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She H, Liu Z, Xu Z, Zhang H, Wu J, Wang X, Cheng F, Charlesworth D, Qian W. Genome sequence of the wild species, Spinacia tetrandra, including a phased sequence of the extensive sex-linked region, revealing partial degeneration in evolutionary strata with unusual properties. THE NEW PHYTOLOGIST 2025; 246:2765-2781. [PMID: 40281666 DOI: 10.1111/nph.70165] [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: 10/10/2024] [Accepted: 04/04/2025] [Indexed: 04/29/2025]
Abstract
Genetic degeneration is a striking feature of Y chromosomes, often involving losses of many genes carried on the X chromosome. However, the time course of gene losses remains unclear. Sex chromosomes of plants evolved more recently than animals' highly degenerated ones, making them ideal for studying degeneration timing. To investigate Spinacia sex chromosome evolution and the time course of degeneration, we compared genome sequences of cultivated Spinacia oleracea, with a small Y-linked region on Chr4, with its two wild relatives. In spinach and its closest relative Spinacia turkestanica, the Y duplication region (YDR) introduced a male-determining factor into Chr4's low-recombining pericentromeric region. In other words, a turnover event occurred in these species' recent common ancestor. The homologous Chr4 of the more distantly related S. tetrandra has a c. 133 Mb completely sex-linked and partially degenerated region, possibly reflecting the ancestral state. Sequence divergence analysis suggests that two 'evolutionary strata' evolved shortly before the two Spinacia lineages split. Consistent with the turnover hypothesis, the YDR of the other two Spinacia species is not within the S. tetrandra older stratum. We discuss the unexpected findings in S. tetrandra that genetic degeneration, genomic rearrangements, and repetitive sequence density are all greatest in the younger stratum.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, 453519, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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2
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Lee C, Epstein L, Kaur S, Henry PM, Postma-Haarsma AD, Monroe JG, Van Deynze A. A well-annotated genome of Apium graveolens var. dulce cv. Challenger, a celery with resistance to Fusarium oxysporum f. sp. apii race 2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 122:e70251. [PMID: 40489902 DOI: 10.1111/tpj.70251] [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: 03/06/2025] [Revised: 05/07/2025] [Accepted: 05/19/2025] [Indexed: 06/11/2025]
Abstract
Celery (Apium graveolens var. dulce) production can be limited by the fungal pathogen Fusarium oxysporum f. sp. apii (Foa), particularly at temperatures above 22°C. Because celery has a narrow genetic base, an intraspecific admixture of Apium graveolens was developed into cv. Challenger, which is resistant to Foa race 2, the causal agent of Fusarium yellows, but susceptible to Foa race 4, a relatively unrelated causal agent of Fusarium wilt. We assembled a high-quality, chromosome-level physical map of Challenger with 40 464 RNA-based, protein-coding gene models in 3.3 Gbp and anchored it with a genetic map. Although there is high gene density and higher recombination at the ends of the chromosomes, an average of 56% of the genes/chromosome are in lower recombination zones (<0.025 cM/Mb). We identified Challenger's nucleotide-binding and leucine-rich repeat receptors (NLRs) and pattern recognition receptors (PRRs), the two gene families that encode most resistance (R) genes. In three treatment groups (mock-infested or infested with either Foa race 2 or race 4), 243 NLRs and 445 PRRs were quantified in the celery crowns via Quant-Seq 3' mRNA-Seq (Tag-Seq). We compared the genomes of Challenger with that of the previously published cv. Ventura, which is moderately susceptible to Foa race 2. We present a toolbox for genome-assisted breeding for celery that includes annotated gene models, a protocol for genotype-by-sequencing, documentation of the expression of NLRs and PRRs, and a straightforward strategy for introgressing selected NLR superclusters, 83% of which are in higher recombination regions.
