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de Lima TM, da Silva SF, Sánchez-Vilas J, Júnior WLS, Mayer JLS, Ribeiro RV, Pinheiro F. Phenotypic plasticity rather than ecotypic differentiation explains the broad realized niche of a Neotropical orchid species. PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 38958955 DOI: 10.1111/plb.13684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
Local adaptation is common in plant species, and knowing whether a population is locally adapted has fundamental and applied relevance. However, local adaptation in tropical plants remains largely less studied, and covering this gap is not simple since reciprocal transplantation - the gold standard for detecting local adaptation - is not feasible for most species. Here, we combined genetic, climatic and phenotypic data to investigate ecotypic differentiation, an important aspect of local adaptation, in coastal and inland populations of the orchid Epidendrum fulgens Brongn., a long-lived tropical plant for which reciprocal transplantation would not be feasible. We used nine microsatellite markers to estimate genetic divergence between inland and coastal populations. Moreover, occurrence data and climate data were used to test for differences in the realized niche of those populations. Finally, we assessed saturated water content, leaf specific area, height, and stomatal density in common garden and in situ to investigate the effects of ecotypic differentiation and plasticity on the phenotype. Coastal and inland groups' niches do not overlap, the former occupying a wetter and warmer area. However, this differentiation does not seem to be driven by ecotypic differentiation since there was no positive correlation between genetic structure and climate dissimilarity. Moreover, specific leaf area and leaf saturated water content, which are important phenotypic traits related to soil fertility and drought stress, were rather plastic. We conclude that ecotypic differentiation is absent, since phenotypic plasticity is an important mechanism explaining the niche broadness of this species.
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Affiliation(s)
- T M de Lima
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - S F da Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Laboratory of Crop Physiology, Department of Plant Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - J Sánchez-Vilas
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building Museum Avenue, Cardiff, UK
- Departamento de Bioloxía Funcional, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - W L S Júnior
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - J L S Mayer
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - R V Ribeiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Laboratory of Crop Physiology, Department of Plant Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - F Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
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2
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Manthey JD, Spellman GM. Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana). Mol Phylogenet Evol 2024; 196:108088. [PMID: 38697377 DOI: 10.1016/j.ympev.2024.108088] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
The nonrandom distribution of chromosomal characteristics and functional elements-genomic architecture-impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure-ordination, clustering, and phylogenetic methods-we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.
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Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University. Lubbock, TX, USA.
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, USA
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3
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Mee JA, Carson B, Yeaman S. Conditionally Deleterious Mutation Load Accumulates in Genomic Islands of Local Adaptation but Can Be Purged with Sufficient Genotypic Redundancy. Am Nat 2024; 204:43-54. [PMID: 38857343 DOI: 10.1086/730186] [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] [Indexed: 06/12/2024]
Abstract
AbstractLocal adaptation frequently evolves in patches or environments that are connected via migration. In these cases, genomic regions that are linked to a locally adapted locus experience reduced effective migration rates. Via individual-based simulations of a two-patch system, we show that this reduced effective migration results in the accumulation of conditionally deleterious mutations, but not universally deleterious mutations, adjacent to adaptive loci. When there is redundancy in the genetic basis of local adaptation (i.e., genotypic redundancy), turnover of locally adapted polymorphisms allows conditionally deleterious mutation load to be purged. The amount of mutational load that accumulates adjacent to locally adapted loci is dependent on redundancy, recombination rate, migration rate, population size, strength of selection, and the phenotypic effect size of adaptive alleles. Our results highlight the need to be cautious when interpreting patterns of local adaptation at the level of phenotype or fitness, as the genetic basis of local adaptation can be transient, and evolution may confer a degree of maladaptation to nonlocal environments.
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Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1408-1426. [PMID: 38578160 DOI: 10.1111/jipb.13653] [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: 09/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.
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Affiliation(s)
- Tianhao Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjing Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuyifu Chen
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yuanyuan Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guo-Feng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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5
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Song X, Zhu G, Su X, Yu Y, Duan Y, Wang H, Shang X, Xu H, Chen Q, Guo W. Combined genome and transcriptome analysis of elite fiber quality in Gossypium barbadense. PLANT PHYSIOLOGY 2024; 195:2158-2175. [PMID: 38513701 DOI: 10.1093/plphys/kiae175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Gossypium barbadense, which is one of several species of cotton, is well known for its superior fiber quality. However, the genetic basis of its high-quality fiber remains largely unexplored. Here, we resequenced 269 G. barbadense accessions. Phylogenetic structure analysis showed that the set of accessions was clustered into 3 groups: G1 and G2 mainly included modern cultivars from Xinjiang, China, and G3 was related to widely introduced accessions in different regions worldwide. A genome-wide association study of 5 fiber quality traits across multiple field environments identified a total of 512 qtls (main-effect QTLs) and 94 qtlEs (QTL-by-environment interactions) related to fiber quality, of which 292 qtls and 57 qtlEs colocated with previous studies. We extracted the genes located in these loci and performed expression comparison, local association analysis, and introgression segment identification. The results showed that high expression of hormone-related genes during fiber development, introgressions from Gossypium hirsutum, and the recombination of domesticated elite allelic variation were 3 major contributors to improve the fiber quality of G. barbadense. In total, 839 candidate genes with encoding region variations associated with elite fiber quality were mined. We confirmed that haplotype GB_D03G0092H traced to G. hirsutum introgression, with a 1-bp deletion leading to a frameshift mutation compared with GB_D03G0092B, significantly improved fiber quality. GB_D03G0092H is localized in the plasma membrane, while GB_D03G0092B is in both the nucleus and plasma membrane. Overexpression of GB_D03G0092H in Arabidopsis (Arabidopsis thaliana) significantly improved the elongation of longitudinal cells. Our study systematically reveals the genetic basis of the superior fiber quality of G. barbadense and provides elite segments and gene resources for breeding high-quality cotton cultivars.
