1
|
Xiang X, Zhou X, Zi H, Wei H, Cao D, Zhang Y, Zhang L, Hu J. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. HORTICULTURE RESEARCH 2024; 11:uhad255. [PMID: 38274646 PMCID: PMC10809908 DOI: 10.1093/hr/uhad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.
Collapse
Affiliation(s)
- Xiaodong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xinglu Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Hantian Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Demei Cao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| |
Collapse
|
2
|
Ding C, Brouard JS. Assisted migration is plausible for a boreal tree species under climate change: A quantitative and population genetics study of trembling aspen ( Populus tremuloides Michx.) in western Canada. Ecol Evol 2022; 12:e9384. [PMID: 36225831 PMCID: PMC9534759 DOI: 10.1002/ece3.9384] [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: 12/09/2021] [Accepted: 09/16/2022] [Indexed: 11/14/2022] Open
Abstract
A novel method was tested for improving tree breeding strategies that integrate quantitative and population genetics based on range‐wide reciprocal transplant experiments. Five reciprocal common garden tests of Populus tremuloides were investigated including 6450 trees across western Canada focusing on adaptation traits and growth. Both genetic parameters and home‐site transplant models were evaluated. We found a genetic trade‐off between growth and early spring leaf flush and late fall senescence. Coefficients of phenotypic variation (CVp) of cell lysis (CL), a measure of freezing injury, shrank from 0.28 to 0.10 during acclimation in the fall, and the CVp slope versus the freezing temperature was significantly different from zero (R2 = 0.33, p = .02). There was more between‐population genetic variation in fall phenology than in spring leaf phenology. We suggest that P. tremuloides demonstrated a discrepancy between the ecological optimum and the physiological optimum minimum winter temperature. The sub‐optimal growing condition of P. tremuloides is potentially caused by the warmer ecological optimum than the physiological optimum. Assisted migration and breeding of fast growers to reforest cooler plantation sites can improve productivity. Transferring the study populations to less than 4°C of extreme minimum temperature appears safe for reforestation aligning with the historical recolonization direction of the species. This is equivalent to a 5–10° latitudinal northward movement. Fall frost hardiness is an effective criterion for family selection in the range tested in this study.
Collapse
Affiliation(s)
- Chen Ding
- Western Gulf Forest Tree Improvement ProgramTexas A&M Forest Service, TAMU SystemCollege StationTexasUSA
| | - Jean S. Brouard
- Isabella Point Forestry Ltd.Salt Spring IslandBritish ColumbiaCanada
| |
Collapse
|
3
|
Dani KGS, Pollastri S, Pinosio S, Reichelt M, Sharkey TD, Schnitzler J, Loreto F. Isoprene enhances leaf cytokinin metabolism and induces early senescence. THE NEW PHYTOLOGIST 2022; 234:961-974. [PMID: 34716577 PMCID: PMC9300082 DOI: 10.1111/nph.17833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/22/2021] [Indexed: 06/02/2023]
Abstract
Isoprene, a major biogenic volatile hydrocarbon of climate-relevance, indisputably mitigates abiotic stresses in emitting plants. However functional relevance of constitutive isoprene emission in unstressed plants remains contested. Isoprene and cytokinins (CKs) are synthesized from a common substrate and pathway in chloroplasts. It was postulated that isoprene emission may affect CK-metabolism. Using transgenic isoprene-emitting (IE) Arabidopsis and isoprene nonemitting (NE) RNA-interference grey poplars (paired with respective NE and IE genotypes), the life of individual IE and NE leaves from emergence to abscission was followed under stress-free conditions. We monitored plant growth rate, aboveground developmental phenotype, modelled leaf photosynthetic energy status, quantified the abundance of leaf CKs, analysed Arabidopsis and poplar leaf transcriptomes by RNA-sequencing in presence and absence of isoprene during leaf senescence. Isoprene emission by unstressed leaves enhanced the abundance of CKs (isopentenyl adenine and its precursor) by > 200%, significantly upregulated genes coding for CK-synthesis, CK-signalling and CK-degradation, hastened plant development, increased chloroplast metabolic rate, altered photosynthetic energy status, induced early leaf senescence in both Arabidopsis and poplar. IE leaves senesced sooner even in decapitated poplars where source-sink relationships and hormone homeostasis were perturbed. Constitutive isoprene emission significantly accelerates CK-led leaf and organismal development and induces early senescence independent of growth constraints. Isoprene emission provides an early-riser evolutionary advantage and shortens lifecycle duration to assist rapid diversification in unstressed emitters.