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Affiliation(s)
- Chaehee Lee
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Sukhwinder Kaur
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Peter M Henry
- United States Department of Agriculture, Agricultural Research Service, 1636 E. Alisal St, Salinas, California, 93905, USA
| | | | - J Grey Monroe
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
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3
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Vi T, Le TN, Cubry P, Phan VH, Dinh TTO, Tran TBN, Nguyen VT, Millet CP, Kambale JL, Karine GKM, Musoli P, Sumirat U, Mahinga JC, Stoffelen P, Zhang D, Marraccini P, Vigouroux Y, Khong NG, Poncet V. Out of Africa: The genomic footprints of Vietnamese Robusta coffee. PLoS One 2025; 20:e0324988. [PMID: 40435003 PMCID: PMC12118859 DOI: 10.1371/journal.pone.0324988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Accepted: 04/28/2025] [Indexed: 06/01/2025] Open
Abstract
Vietnam is the main producer of Robusta (Coffea canephora) coffee, but faces several future agronomic challenges. These may be addressed through breeding for improved cultivars and more sustainable cropping systems. For such efforts to be successful and efficient, locally available genetic resources must be understood. Indeed, while C. canephora exhibits high genetic diversity in its native tropical African forests, only a part of it contributed to the worldwide diffusion of Robusta. Here we traced the African origins of Robusta accessions cultivated in the Central Highlands of Vietnam. A total of 126 Robusta accessions from the Vietnam coffee germplasm collection were characterized, including historical, elite and local cultivated clones. Their genetic diversity and origins were inferred through comparisons with wild reference samples using a new set of 261 genome-wide SNPs. A core set of 45 accessions that maximize the genetic distance and allelic richness were identified for conservation and breeding priorities. Full genome sequencing of these individuals helped to closely trace the origins of chromosomal segments back to different, geographically-structured wild African genetic groups. All Vietnamese Robusta accessions displayed Congo Basin (ER group) origins, albeit to various extents. However, we also uncovered contribution from several other genetic groups, variously from the Guinean region (D), the central African Atlantic coast (AG), and Eastern CAR/Uganda (OB), in 31 hybrid individuals. These source groups have been widely used in crossbreeding to develop elite clones. In addition, using whole-genome sequencing data, we also identified various admixture patterns at the chromosome level among the hybrids, which might provide valuable information for selecting breeding materials.
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Affiliation(s)
- Tram Vi
- UMR DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
- National Key Laboratory for Plant Cellular Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Thi Nhu Le
- National Key Laboratory for Plant Cellular Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Philippe Cubry
- UMR DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
| | - Viet Ha Phan
- Western Highlands Agriculture & Forestry Science Institute (WASI), Buon Ma Thuot, Vietnam
| | - Thi Tieu Oanh Dinh
- Western Highlands Agriculture & Forestry Science Institute (WASI), Buon Ma Thuot, Vietnam
| | - Thi Bich Ngoc Tran
- Western Highlands Agriculture & Forestry Science Institute (WASI), Buon Ma Thuot, Vietnam
| | - Van Toan Nguyen
- National Key Laboratory for Plant Cellular Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Pascal Musoli
- National Agricultural Research Organization (NARO), Mukono, Uganda
| | - Ucu Sumirat
- Starbucks Farmer Support Center, North Sumatra, Indonesia
| | | | | | - Dapeng Zhang
- USDA-ARS, SPCL, Beltsville, Maryland, United States of America
| | - Pierre Marraccini
- UMR DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
- CIRAD, Montpellier, France
| | - Yves Vigouroux
- UMR DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
| | - Ngan Giang Khong
- National Key Laboratory for Plant Cellular Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Valerie Poncet
- UMR DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
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4
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Postel Z, Martin H, Roux C, Godé C, Genete M, Schmitt É, Monnet F, Vekemans X, Touzet P. Genetic Isolation among Four Lineages of Silene nutans. PLANT & CELL PHYSIOLOGY 2025; 66:514-528. [PMID: 39324423 PMCID: PMC12085096 DOI: 10.1093/pcp/pcae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 09/12/2024] [Accepted: 09/24/2024] [Indexed: 09/27/2024]
Abstract
Speciation is the process leading to the emergence of new species. While being usually progressive, it can sometimes be fast with rapid emergence of reproductive barriers leading to high level of reproductive isolation. Some reproductive barriers might leave signatures in the genome, through elevated level of genetic differentiation at specific loci. Similar signatures might also be the results of linked selection acting in low recombination regions. Nottingham catchfly (Silene nutans) is a Caryophyllaceae species composed of four genetically differentiated lineages for which strong and asymmetric levels of reproductive isolation have been identified. Using population transcriptomic data from several individuals of the four lineages, we inferred the best evo-demographic scenario leading to the current reproductive isolation of these four lineages. We also tested whether loci exhibiting high level of genetic differentiation represented barrier loci or were located in low recombination regions, evolving under strong influence of linked selection. Overall, the four lineages of S. nutans have diverged in strict isolation, likely during the different glacial period, through migration in distinct glacial refugia. Speciation between these four lineages appeared to be particularly fast, likely due to fast evolving plastid genome accelerating plastid-nuclear co-evolution and the probability of plastid-nuclear incompatibilities in inter-lineage hybrids.