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Affiliation(s)
- Xiaohui Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiujuan Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yujia Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujia Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Haitang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijiang Xu
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China
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Ahrens CW, Murray K, Mazanec RA, Ferguson S, Jones A, Tissue DT, Byrne M, Borevitz JO, Rymer PD. Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla. BMC Genomics 2024; 25:640. [PMID: 38937661 PMCID: PMC11209971 DOI: 10.1186/s12864-024-10531-8] [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: 09/15/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. RESULTS We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. CONCLUSIONS Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
- Cesar Australia, Brunswick, VIC, 3058, Australia.
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Richard A Mazanec
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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7
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Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, Yant L. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat Commun 2024; 15:5377. [PMID: 38918389 PMCID: PMC11199601 DOI: 10.1038/s41467-024-49679-y] [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: 10/08/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
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Affiliation(s)
- Tuomas Hämälä
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland.
| | | | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Carlile
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
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Dorey T, Frachon L, Rieseberg LH, Kreiner JM, Schiestl FP. Biotic interactions promote local adaptation to soil in plants. Nat Commun 2024; 15:5186. [PMID: 38890322 PMCID: PMC11189560 DOI: 10.1038/s41467-024-49383-x] [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: 09/01/2023] [Accepted: 05/30/2024] [Indexed: 06/20/2024] Open
Abstract
Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing Brassica rapa plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the "number of open flowers", a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy.
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Affiliation(s)
- Thomas Dorey
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Léa Frachon
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland.
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Vangestel C, Swaegers J, De Corte Z, Dekoninck W, Gharbi K, Gillespie R, Vandekerckhove M, Van Belleghem SM, Hendrickx F. Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles. SCIENCE ADVANCES 2024; 10:eadk7906. [PMID: 38820159 PMCID: PMC11141621 DOI: 10.1126/sciadv.adk7906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we study a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of Calosoma beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities.
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Affiliation(s)
- Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Janne Swaegers
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Zoë De Corte
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, United Kingdom
| | - Rosemary Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Vandekerckhove
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Steven M. Van Belleghem
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
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10
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Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [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: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
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Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
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11
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Nosil P, de Carvalho CF, Villoutreix R, Zamorano LS, Sinclair-Waters M, Planidin NP, Parchman TL, Feder J, Gompert Z. Evolution repeats itself in replicate long-term studies in the wild. SCIENCE ADVANCES 2024; 10:eadl3149. [PMID: 38787954 PMCID: PMC11122682 DOI: 10.1126/sciadv.adl3149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
The extent to which evolution is repeatable remains debated. Here, we study changes over time in the frequency of cryptic color-pattern morphs in 10 replicate long-term field studies of a stick insect, each spanning at least a decade (across 30 years of total data). We find predictable "up-and-down" fluctuations in stripe frequency in all populations, representing repeatable evolutionary dynamics based on standing genetic variation. A field experiment demonstrates that these fluctuations involve negative frequency-dependent natural selection (NFDS). These fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they can reliably move back toward it via NFDS. Last, we show that the origin of new cryptic forms is associated with multiple structural genomic variants such that which mutations arise affects evolution at larger temporal scales. Thus, evolution from existing variation is predictable and repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection.
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Affiliation(s)
- Patrik Nosil
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Laura S. Zamorano
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | | | - Jeffrey Feder
- Department of Biology, Notre Dame University, South Bend, IN 11111, USA
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA
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12
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Han Z, Si Z, Rahman MU, He L, Li Y, Khan AQ, Mao Y, Zulfiqar S, Ishfaq S, Mohsan M, Iqbal MA, Zafar S, Hu Y, Zhang T. Genomic insights into local adaptation of upland cotton in China and Pakistan. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:136. [PMID: 38764078 DOI: 10.1007/s00122-024-04624-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/14/2024] [Indexed: 05/21/2024]
Abstract
KEY MESSAGE Different kinship and resistance to cotton leaf curl disease (CLCuD) and heat were found between upland cotton cultivars from China and Pakistan. 175 SNPs and 82 InDels loci related to yield, fiber quality, CLCuD, and heat resistance were identified. Elite alleles found in Pakistani accessions aided local adaptation to climatic condition of two countries. Adaptation of upland cotton (Gossypium hirsutum) beyond its center of origin is expected to be driven by tailoring of the genome and genes to enhance yield and quality in new ecological niches. Here, resequencing of 456 upland cotton accessions revealed two distinct kinships according to the associated country. Fiber quality and lint percentage were consistent across kinships, but resistance to cotton leaf curl disease (CLCuD) and heat was distinctly exhibited by accessions from Pakistan, illustrating highly local adaption. A total of 175 SNP and 82 InDel loci related to yield, fiber quality, CLCuD and heat resistance were identified; among them, only two overlapped between Pakistani and Chinese accessions underscoring the divergent domestication and improvement targets in each country. Loci associated with resistance alleles to leaf curl disease and high temperature were largely found in Pakistani accessions to counter these stresses prevalent in Pakistan. These results revealed that breeding activities led to the accumulation of unique alleles and helped upland cotton become adapted to the respective climatic conditions, which will contribute to elucidating the genetic mechanisms that underlie resilience traits and help develop climate-resilient cotton cultivars for use worldwide.