Collapse
Affiliation(s)
- Kaidala Ganesha Srikanta Dani
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyVia Madonna del Piano 1050019Sesto FiorentinoFlorenceItaly
- Department of Biology, Agriculture and Food SciencesNational Research Council of ItalyPiazzale Aldo Moro 700185RomeItaly
| | - Susanna Pollastri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyVia Madonna del Piano 1050019Sesto FiorentinoFlorenceItaly
| | - Sara Pinosio
- Institute of Biosciences and BioresourcesNational Research Council of ItalyVia Madonna del Piano 1050019Sesto FiorentinoFlorenceItaly
- Institute for Applied GenomicsVia Jacopo Linussio 5133100UdineItaly
| | - Michael Reichelt
- Department of BiochemistryMax Planck Institute for Chemical EcologyHans‐Knöll Strasse 8D‐07745JenaGermany
| | - Thomas D. Sharkey
- MSU‐DOE Plant Research LaboratoryDepartment of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| | - Jörg‐Peter Schnitzler
- Research Unit Environmental SimulationInstitute of Biochemical Plant PathologyHelmholtz Zentrum MünchenGerman Research Center for Environmental Health85764NeuherbergGermany
| | - Francesco Loreto
- Department of Biology, Agriculture and Food SciencesNational Research Council of ItalyPiazzale Aldo Moro 700185RomeItaly
- Department of BiologyUniversity of Naples Federico IIVia Cinthia80126NaplesItaly
| |
Collapse
|
4
|
Satake A, Nagahama A, Sasaki E. A cross-scale approach to unravel the molecular basis of plant phenology in temperate and tropical climates. THE NEW PHYTOLOGIST 2022; 233:2340-2353. [PMID: 34862973 DOI: 10.1111/nph.17897] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Plants have evolved to time their leafing, flowering and fruiting in appropriate seasons for growth, reproduction and resting. As a consequence of their adaptation to geographically different environments, there is a rich diversity in plant phenology from temperate and tropical climates. Recent progress in genetic and molecular studies will provide numerous opportunities to study the genetic basis of phenological traits and the history of adaptation of phenological traits to seasonal and aseasonal environments. Integrating molecular data with long-term phenology and climate data into predictive models will be a powerful tool to forecast future phenological changes in the face of global environmental change. Here, we review the cross-scale approach from genes to plant communities from three aspects: the latitudinal gradient of plant phenology at the community level, the environmental and genetic factors underlying the diversity of plant phenology, and an integrated approach to forecast future plant phenology based on genetically informed knowledge. Synthesizing the latest knowledge about plant phenology from molecular, ecological and mathematical perspectives will help us understand how natural selection can lead to the further evolution of the gene regulatory mechanisms in phenological traits in future forest ecosystems.
Collapse
Affiliation(s)
- Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Ai Nagahama
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Eriko Sasaki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| |
Collapse
|
5
|
Apuli RP, Richards T, Rendón-Anaya M, Karacic A, Rönnberg-Wästljung AC, Ingvarsson PK. The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray). BMC PLANT BIOLOGY 2021; 21:317. [PMID: 34215191 PMCID: PMC8252265 DOI: 10.1186/s12870-021-03103-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment. RESULTS We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions. CONCLUSIONS In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.
Collapse
Affiliation(s)
- Rami-Petteri Apuli
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Thomas Richards
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Martha Rendón-Anaya
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Almir Karacic
- Institute for Crop Production Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
| |
Collapse
|
6
|
Bentley AR, Compton LJ. Theory into practice: opportunities & applications of quantitative genetics in plants. Heredity (Edinb) 2020; 125:373-374. [PMID: 33168960 DOI: 10.1038/s41437-020-00374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Lindsey J Compton
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|