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Affiliation(s)
- Zoé Postel
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Hélène Martin
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Camille Roux
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Cécile Godé
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Mathieu Genete
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Éric Schmitt
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - François Monnet
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Xavier Vekemans
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
| | - Pascal Touzet
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille F-59000, France
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5
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Bursell M, Rohilla M, Ramirez L, Cheng Y, Schwarzkopf EJ, Guerrero RF, Smukowski Heil C. Mixed Outcomes in Recombination Rates After Domestication: Revisiting Theory and Data. Mol Ecol 2025:e17773. [PMID: 40271548 DOI: 10.1111/mec.17773] [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: 07/01/2024] [Revised: 04/07/2025] [Accepted: 04/14/2025] [Indexed: 04/25/2025]
Abstract
The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesised to indirectly select for increases in the genome-wide recombination rate. This hypothesis is potentially consistent with theory on the evolution of the recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilise population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domesticated goats compared to bezoars but more mixed results in chicken and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in genome-wide recombination with domestication.
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Affiliation(s)
- Madeline Bursell
- Department of Plant Pathology and Entomology, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Manav Rohilla
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Lucia Ramirez
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Yuhuan Cheng
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Enrique J Schwarzkopf
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Rafael F Guerrero
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
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6
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Pelé A, Falque M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Martin OC, Chèvre AM, Rousseau-Gueutin M. Genomic Divergence Shaped the Genetic Regulation of Meiotic Homologous Recombination in Brassica Allopolyploids. Mol Biol Evol 2025; 42:msaf073. [PMID: 40173423 PMCID: PMC11982612 DOI: 10.1093/molbev/msaf073] [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: 12/21/2024] [Revised: 03/05/2025] [Accepted: 03/06/2025] [Indexed: 04/04/2025] Open
Abstract
The tight regulation of meiotic recombination between homologs is disrupted in Brassica AAC allotriploids, a genomic configuration that may have facilitated the formation of rapeseed (Brassica napus L.) ∼7,500 years ago. Indeed, the presence of the haploid C genome induces supernumerary crossovers between homologous A chromosomes with dramatically reshaped distribution. However, the genetic mechanisms driving this phenomenon and their divergence between nascent and established lineages remain unclear. To address these concerns, we generated hybrids carrying additional C chromosomes derived either from an established lineage of the allotetraploid B. napus or from its diploid progenitor B. oleracea. We then assessed recombination variation across twelve populations by mapping male meiotic crossovers using single nucleotide polymorphism markers evenly distributed across the sequenced A genome. Our findings reveal that the C09 chromosome of B. oleracea is responsible for the formation of additional crossovers near pericentromeric regions. Interestingly, its counterpart from an established lineage of B. napus shows no significant effect on its own, despite having a similar content of meiotic genes. However, we showed that the B. napus C09 chromosome influences crossover formation through inter-chromosomal epistatic interactions with other specific C chromosomes. These results provide new insights into the genetic regulation of homologous recombination in Brassica and emphasize the role of genomic divergence since the formation of the allopolyploid B. napus.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poznan 61-614, Poland
| | - Matthieu Falque
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | | | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
| | - Olivier C Martin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette 91190, France
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7
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Brekke C, Gjuvsland AB, Berg P, Johnston SE. Independent genetic basis of meiotic crossover positioning and interference in domestic pigs. Sci Rep 2025; 15:9260. [PMID: 40102600 PMCID: PMC11920276 DOI: 10.1038/s41598-025-93003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 03/04/2025] [Indexed: 03/20/2025] Open
Abstract