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Affiliation(s)
- Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mehboob-Ur Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Lu He
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ali Qaiser Khan
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Yun Mao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Shumila Ishfaq
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Mohsan
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Atif Iqbal
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Saba Zafar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences, (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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13
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Bock DG, Baeckens S, Kolbe JJ, Losos JB. When adaptation is slowed down: Genomic analysis of evolutionary stasis in thermal tolerance during biological invasion in a novel climate. Mol Ecol 2024; 33:e17075. [PMID: 37489260 DOI: 10.1111/mec.17075] [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: 01/30/2023] [Revised: 06/25/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023]
Abstract
Research conducted during the past two decades has demonstrated that biological invasions are excellent models of rapid evolution. Even so, characteristics of invasive populations such as a short time for recombination to assemble optimal combinations of alleles may occasionally limit adaptation to new environments. Here, we investigated such genetic constraints to adaptation in the invasive brown anole (Anolis sagrei)-a tropical ectotherm that was introduced to the southeastern United States, a region with a much colder climate than in its native Caribbean range. We examined thermal physiology for 30 invasive populations and tested for a climatic cline in cold tolerance. Also, we used genomics to identify mechanisms that may limit adaptation. We found no support for a climatic cline, indicating that thermal tolerance did not shift adaptively. Concomitantly, population genomic results were consistent with the occurrence of recombination cold spots that comprise more than half of the genome and maintain long-range associations among alleles in invasive populations. These genomic regions overlap with both candidate thermal tolerance loci that we identified using a standard genome-wide association test. Moreover, we found that recombination cold spots do not have a large contribution to population differentiation in the invasive range, contrary to observations in the native range. We suggest that limited recombination is constraining the contribution of large swaths of the genome to adaptation in invasive brown anoles. Our study provides an example of evolutionary stasis during invasion and highlights the possibility that reduced recombination occasionally slows down adaptation in invasive populations.
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Affiliation(s)
- Dan G Bock
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Simon Baeckens
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Evolution and Optics of Nanostructures Lab, Department of Biology, Ghent University, Ghent, Belgium
- Functional Morphology Lab, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Jonathan B Losos
- Department of Biology, Washington University, St. Louis, Missouri, USA
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14
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Justen HC, Easton WE, Delmore KE. Mapping seasonal migration in a songbird hybrid zone -- heritability, genetic correlations, and genomic patterns linked to speciation. Proc Natl Acad Sci U S A 2024; 121:e2313442121. [PMID: 38648483 PMCID: PMC11067064 DOI: 10.1073/pnas.2313442121] [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: 08/06/2023] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Seasonal migration is a widespread behavior relevant for adaptation and speciation, yet knowledge of its genetic basis is limited. We leveraged advances in tracking and sequencing technologies to bridge this gap in a well-characterized hybrid zone between songbirds that differ in migratory behavior. Migration requires the coordinated action of many traits, including orientation, timing, and wing morphology. We used genetic mapping to show these traits are highly heritable and genetically correlated, explaining how migration has evolved so rapidly in the past and suggesting future responses to climate change may be possible. Many of these traits mapped to the same genomic regions and small structural variants indicating the same, or tightly linked, genes underlie them. Analyses integrating transcriptomic data indicate cholinergic receptors could control multiple traits. Furthermore, analyses integrating genomic differentiation further suggested genes underlying migratory traits help maintain reproductive isolation in this hybrid zone.
