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Zhao B, Wang JW. Perenniality: From model plants to applications in agriculture. MOLECULAR PLANT 2024; 17:141-157. [PMID: 38115580 DOI: 10.1016/j.molp.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; New Cornerstone Science Laboratory, Shanghai 200032, China.
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2
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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Liu Y, Ma D, Constabel CP. CRISPR/Cas9 Disruption of MYB134 and MYB115 in Transgenic Poplar Leads to Differential Reduction of Proanthocyanidin Synthesis in Roots and Leaves. PLANT & CELL PHYSIOLOGY 2023; 64:1189-1203. [PMID: 37522631 DOI: 10.1093/pcp/pcad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/01/2023]
Abstract
Proanthocyanidins (PAs) are common specialized metabolites and particularly abundant in trees and woody plants. In poplar (Populus spp.), PA biosynthesis is stress-induced and regulated by two previously studied transcription factors MYB115 and MYB134. To determine the relative contribution of these regulators to PA biosynthesis, we created single- and double-knockout (KO) mutants for both genes in transgenic poplars using CRISPR/Cas9. Knocking out either MYB134 or MYB115 showed reduced PA accumulation and downregulated flavonoid genes in leaves, but MYB134 disruption had the greatest impact and reduced PAs to 30% of controls. In roots, by contrast, only the MYB134/MYB115 double-KOs showed a significant change in PA concentration. The loss of PAs paralleled the lower expression of PA biosynthesis genes and concentrations of flavan-3-ol PA precursors catechin and epicatechin. Interestingly, salicinoids were also affected in double-KOs, with distinct patterns in roots and shoots. We conclude that the regulatory pathways for PA biosynthesis differ in poplar leaves and roots. The residual PA content in the double-KO plants indicates that other transcription factors must also be involved in control of the PA pathway.
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Affiliation(s)
- Yalin Liu
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P5C3, Canada
| | - Dawei Ma
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P5C3, Canada
| | - C Peter Constabel
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P5C3, Canada
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Klocko AL, Elorriaga E, Ma C, Strauss SH. Variation in floral form of CRISPR knock-outs of the poplar homologs of LEAFY and AGAMOUS after FT heat-induced early flowering. HORTICULTURE RESEARCH 2023; 10:uhad132. [PMID: 37564267 PMCID: PMC10410293 DOI: 10.1093/hr/uhad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/20/2023] [Indexed: 08/12/2023]
Abstract
Plant migration and gene flow from genetically modified or exotic trees to nearby lands or by crossing with wild relatives is a major public and regulatory concern. Many genetic strategies exist to mitigate potential gene flow; however, the long delay in onset of flowering is a severe constraint to research progress. We used heat-induced FT overexpression to speed assessment of the expected floral phenotypes after CRISPR knockout of poplar homologs of the key floral genes, LEAFY and AGAMOUS. We selected events with previously characterized CRISPR-Cas9 induced biallelic changes then re-transformed them with the Arabidopsis thaliana FLOWERING LOCUS T (AtFT) gene under control of either a strong constitutive promoter or a heat-inducible promoter. We successfully obtained flowering in both a male and female clones of poplar, observing a wide range of inflorescence and floral forms among flowers, ramets, and insertion events. Overall, flowers obtained from the selected LFY and AG targeted events were consistent with what would be predicted for loss-of-function of these genes. LFY-targeted events showed small catkins with leaf-like organs, AG-targeted events had nested floral organs consistent with reduction in floral determinacy and absence of well-formed carpels or anthers. These findings demonstrate the great developmental plasticity of Populus flowers during genetically accelerated flowering, which may be of horticultural value. They also provide an informative early view of floral phenotypes and apparent sterility from knockouts of both these gene targets.
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Affiliation(s)
- Amy L Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Estefania Elorriaga
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
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Zhou F, Wu H, Chen Y, Wang M, Tuskan GA, Yin T. Function and molecular mechanism of a poplar placenta limited MIXTA gene in regulating differentiation of plant epidermal cells. Int J Biol Macromol 2023; 242:124743. [PMID: 37150377 DOI: 10.1016/j.ijbiomac.2023.124743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/20/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
The placenta in fruits of most plants either desiccate and shrink as the fruits mature or develop further to form the fleshy tissues. In poplars, placental epidermal cells protrude collectively to produce catkin fibers. In this study, three carpel limited MIXTA genes, PdeMIXTA02, PdeMIXTA03, PdeMIXTA04, were find to specifically expressed in carpel immediately after pollination. Heterologous expression of the three genes in Arabidopsis demonstrated that PdeMIXTA04 significantly promoted trichomes density and could restore trichomes in the trichomeless mutant. By contrast, such functions were not observed with PdeMIXTA02, PdeMIXTA03. In situ hybridization revealed that PdeMIXTA04 was explicitly expressed in poplar placental epidermal cells. We also confirmed trichome-specific expression of the PdeMIXTA04 promoter. Multiple experimental proofs have confirmed the interaction between PdeMIXTA04, PdeMYC and PdeWD40, indicating PdeMIXTA04 functioned through the MYB-bHLH-WD40 ternary complex. Our work provided distinctive understanding of the molecular mechanism triggering differentiation of poplar catkins.
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Affiliation(s)
- Fangwei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Huaitong Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Yingnan Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Mingxiu Wang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Tongming Yin
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
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Sheng X, Mahendra RA, Wang CT, Brunner AM. CRISPR/Cas9 mutants delineate roles of Populus FT and TFL1/CEN/BFT family members in growth, dormancy release and flowering. TREE PHYSIOLOGY 2023; 43:1042-1054. [PMID: 36892416 DOI: 10.1093/treephys/tpad027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/21/2023] [Indexed: 06/11/2023]
Abstract
Vegetative and reproductive phase change and phenology are economically and ecologically important traits. Trees typically require several years of growth before flowering and, once mature, seasonal control of the transition to flowering and flower development is necessary to maintain vegetative meristems and for reproductive success. Members of two related gene subfamilies, FLOWERING LOCUST (FT) and TERMINAL FLOWER1 (TFL1)/CENTRORADIALIS (CEN)/BROTHER OF FT AND TFL1 (BFT), have antagonistic roles in flowering in diverse species and roles in vegetative phenology in trees, but many details of their functions in trees have yet to be resolved. Here, we used CRISPR/Cas9 to generate single and double mutants involving the five Populus FT and TFL1/CEN/BFT genes. The ft1 mutants exhibited wild-type-like phenotypes in long days and short days, but after chilling, to release dormancy, they showed delayed bud flush and GA3 could compensate for the ft1 mutation. After rooting and generating some phytomers in tissue culture, both cen1 and cen1ft1 mutants produced terminal as well as axillary flowers, indicating that the cen1 flowering phenotype is independent of FT1. The CEN1 showed distinct circannual expression patterns in vegetative and reproductive tissues and comparison with the expression patterns of FT1 and FT2 suggests that the relative levels of CEN1 compared with FT1 and FT2 regulate multiple phases of vegetative and reproductive seasonal development.
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Affiliation(s)
- Xiaoyan Sheng
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA 24061, USA
| | - R Ayeshan Mahendra
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA 24061, USA
| | - Chieh-Ting Wang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA 24061, USA
| | - Amy M Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA 24061, USA
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