Meiotic crossover patterning shows huge variation within and between chromosomes, individuals, and species, yet the molecular and evolutionary causes and consequences of this variation remain poorly understood. A key step is to understand the genetic architecture of the crossover rate, positioning, and interference to determine if these factors are governed by common or distinct genetic processes. Here, we investigate individual variation in autosomal crossover count, crossover position (measured as both intra-chromosomal shuffling and distance to telomere), and crossover interference in a large breeding population of domestic pigs (N = 82,474 gametes). We show that all traits are heritable in females at the gamete (h2 = 0.07-0.11) and individual mean levels (h2 = 0.08-0.41). In females, crossover count, and interference are strongly associated with RNF212, but crossover positioning is associated with SYCP2, MEI4, and PRDM9. Our results show that crossover positioning and rate/interference are driven by distinct genetic processes in female pigs and have the capacity to evolve independently.
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Affiliation(s)
- Cathrine Brekke
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, Ås, 1433, Norway.
| | - Arne B Gjuvsland
- Norsvin, Storhamargata 44, Hamar, 2317, Norway
- Geno, Storhamargata 44, Hamar, 2317, Norway
| | - Peer Berg
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, Ås, 1433, Norway
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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8
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Malinsky M, Talbi M, Zhou C, Maurer N, Sacco S, Shapiro B, Peichel CL, Seehausen O, Salzburger W, Weber JN, Bolnick DI, Green RE, Durbin R. Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.06.641907. [PMID: 40161681 PMCID: PMC11952307 DOI: 10.1101/2025.03.06.641907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Recombination is central to genetics and to evolution of sexually reproducing organisms. However, obtaining accurate estimates of recombination rates, and of how they vary along chromosomes, continues to be challenging. To advance our ability to estimate recombination rates, we present Hi-reComb, a new method and software for estimation of recombination maps from bulk gamete chromosome conformation capture sequencing (Hi-C). Simulations show that Hi-reComb produces robust, accurate recombination landscapes. With empirical data from sperm of five fish species we show the advantages of this approach, including joint assessment of recombination maps and large structural variants, map comparisons using bootstrap, and workflows with trio phasing vs. Hi-C phasing. With off-the-shelf library construction and a straightforward rapid workflow, our approach will facilitate routine recombination landscape estimation for a broad range of studies and model organisms in genetics and evolutionary biology. Hi-reComb is open-source and freely available at https://github.com/millanek/Hi-reComb.
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Affiliation(s)
- Milan Malinsky
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Marion Talbi
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Chenxi Zhou
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Nicholas Maurer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Samuel Sacco
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Beth Shapiro
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Walter Salzburger
- Department of Environmental Sciences, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Jesse N. Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
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9
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Booker WW, Schrider DR. Recombination and the role of pseudo-overdominance in polyploid evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.28.640841. [PMID: 40093174 PMCID: PMC11908147 DOI: 10.1101/2025.02.28.640841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Natural selection is an imperfect force that can under some conditions fail to prevent the buildup of deleterious mutations. Small population sizes and the lack of recombination are two such scenarios that reduce the efficiency of selection. Under these conditions, the disconnect between deleterious genetic load and individual fitness due to the masking of recessive deleterious mutations in heterozygous individuals may result in the emergence of pseudo-overdominance, wherein the buildup of haplotypes with complementary sets of deleterious mutations results in apparent heterozygote advantage and an increase in linked neutral diversity. In polyploids, the presence of additional allelic copies magnifies this masking effect and may therefore increase the probability of pseudo-overdominance. Here, we simulate the evolution of small diploid and autotetraploid populations to identify the conditions that support the evolution of pseudo-overdominance. We discover that pseudo-overdominance evolves under a much wider range of parameters in autotetraploids than in diploids with identical population sizes, and that in many parts of parameter space there is an inverse relationship between fitness and recombination rate. These results imply that pseudo-overdominance may be more common than previously thought. We conclude by discussing the current evidence for pseudo-overdominance in species with polyploid histories, as well as its implications in agriculture due to the prevalence of polyploidy in crops.