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Affiliation(s)
- Hannah C. Justen
- Biology Department, Texas Agricultural and Mechanical University, TAMUCollege Station, TX3528
| | - Wendy E. Easton
- Environment and Climate Change Canada, Canadian Wildlife Service-Pacific Region, Delta, BCV4K 3N2, Canada
| | - Kira E. Delmore
- Biology Department, Texas Agricultural and Mechanical University, TAMUCollege Station, TX3528
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15
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Temme AA, Kerr KL, Nolting KM, Dittmar EL, Masalia RR, Bucksch AK, Burke JM, Donovan LA. The genomic basis of nitrogen utilization efficiency and trait plasticity to improve nutrient stress tolerance in cultivated sunflower. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2527-2544. [PMID: 38270266 DOI: 10.1093/jxb/erae025] [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: 12/12/2022] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
Maintaining crop productivity is challenging as population growth, climate change, and increasing fertilizer costs necessitate expanding crop production to poorer lands whilst reducing inputs. Enhancing crops' nutrient use efficiency is thus an important goal, but requires a better understanding of related traits and their genetic basis. We investigated variation in low nutrient stress tolerance in a diverse panel of cultivated sunflower genotypes grown under high and low nutrient conditions, assessing relative growth rate (RGR) as performance. We assessed variation in traits related to nitrogen utilization efficiency (NUtE), mass allocation, and leaf elemental content. Across genotypes, nutrient limitation generally reduced RGR. Moreover, there was a negative correlation between vigor (RGR in control) and decline in RGR in response to stress. Given this trade-off, we focused on nutrient stress tolerance independent of vigor. This tolerance metric correlated with the change in NUtE, plasticity for a suite of morphological traits, and leaf element content. Genome-wide associations revealed regions associated with variation and plasticity in multiple traits, including two regions with seemingly additive effects on NUtE change. Our results demonstrate potential avenues for improving sunflower nutrient stress tolerance independent of vigor, and highlight specific traits and genomic regions that could play a role in enhancing tolerance.
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Affiliation(s)
- Andries A Temme
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Plant Breeding, Wageningen University & Research, 6700 HB Wageningen, The Netherlands
| | - Kelly L Kerr
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kristen M Nolting
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily L Dittmar
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Rishi R Masalia
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Lisa A Donovan
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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16
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Sacchi B, Humphries Z, Kružlicová J, Bodláková M, Pyne C, Choudhury BI, Gong Y, Bačovský V, Hobza R, Barrett SCH, Wright SI. Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus. Mol Biol Evol 2024; 41:msae074. [PMID: 38606901 PMCID: PMC11057207 DOI: 10.1093/molbev/msae074] [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: 10/06/2023] [Revised: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10 MYA) and neo (<200,000 yr) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup Rumex salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 Mb) and two Y chromosomes (503 Mb) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo-sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.
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Affiliation(s)
- Bianca Sacchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Jana Kružlicová
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Cassandre Pyne
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Department of Biology, Queen’s University, Kingston, Canada
| | - Yunchen Gong
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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17
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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18
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Exciting times for evolutionary biology. Nat Ecol Evol 2024; 8:593-594. [PMID: 38605230 DOI: 10.1038/s41559-024-02402-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
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19
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He W, He H, Yuan Q, Zhang H, Li X, Wang T, Yang Y, Yang L, Yang Y, Liu X, Wei H, Zhang H, Zhang B, Guo M, Leng Y, Shi C, Lv Y, Chen W, Wang X, Zhang Z, Yu B, Zhang B, Xu Q, Qian H, Zhou Y, Wang S, Qian Q, Shang L. Widespread inversions shape the genetic and phenotypic diversity in rice. Sci Bull (Beijing) 2024; 69:593-596. [PMID: 38233278 DOI: 10.1016/j.scib.2023.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/19/2024]
Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hai Zhang
- School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Tianyi Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yingxue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Longbo Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuting Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingliang Guo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yue Leng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yang Lv
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wu Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xianmeng Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhipeng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bohui Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bintao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qiang Xu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongge Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shaokui Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Yazhouwan National Laboratory, Sanya 572024, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Yazhouwan National Laboratory, Sanya 572024, China.
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20
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Nosil P, Gompert Z, Funk DJ. Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species. Nat Commun 2024; 15:2273. [PMID: 38480699 PMCID: PMC10937975 DOI: 10.1038/s41467-024-46294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in fits and bursts, rather than being uniform and gradual. We show in Timema stick insects that one component of reproductive isolation evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum, and thus exhibits similar dynamics to morphological traits not implicated in reproductive isolation. The results show different evolutionary dynamics for different components of reproductive isolation and highlight a special relevance for species status in the process of speciation.
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Affiliation(s)
- Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Daniel J Funk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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21
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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579721. [PMID: 38496530 PMCID: PMC10942266 DOI: 10.1101/2024.02.10.579721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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22
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Ma LJ, Cao LJ, Chen JC, Tang MQ, Song W, Yang FY, Shen XJ, Ren YJ, Yang Q, Li H, Hoffmann AA, Wei SJ. Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect. Mol Biol Evol 2024; 41:msae044. [PMID: 38401527 PMCID: PMC10924284 DOI: 10.1093/molbev/msae044] [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: 10/25/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.
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Affiliation(s)
- Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Meng-Qing Tang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fang-Yuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ya-Jing Ren
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiong Yang
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ary Anthony Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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23
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Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [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: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
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24
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Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
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25
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Innes PA, Goebl AM, Smith CCR, Rosenberger K, Kane NC. Gene expression and alternative splicing contribute to adaptive divergence of ecotypes. Heredity (Edinb) 2024; 132:120-132. [PMID: 38071268 PMCID: PMC10924094 DOI: 10.1038/s41437-023-00665-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 03/10/2024] Open
Abstract
Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.
