1
|
Meucci S, Kruse S, Haupt S, Stoof‐Leichsenring KR, Krutovsky KV, Bernhardt N, Harpke D, Herzschuh U. Biological Processes Underlying Genetic Adaptation of Larches to Cold and Dry Winter Conditions in Eastern Siberia. Ecol Evol 2025; 15:e70940. [PMID: 39949889 PMCID: PMC11821550 DOI: 10.1002/ece3.70940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 12/17/2024] [Accepted: 01/20/2025] [Indexed: 02/16/2025] Open
Abstract
The boreal forests of central and eastern Siberia, dominated by larches, are challenged by increasingly harsher continental conditions and more frequent droughts. Despite the crucial ecosystem services provided by these Siberian boreal forests, the major stressors driving the selective factors as well as the genetic adaptation mechanisms of larches are still unknown. Here we present a landscape genomics study on 243 individuals of the dominant larch tree species, Larix gmelinii and L. cajanderi. We assessed genotype-environment associations (GEAs) between genetic variation of individual markers based on genotyping-by-sequencing (GBS) data and bioclimatic variables recorded at the sampling locations. We find that the cold and dry winter conditions of eastern Siberia are likely the main selective factor driving the genetic adaptation of larches. Gene ontology (GO) enrichment analysis identified metabolic, transmembrane transport, and homeostatic, as well as developmental processes among the main biological processes underlying genetic adaptation driven by cold and dry winter conditions.
Collapse
Affiliation(s)
- Stefano Meucci
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPolar Terrestrial Environmental SystemsPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Stefan Kruse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPolar Terrestrial Environmental SystemsPotsdamGermany
| | - Sarah Haupt
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPolar Terrestrial Environmental SystemsPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Kathleen R. Stoof‐Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPolar Terrestrial Environmental SystemsPotsdamGermany
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree BreedingGeorge‐August University of GöttingenGöttingenGermany
- Center for Integrated Breeding ResearchGeorg‐August University of GöttingenGöttingenGermany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussian Federation
- Laboratory of Forest Genomics, Genome Research and Education Center, Department of Genomics and Bioinformatics, Institute of Fundamental Biology and BiotechnologySiberian Federal UniversityKrasnoyarskRussian Federation
- Scientific and Methodological CenterG. F. Morozov Voronezh State University of Forestry and TechnologiesVoronezhRussian Federation
| | - Nadine Bernhardt
- Julius Kühn‐Institut, Federal Research Centre for Cultivated PlantsInstitute for Resistance Research and Stress ToleranceQuedlinburgGermany
| | - Dörte Harpke
- Leibniz Institute of Plant Genetics and Crop Plant Research GaterslebenStadt SeelandGermany
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPolar Terrestrial Environmental SystemsPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Institute of Environmental Science and GeographyUniversity of PotsdamPotsdamGermany
| |
Collapse
|
2
|
Qiu XF, Liu YY, Wu G, Xu CH, Liu XQ, Xiang XY, Wei XX, Wang XQ. Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests. Mol Phylogenet Evol 2025; 202:108240. [PMID: 39549977 DOI: 10.1016/j.ympev.2024.108240] [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: 10/11/2023] [Revised: 09/28/2024] [Accepted: 11/10/2024] [Indexed: 11/18/2024]
Abstract
As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today's forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time. We first reconstructed a highly resolved and robust phylogeny of Larix covering all widely recognized species, using both transcriptome-based 1,301 orthologous genes (OGs) and plastid genomes. In sharp contrast to previous studies, an unexpected deep split between the circumboreal and Qinghai-Tibetan Plateau (QTP) larches was revealed in our study. Within each lineage, two geographically distinct clades were further resolved. Biogeographical analyses suggest that Larix might have an origin of Eocene in high-latitude uplands, and during the Miocene, all extant species have appeared. Cenozoic climate- and orogeny-triggered vicariance likely played a major role in the divergence of global larches. Our results also demonstrate that the proto-boreal forest biome may have a relatively old origin back to the early Miocene, and significant winnowing and species alteration would have occurred as the climate shifted to much colder and drier conditions during the Neogene. Ecological niche analyses show various responses of the circumboreal and QTP larches under different climate scenarios, but both lineages are negatively impacted by warming climates. These findings have important conservation implications given the sensitivity of boreal forests in the face of global warming. Our work further emphasizes the importance of a solid phylogenetic framework for evolutionary and biogeographical inferences.
Collapse
Affiliation(s)
- Xiu-Fei Qiu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Yan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Ge Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong-Hui Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Quan Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Yan Xiang
- College of Life Sciences, Anqing Normal University, Anqing 246133, China
| | - Xiao-Xin Wei
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
3
|
Orlov YL, Chen M. Special Issue on "Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0". Int J Mol Sci 2023; 24:17588. [PMID: 38139417 PMCID: PMC10743833 DOI: 10.3390/ijms242417588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The analysis of molecular mechanisms underlying plant adaptation to environmental changes and stress response is crucial for plant biotechnology [...].
Collapse
Affiliation(s)
- Yuriy L. Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
4
|
Xiao Y, Zhang XX, Hu Y, Wang X, Li P, He ZH, Lv YW, Chen XY, Hu XS. Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers. Genes (Basel) 2022; 14:116. [PMID: 36672857 PMCID: PMC9858616 DOI: 10.3390/genes14010116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.
Collapse
Affiliation(s)
- Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Xin Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Ying Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Yang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|