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Affiliation(s)
- William W Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27514-2916, United States of America
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27514-2916, United States of America
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10
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Talbi M, Turner GF, Malinsky M. Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko. Evolution 2025; 79:364-379. [PMID: 39589917 DOI: 10.1093/evolut/qpae169] [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: 04/30/2024] [Revised: 11/06/2024] [Accepted: 11/25/2024] [Indexed: 11/28/2024]
Abstract
Variation of recombination rate along the genome is of crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how and why recombination landscapes evolve in nature. Here, we reconstruct recombination maps based on linkage disequilibrium and use subsampling and simulations to derive a new measure of recombination landscape evolution: the Population Recombination Divergence Index (PRDI). Using PRDI, we show that fine-scale recombination landscapes differ substantially between two cichlid fish ecotypes of Astatotilapia calliptera that diverged only ~2,500 generations ago. Perhaps surprisingly, recombination landscape differences are not driven by divergence in terms of allele frequency (FST) and nucleotide diversity (Δ(π)): although there is some association, we observe positive PRDI in regions where FST and Δ(π) are zero. We found a stronger association between the evolution of recombination and 47 large haplotype blocks that are polymorphic in Lake Masoko, cover 21% of the genome, and appear to include multiple inversions. Among haplotype blocks, there is a strong and clear association between the degree of recombination divergence and differences between ecotypes in heterozygosity, consistent with recombination suppression in heterozygotes. Overall, our work provides a holistic view of changes in population recombination landscapes during the early stages of speciation with gene flow.
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Affiliation(s)
- Marion Talbi
- Biology Department, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland
| | - George F Turner
- School of Natural & Environmental Sciences, Bangor University, Bangor, United Kingdom
| | - Milan Malinsky
- Biology Department, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland
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11
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Steckenborn S, Marques A. Centromere diversity and its evolutionary impacts on plant karyotypes and plant reproduction. THE NEW PHYTOLOGIST 2025; 245:1879-1886. [PMID: 39763092 PMCID: PMC11798908 DOI: 10.1111/nph.20376] [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: 07/31/2024] [Accepted: 12/11/2024] [Indexed: 02/07/2025]
Abstract
Karyotype changes are a formidable evolutionary force by directly impacting cross-incompatibility, gene dosage, genetic linkage, chromosome segregation, and meiotic recombination landscape. These changes often arise spontaneously and are commonly detected within plant lineages, even between closely related accessions. One element that can influence drastic karyotype changes after only one (or few) plant generations is the alteration of the centromere position, number, distribution, or even its strength. Here, we briefly explore how these different centromere configurations can directly result in karyotype rearrangements, impacting plant reproduction and meiotic recombination.
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Affiliation(s)
- Stefan Steckenborn
- Department of Chromosome BiologyMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829CologneGermany
| | - André Marques
- Department of Chromosome BiologyMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829CologneGermany
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12
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Stack GM, Quade MA, Wilkerson DG, Monserrate LA, Bentz PC, Carey SB, Grimwood J, Toth JA, Crawford S, Harkess A, Smart LB. Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies. Int J Mol Sci 2025; 26:1165. [PMID: 39940933 PMCID: PMC11818205 DOI: 10.3390/ijms26031165] [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: 11/20/2024] [Revised: 01/20/2025] [Accepted: 01/27/2025] [Indexed: 02/16/2025] Open
Abstract
Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a k-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among Cannabis sativa genotypes. We leveraged linkage maps constructed from F2 progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts.