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Affiliation(s)
- Peter A Innes
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA.
| | - April M Goebl
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
- Research and Conservation Department, Denver Botanic Gardens, Denver, CO, USA
| | - Chris C R Smith
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Kaylee Rosenberger
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
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26
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Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
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Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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27
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Goebl AM, Kane NC, Doak DF, Rieseberg LH, Ostevik KL. Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes. Mol Ecol 2024; 33:e16785. [PMID: 36374153 DOI: 10.1111/mec.16785] [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: 07/12/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth (λ > 1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes.
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Affiliation(s)
- April M Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniel F Doak
- Environmental Studies Programme, University of Colorado, Boulder, Colorado, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, USA
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28
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Mantel SJ, Sweigart AL. Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species. Mol Ecol 2024; 33:e17261. [PMID: 38174628 PMCID: PMC10922885 DOI: 10.1111/mec.17261] [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: 09/27/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
The evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in naturally hybridizing species are not well understood. Here, we explore these issues using genetic mapping in three independent populations of recombinant inbred lines between naturally hybridizing monkeyflowers, Mimulus guttatus and Mimulus nasutus, from the sympatric Catherine Creek population. We discover that the three M. guttatus founders differ dramatically in admixture history, with nearly a quarter of one founder's genome introgressed from M. nasutus. Comparative genetic mapping in the three RIL populations reveals three new putative inversions, each one segregating among the M. guttatus founders, two due to admixture. We find strong, genome-wide transmission ratio distortion in all RILs, but patterns are highly variable among the three populations. At least some of this distortion appears to be explained by epistatic selection favouring parental genotypes, but tests of inter-chromosomal linkage disequilibrium also reveal multiple candidate Dobzhansky-Muller incompatibilities. We also map several genetic loci for hybrid pollen viability, including two interacting pairs that coincide with peaks of distortion. Remarkably, even with this limited sample of three M. guttatus lines, we discover abundant segregating variation for hybrid incompatibilities with M. nasutus, suggesting this population harbours diverse contributors to postzygotic isolation. Moreover, even with substantial admixture, hybrid incompatibilities between Mimulus species persist, suggesting postzygotic isolation might be a potent force in maintaining species barriers in this system.
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Affiliation(s)
- Samuel J. Mantel
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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29
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James ME, Ortiz-Barrientos D. The genomic consequences of selection across development. Mol Ecol 2024; 33:e17280. [PMID: 38247305 DOI: 10.1111/mec.17280] [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: 09/25/2023] [Revised: 01/01/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Understanding how natural selection drives diversification in nature has been at the forefront of biological research for over a century. The main idea is simple: natural selection favours individuals best suited to pass on their genes. However, the journey from birth to reproduction is complex as organisms experience multiple developmental stages, each influenced by genetic and environmental factors (Orr, 2009). These complexities compound even further as each stage of development might be governed by a unique underlying set of alleles and genes. In this issue of Molecular Ecology, Goebl et al. (2022) examine the role of natural selection in driving ecotypic divergence across different life history stages of the prairie sunflower Helianthus petiolaris. The authors used reciprocal transplant experiments, demographic models, and genomic sequencing to explore fitness variation across developmental stages. They show how natural selection impacts population divergence across multiple life history stages and evaluate the resulting allele frequency changes. Goebl et al. link these results to the role of chromosomal inversions, thus furthering our understanding of how ecological divergence proceeds in the face of gene flow. Below, we explore these results in detail and complement their interpretation by considering the evolution of genetic correlations amongst traits governing fitness.
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Affiliation(s)
- Maddie E James
- School of the Environment, The University of Queensland, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, The University of Queensland, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD, Australia
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30
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Li Y, Li X, Nie S, Zhang M, Yang Q, Xu W, Duan Y, Wang X. Reticulate evolution of the tertiary relict Osmanthus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:145-160. [PMID: 37837261 DOI: 10.1111/tpj.16480] [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: 02/07/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.
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Affiliation(s)
- Yongfu Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qinghua Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Wenbin Xu
- Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yifan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xianrong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Soudi S, Jahani M, Todesco M, Owens GL, Bercovich N, Rieseberg LH, Yeaman S. Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion. eLife 2023; 12:RP88604. [PMID: 38095362 PMCID: PMC10721221 DOI: 10.7554/elife.88604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.
