. The FtTH characteristics of the gene expression patterns indicate functional diversity in the time and space in the tartary buckwheat life process. Based on the discussion and analysis of FtTH gene function, we screened some genes closely related to the growth and development of tartary buckwheat. This will help us to further study the function of FtTH genes through experimental exploration in tartary buckwheat growth and improve the fruit of tartary buckwheat.
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Affiliation(s)
- Zhaotang Ma
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Moyang Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Li Huang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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48
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O'Neill JP, Colon KT, Jenik PD. The onset of embryo maturation in Arabidopsis is determined by its developmental stage and does not depend on endosperm cellularization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:286-301. [PMID: 30900325 PMCID: PMC6635039 DOI: 10.1111/tpj.14324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 05/06/2023]
Abstract
Seeds are dormant and desiccated structures, filled with storage products to be used after germination. These properties are determined by the maturation program, which starts, in Arabidopsis thaliana, mid-embryogenesis, at about the same time and developmental stage in all the seeds in a fruit. The two factors, chronological and developmental time, are closely entangled during seed development, so their relative contribution to the transition to maturation is not well understood. It is also unclear whether that transition is determined autonomously by each seed or whether it depends on signals from the fruit. The onset of maturation follows the cellularization of the endosperm, and it has been proposed that there exists a causal relationship between both processes. We explored all these issues by analyzing markers for maturation in Arabidopsis mutant seeds that develop at a slower pace, or where endosperm cellularization happens too early, too late, or not at all. Our data show that the developmental stage of the embryo is the key determinant of the initiation of maturation, and that each seed makes that transition autonomously. We also found that, in contrast with previous models, endosperm cellularization is not required for the onset of maturation, suggesting that this transition is independent of the hexose/sucrose ratio in the seed. Our observations indicate that the mechanisms that control endosperm cellularization, embryo growth, and embryo maturation act independently of each other.
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Affiliation(s)
- John P O'Neill
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA, 17604-3003, USA
| | - Kristen T Colon
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA, 17604-3003, USA
| | - Pablo D Jenik
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA, 17604-3003, USA
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49
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Cheng X, Xiong R, Yan H, Gao Y, Liu H, Wu M, Xiang Y. The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis). BMC PLANT BIOLOGY 2019; 19:154. [PMID: 31023225 PMCID: PMC6482567 DOI: 10.1186/s12870-019-1744-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/28/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Trihelix transcription factors (TTFs) are photoresponsive proteins that have a representative three-helix structure (helix-loop-helix-loop-helix). Members of this gene family have been reported to play roles in many plant processes. RESULTS In this study, we performed a functional and evolutionary analysis of the TTFs in Moso bamboo (Phyllostachys edulis). A total of 35 genes were identified and grouped into five subfamilies (GT-1, GT-γ, GT-2, SIP1 and SH4) according to their structural properties. Gene structure analysis showed that most genes in the PeTTF family had fewer introns. A unique motif (Motif 16) to the GT-γ subfamily was identified by conserved motif analysis. Promoter analysis revealed various cis-acting elements related to plant growth and development, abiotic and biotic stresses, and phytohormone responses. Data for the 35 Moso bamboo TTF genes were used to generate heat maps, which indicated that these genes were expressed in different tissues or developmental stages. Most of the TTF genes identified here had high expression in leaves and panicles according to the expression profile analysis. The expression levels of the TTF members in young leaves were studied using quantitative real-time PCR to determine their tissue specificity and stress-related expression patterns to help functionally characterize individual members. CONCLUSIONS The results indicated that members of the TTF gene family may be involved in plant responses to stress conditions. Additionally, PeTTF29 was shown to be located in the nucleus by subcellular localization analysis and to have transcriptional activity in a transcriptional activity assay. Our research provides a comprehensive summary of the PeTTF gene family, including functional and evolutionary perspectives, and provides a basis for functionally characterizing these genes.
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Affiliation(s)
- Xinran Cheng
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 China
| | - Rui Xiong
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
| | - Yameng Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
| | - Huanlong Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
| | - Min Wu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 China
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50
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Na G, Mu X, Grabowski P, Schmutz J, Lu C. Enhancing microRNA167A expression in seed decreases the α-linolenic acid content and increases seed size in Camelina sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:346-358. [PMID: 30604453 DOI: 10.1111/tpj.14223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 05/20/2023]
Abstract
Despite well established roles of microRNAs in plant development, few aspects have been addressed to understand their effects in seeds especially on lipid metabolism. In this study, we showed that overexpressing microRNA167A (miR167OE) in camelina (Camelina sativa) under a seed-specific promoter changed fatty acid composition and increased seed size. Specifically, the miR167OE seeds had a lower α-linolenic acid with a concomitantly higher linoleic acid content than the wild-type. This decreased level of fatty acid desaturation corresponded to a decreased transcriptional expression of the camelina fatty acid desaturase3 (CsFAD3) in developing seeds. MiR167 targeted the transcription factor auxin response factor (CsARF8) in camelina, as had been reported previously in Arabidopsis. Chromatin immunoprecipitation experiments combined with transcriptome analysis indicated that CsARF8 bound to promoters of camelina bZIP67 and ABI3 genes. These transcription factors directly or through the ABI3-bZIP12 pathway regulate CsFAD3 expression and affect α-linolenic acid accumulation. In addition, to decipher the miR167A-CsARF8 mediated transcriptional cascade for CsFAD3 suppression, transcriptome analysis was conducted to implicate mechanisms that regulate seed size in camelina. Expression levels of many genes were altered in miR167OE, including orthologs that have previously been identified to affect seed size in other plants. Most notably, genes for seed coat development such as suberin and lignin biosynthesis were down-regulated. This study provides valuable insights into the regulatory mechanism of fatty acid metabolism and seed size determination, and suggests possible approaches to improve these important traits in camelina.
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Affiliation(s)
- GunNam Na
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Xiaopeng Mu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Paul Grabowski
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
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