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Sezen UU, Shue JE, Worthy SJ, Davies SJ, McMahon SM, Swenson NG. Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech. Proc Biol Sci 2024; 291:20232338. [PMID: 38593851 PMCID: PMC11003779 DOI: 10.1098/rspb.2023.2338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024] Open
Abstract
Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.
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Affiliation(s)
- U. Uzay Sezen
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
| | - Jessica E. Shue
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
| | - Samantha J. Worthy
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Stuart J. Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Sean M. McMahon
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Nathan G. Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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Liao X, Su Y, Klintenäs M, Li Y, Sane S, Wu Z, Chen Q, Zhang B, Nilsson O, Ding J. Age-dependent seasonal growth cessation in Populus. Proc Natl Acad Sci U S A 2023; 120:e2311226120. [PMID: 37991940 PMCID: PMC10691234 DOI: 10.1073/pnas.2311226120] [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: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023] Open
Abstract
In temperate and boreal regions, perennial plants adapt their annual growth cycle to the change of seasons. In natural forests, juvenile seedlings usually display longer growth seasons compared to adult trees to ensure their establishment and survival under canopy shade. However, how trees adjust their annual growth according to their age is not known. In this study, we show that age-dependent seasonal growth cessation is genetically controlled and found that the miR156-SPL3/5 module, a key regulon of vegetative phase change (VPC), also triggers age-dependent growth cessation in Populus trees. We show that miR156 promotes shoot elongation during vegetative growth, and its targets SPL3/5s function in the same pathway but as repressors. We find that the miR156-SPL3/5s regulon controls growth cessation in both leaves and shoot apices and through multiple pathways, but with a different mechanism compared to how the miR156-SPL regulon controls VPC in annual plants. Taken together, our results reveal an age-dependent genetic network in mediating seasonal growth cessation, a key phenological process in the climate adaptation of perennial trees.
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Affiliation(s)
- Xiaoli Liao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Hubei Engineering Technology Research Center for Forestry Information, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
| | - Yunjie Su
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Hubei Engineering Technology Research Center for Forestry Information, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
| | - Maria Klintenäs
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå901 83, Sweden
| | - Yue Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Hubei Engineering Technology Research Center for Forestry Information, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
| | - Shashank Sane
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå901 83, Sweden
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Hubei Engineering Technology Research Center for Forestry Information, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
| | - Qihui Chen
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Hubei Engineering Technology Research Center for Forestry Information, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
| | - Bo Zhang
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå901 83, Sweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå901 83, Sweden
| | - Jihua Ding
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Hubei Engineering Technology Research Center for Forestry Information, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan430070, 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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