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Affiliation(s)
- Shaghayegh Soudi
- Department of Biological Sciences, University of CalgaryCalgaryCanada
| | - Mojtaba Jahani
- Department of Biological Sciences, University of CalgaryCalgaryCanada
- Department of Botany, University of British ColumbiaVancouverCanada
| | - Marco Todesco
- Department of Botany, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
- Irving K. Barber Faculty of Science, University of British Columbia OkanaganKelownaCanada
| | | | | | | | - Sam Yeaman
- Department of Biological Sciences, University of CalgaryCalgaryCanada
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Wong ELY, Filatov DA. Pericentromeric recombination suppression and the 'large X effect' in plants. Sci Rep 2023; 13:21682. [PMID: 38066067 PMCID: PMC10709461 DOI: 10.1038/s41598-023-48870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
X chromosome was reported to be a major contributor to isolation between closely related species-the 'large X' effect (LXE). The causes of LXE are not clear, but the leading theory is that it is caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. However, the LXE was also reported in species with relatively recently evolved sex chromosomes where Y chromosome is not completely degenerate and X-linked genes are not hemizygous, such as the plant Silene latifolia. Recent genome sequencing and detailed genetic mapping in this species revealed a massive (> 330 Mb) non- or rarely-recombining pericentromeric region on the X chromosome (Xpr) that comprises ~ 90% of the chromosome and over 13% of the entire genome. If any of the Xpr genes are involved in species incompatibilities, this would oppose interspecific gene flow for other genes tightly linked in the Xpr. Here we test the hypothesis that the previously reported LXE in S. latifolia is caused by the lack of recombination on most of the X chromosome. Based on genome-wide analysis of DNA polymorphism and gene expression in S. latifolia and its close cross-compatible relative S. dioica, we report that the rarely-recombining regions represent a significant barrier for interspecific gene flow. We found little evidence for any additional factors contributing to the LXE, suggesting that extensive pericentromeric recombination suppression on the X-chromosome is the major if not the only cause of the LXE in S. latifolia and S. dioica.
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Affiliation(s)
- Edgar L Y Wong
- Department of Biology, University of Oxford, Oxford, UK
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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Wang N, Li Y, Meng Q, Chen M, Wu M, Zhang R, Xu Z, Sun J, Zhang X, Nie X, Yuan D, Lin Z. Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense. J Adv Res 2023; 54:15-27. [PMID: 36775017 DOI: 10.1016/j.jare.2023.02.002] [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: 11/07/2022] [Revised: 01/10/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
INTRODUCTION Sea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare. OBJECTIVES We aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton. METHODS Through genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3-79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton. RESULTS One reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian. CONCLUSION Our study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.
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Affiliation(s)
- Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Yuanxue Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Meilin Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Mi Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhiyong Xu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
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Dallaire X, Bouchard R, Hénault P, Ulmo-Diaz G, Normandeau E, Mérot C, Bernatchez L, Moore JS. Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication. Genome Biol Evol 2023; 15:evad229. [PMID: 38085037 PMCID: PMC10752349 DOI: 10.1093/gbe/evad229] [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] [Accepted: 11/30/2023] [Indexed: 12/28/2023] Open
Abstract
Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.
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Affiliation(s)
- Xavier Dallaire
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Centre d'Études Nordiques, Université Laval, Québec, Canada
| | - Raphael Bouchard
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Philippe Hénault
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Gabriela Ulmo-Diaz
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Eric Normandeau
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
- Plateforme de bio-informatique de l’IBIS, Université Laval, Québec, Canada
| | - Claire Mérot
- CNRS, UMR 6553 ECOBIO, Université de Rennes, Rennes, France
| | - Louis Bernatchez
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Jean-Sébastien Moore
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Centre d'Études Nordiques, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [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] [Indexed: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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Pinsky ML, Clark RD, Bos JT. Coral Reef Population Genomics in an Age of Global Change. Annu Rev Genet 2023; 57:87-115. [PMID: 37384733 DOI: 10.1146/annurev-genet-022123-102748] [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] [Indexed: 07/01/2023]
Abstract
Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.
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Affiliation(s)
- Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA;
| | - René D Clark
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - Jaelyn T Bos
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
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Busoms S, Fischer S, Yant L. Chasing the mechanisms of ecologically adaptive salinity tolerance. PLANT COMMUNICATIONS 2023; 4:100571. [PMID: 36883005 PMCID: PMC10721451 DOI: 10.1016/j.xplc.2023.100571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona E-08193, Spain
| | - Sina Fischer
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
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Feng S, Xi E, Wan W, Ru D. Genomic signals of local adaptation in Picea crassifolia. BMC PLANT BIOLOGY 2023; 23:534. [PMID: 37919677 PMCID: PMC10623705 DOI: 10.1186/s12870-023-04539-7] [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: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. RESULTS Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. CONCLUSIONS Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Dutta A, McDonald BA, Croll D. Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011801. [PMID: 37972199 PMCID: PMC10688896 DOI: 10.1371/journal.ppat.1011801] [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: 05/10/2023] [Revised: 11/30/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.
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Affiliation(s)
- Anik Dutta
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- 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
| | - Lingfeng Miao
- 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
| | - 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
| | - 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
| | - 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.
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Dowell JA, Mason C. Candidate pathway association and genome-wide association approaches reveal alternative genetic architectures of carotenoid content in cultivated sunflower ( Helianthus annuus). APPLICATIONS IN PLANT SCIENCES 2023; 11:e11558. [PMID: 38106540 PMCID: PMC10719882 DOI: 10.1002/aps3.11558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/10/2023] [Accepted: 05/19/2023] [Indexed: 12/19/2023]
Abstract
Premise The explosion of available genomic data poses significant opportunities and challenges for genome-wide association studies. Current approaches via linear mixed models (LMM) are straightforward but prevent flexible assumptions of an a priori genomic architecture, while Bayesian sparse LMMs (BSLMMs) allow this flexibility. Complex traits, such as specialized metabolites, are subject to various hierarchical effects, including gene regulation, enzyme efficiency, and the availability of reactants. Methods To identify alternative genetic architectures, we examined the genetic architecture underlying the carotenoid content of an association mapping panel of Helianthus annuus individuals using multiple BSLMM and LMM frameworks. Results The LMMs of genome-wide single-nucleotide polymorphisms (SNPs) identified a single transcription factor responsible for the observed variations in the carotenoid content; however, a BSLMM of the SNPs with the bottom 1% of effect sizes from the results of the LMM identified multiple biologically relevant quantitative trait loci (QTLs) for carotenoid content external to the known (annotated) carotenoid pathway. A candidate pathway analysis (CPA) suggested a β-carotene isomerase to be the enzyme with the highest impact on the observed carotenoid content within the carotenoid pathway. Discussion While traditional LMM approaches suggested a single unknown transcription factor associated with carotenoid content variation in sunflower petals, BSLMM proposed several QTLs with interpretable biological relevance to this trait. In addition, the CPA allowed for the dissection of the regulatory vs. biosynthetic genetic architectures underlying this metabolic trait.
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Affiliation(s)
- Jordan A. Dowell
- Department of Plant SciencesUniversity of CaliforniaDavisCalifornia95616USA
- Present address:
Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana70803USA
| | - Chase Mason
- Department of BiologyUniversity of Central FloridaOrlandoFlorida32816USA
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Pichler V, Sanou A, Love RR, Caputo B, Pombi M, Toe KH, Guelbeogo MW, Sagnon N, Ferguson HM, Ranson H, Torre AD, Besansky NJ. A novel tetra-primer ARMS-PCR approach for the molecular karyotyping of chromosomal inversion 2Ru in the main malaria vectors Anopheles gambiae and Anopheles coluzzii. Parasit Vectors 2023; 16:388. [PMID: 37891582 PMCID: PMC10605393 DOI: 10.1186/s13071-023-06014-6] [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: 07/31/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Chromosomal inversion polymorphisms have been associated with adaptive behavioral, physiological, morphological and life history traits in the two main Afrotropical malaria vectors, Anopheles coluzzii and Anopheles gambiae. The understanding of the adaptive value of chromosomal inversion systems is constrained by the feasibility of cytological karyotyping. In recent years in silico and molecular approaches have been developed for the genotyping of most widespread inversions (2La, 2Rb and 2Rc). The 2Ru inversion, spanning roughly 8% of chromosome 2R, is commonly polymorphic in West African populations of An. coluzzii and An. gambiae and shows clear increases in frequency with increasing rainfall seasonally and geographically. The aim of this work was to overcome the constraints of currently available cytological and high-throughput molecular assays by developing a simple PCR assay for genotyping the 2Ru inversion in individual specimens of both mosquito species. METHODS We designed tetra-primer amplification refractory mutation system (ARMS)-PCR assays based on five tag single-nucleotide polymorphisms (SNPs) previously shown to be strongly correlated with 2Ru inversion orientation. The most promising assay was validated against laboratory and field samples of An. coluzzii and An. gambiae karyotyped either cytogenetically or molecularly using a genotyping-in-thousands by sequencing (GT-seq) high-throughput approach that employs targeted sequencing of multiplexed PCR amplicons. RESULTS A successful assay was designed based on the tag SNP at position 2R, 31710303, which is highly predictive of the 2Ru genotype. The assay, which requires only one PCR, and no additional post-PCR processing other than electrophoresis, produced a clear banding pattern for 98.5% of the 454 specimens tested, which is a 96.7% agreement with established karyotyping methods. Sequences were obtained for nine of the An. coluzzii specimens manifesting 2Ru genotype discrepancies with GT-seq. Possible sources of these discordances are discussed. CONCLUSIONS The tetra-primer ARMS-PCR assay represents an accurate, streamlined and cost-effective method for the molecular karyotyping of the 2Ru inversion in An. coluzzii and An. gambiae. Together with approaches already available for the other common polymorphic inversions, 2La, 2Rb and 2Rc, this assay will allow investigations of the adaptive value of the complex set of inversion systems observed in the two major malaria vectors in the Afrotropical region.
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Affiliation(s)
- Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy.
| | - Antoine Sanou
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
- Institute of Biodiversity, Animal Health & Comparative Medicine, Glasgow University, Glasgow, G128QQ, UK
| | - R Rebecca Love
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
- Entomology Branch, Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30333, USA
| | - Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy
| | - Kobie Hyacinth Toe
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
| | - Moussa W Guelbeogo
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health & Comparative Medicine, Glasgow University, Glasgow, G128QQ, UK
| | - Hilary Ranson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy
| | - Nora J Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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44
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James ME, Allsopp RN, Groh JS, Kaur A, Wilkinson MJ, Ortiz-Barrientos D. Uncovering the genetic architecture of parallel evolution. Mol Ecol 2023; 32:5575-5589. [PMID: 37740681 DOI: 10.1111/mec.17134] [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: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/25/2023]
Abstract
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin N Allsopp
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Avneet Kaur
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
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45
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [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: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Lv R, Gou X, Li N, Zhang Z, Wang C, Wang R, Wang B, Yang C, Gong L, Zhang H, Liu B. Chromosome translocation affects multiple phenotypes, causes genome-wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1564-1582. [PMID: 37265000 DOI: 10.1111/tpj.16338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated in polyploids allowing their longer-term retention and hence potential spreading/fixation within a lineage. The direct functional consequences of CRs in plant polyploids remain unexplored. Here, we identified a heterozygous individual from a synthetic allohexaploid wheat in which the terminal parts of the long-arms of chromosomes 2D (approximately 193 Mb) and 4A (approximately 167 Mb) were reciprocally translocated. Five homogeneous translocation lines including both unbalanced and balanced types were developed by selfing fertilization of the founder mutant (RT [2DL; 4AL]-ter/1, reciprocal translocation). We investigated impacts of these translocations on phenotype, genome-wide gene expression and metabolome. We find that, compared with sibling wild-type, CRs in the form of both unbalanced and balanced translocations induced substantial changes of gene expression primarily via trans-regulation in the nascent allopolyploid wheat. The CRs also manifested clear phenotypic and metabolic consequences. In particular, the genetically balanced, stable reciprocal translocations lines showed immediate enhanced reproductive fitness relative to wild type. Our results underscore the profound impact of CRs on gene expression in nascent allopolyploids with wide-ranging phenotypic and metabolic consequences, suggesting CRs are an important source of genetic variation that can be exploited for crop breeding.
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Affiliation(s)
- Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Changyi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Jing CY, Zhang FM, Wang XH, Wang MX, Zhou L, Cai Z, Han JD, Geng MF, Yu WH, Jiao ZH, Huang L, Liu R, Zheng XM, Meng QL, Ren NN, Zhang HX, Du YS, Wang X, Qiang CG, Zou XH, Gaut BS, Ge S. Multiple domestications of Asian rice. NATURE PLANTS 2023; 9:1221-1235. [PMID: 37550371 DOI: 10.1038/s41477-023-01476-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
Abstract
The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.
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Affiliation(s)
- Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing-Dan Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Xiang Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Wong ELY, Filatov DA. The role of recombination landscape in species hybridisation and speciation. FRONTIERS IN PLANT SCIENCE 2023; 14:1223148. [PMID: 37484464 PMCID: PMC10361763 DOI: 10.3389/fpls.2023.1223148] [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: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
It is now well recognised that closely related species can hybridize and exchange genetic material, which may promote or oppose adaptation and speciation. In some cases, interspecific hybridisation is very common, making it surprising that species identity is preserved despite active gene exchange. The genomes of most eukaryotic species are highly heterogeneous with regard to gene density, abundance of repetitive DNA, chromatin compactisation etc, which can make certain genomic regions more prone or more resistant to introgression of genetic material from other species. Heterogeneity in local recombination rate underpins many of the observed patterns across the genome (e.g. actively recombining regions are typically gene rich and depleted for repetitive DNA) and it can strongly affect the permeability of genomic regions to interspecific introgression. The larger the region lacking recombination, the higher the chance for the presence of species incompatibility gene(s) in that region, making the entire non- or rarely recombining block impermeable to interspecific introgression. Large plant genomes tend to have highly heterogeneous recombination landscape, with recombination frequently occurring at the ends of the chromosomes and central regions lacking recombination. In this paper we review the relationship between recombination and introgression in plants and argue that large rarely recombining regions likely play a major role in preserving species identity in actively hybridising plant species.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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Makarenko MS, Azarin KV, Gavrilova VA. Mitogenomic Research of Silverleaf Sunflower ( Helianthus argophyllus) and Its Interspecific Hybrids. Curr Issues Mol Biol 2023; 45:4841-4849. [PMID: 37367057 DOI: 10.3390/cimb45060308] [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: 03/22/2023] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Interspecific hybridization is widespread for sunflowers, both in wild populations and commercial breeding. One of the most common species that can efficiently cross with Helianthus annuus is the Silverleaf sunflower-Helianthus argophyllus. The current study carried out structural and functional organization analyses of mitochondrial DNA in H. argophyllus and the interspecific hybrid, H. annuus (VIR114A line) × H. argophyllus. The complete mitogenome of H. argophyllus counts 300,843 bp, has a similar organization to the mitogenome of cultivated sunflower, and holds SNPs typical for wild sunflowers. RNA editing analysis predicted 484 sites in H. argophyllus mitochondrial CDS. The mitochondrial genome of the H. annuus × H. argophyllus hybrid is identical to the maternal line (VIR114A). We expected that significant rearrangements in the mitochondrial DNA of the hybrid would occur, due to the frequent recombination. However, the hybrid mitogenome lacks rearrangements, presumably due to the preservation of nuclear-cytoplasmic interaction paths.
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Affiliation(s)
- Maksim S Makarenko
- The Laboratory of Plant Genomics, The Institute for Information Transmission Problems, 127051 Moscow, Russia
| | - Kirill V Azarin
- The Laboratory of Molecular Genetics, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Vera A Gavrilova
- Oil and Fiber Crops Genetic Resources Department, The N.I. Vavilov All Russian Institute of Plant Genetic Resources, 190031 Saint Petersburg, Russia
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