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Affiliation(s)
- George M. Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Michael A. Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Dustin G. Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Luis A. Monserrate
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Philip C. Bentz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Sarah B. Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Jacob A. Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | | | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
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13
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Topaloudis A, Cumer T, Lavanchy E, Ducrest AL, Simon C, Machado AP, Paposhvili N, Roulin A, Goudet J. The recombination landscape of the barn owl, from families to populations. Genetics 2025; 229:1-50. [PMID: 39545468 PMCID: PMC11708917 DOI: 10.1093/genetics/iyae190] [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: 07/26/2024] [Accepted: 11/01/2024] [Indexed: 11/17/2024] Open
Abstract
Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and limited data. Frequently used approaches include linkage mapping based on familial data that provides sex-specific broad-scale estimates of realized recombination and inferences based on population linkage disequilibrium that reveal a more fine-scale resolution of the recombination landscape, albeit dependent on the effective population size and the selective forces acting on the population. In this study, we use a combination of these 2 methods to elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). We find subtle differences in crossover placement between sexes that lead to differential effective shuffling of alleles. Linkage disequilibrium-based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates, while smaller chromosomes have a universally high rate that shapes the diversity landscape. We find that recombination rates are correlated with gene content, genetic diversity, and GC content. We find no conclusive differences in the recombination landscapes between populations. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics.
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Affiliation(s)
- Alexandros Topaloudis
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Eléonore Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Anne-Lyse Ducrest
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Celine Simon
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Nika Paposhvili
- Institute of Ecology, Ilia State University, Tbilisi 0162, Georgia
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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14
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Parée T, Noble L, Roze D, Teotónio H. Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation. Mol Biol Evol 2025; 42:msae273. [PMID: 39776196 PMCID: PMC11739800 DOI: 10.1093/molbev/msae273] [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: 10/26/2024] [Revised: 12/05/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
Modifiers of recombination rates have been described but the selective pressures acting on them and their effect on adaptation to novel environments remain unclear. We performed experimental evolution in the nematode Caenorhabditis elegans using alternative rec-1 alleles modifying the position of meiotic crossovers along chromosomes without detectable direct fitness effects. We show that adaptation to a novel environment is impaired by the allele that decreases recombination rates in the genomic regions containing fitness variation. However, the allele that impairs adaptation is indirectly favored by selection, because it increases recombination rates and reduces the associations among beneficial and deleterious variation located in its chromosomal vicinity. These results validate theoretical expectations about the evolution of recombination but suggest that genome-wide polygenic adaptation is of little consequence to indirect selection on recombination rate modifiers.
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Affiliation(s)
- Tom Parée
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, Paris 75005, France
- Department of Biology, New York University, New York, NY 10003, USA
| | - Luke Noble
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, Paris 75005, France
- EnviroDNA, 95 Albert St Brunswick, Melbourne, Victoria 3065, Australia
| | - Denis Roze
- Adaptation et Diversité en Milieu Marin CNRS UMR 7144, Station Biologique de Roscoff, Sorbonne University, Roscoff 29688, France
| | - Henrique Teotónio
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, Paris 75005, France
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15
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Rafiei N, Ronceret A. The plant early recombinosome: a high security complex to break DNA during meiosis. PLANT REPRODUCTION 2024; 37:421-440. [PMID: 39331138 PMCID: PMC11511760 DOI: 10.1007/s00497-024-00509-7] [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: 08/17/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
KEY MESSAGE The formacion of numerous unpredictable DNA Double Strand Breaks (DSBs) on chromosomes iniciates meiotic recombination. In this perspective, we propose a 'multi-key lock' model to secure the risky but necesary breaks as well as a 'one per pair of cromatids' model for the topoisomerase-like early recombinosome. During meiosis, homologous chromosomes recombine at few sites of crossing-overs (COs) to ensure correct segregation. The initiation of meiotic recombination involves the formation of DNA double strand breaks (DSBs) during prophase I. Too many DSBs are dangerous for genome integrity: if these DSBs are not properly repaired, it could potentially lead to chromosomal fragmentation. Too few DSBs are also problematic: if the obligate CO cannot form between bivalents, catastrophic unequal segregation of univalents lead to the formation of sterile aneuploid spores. Research on the regulation of the formation of these necessary but risky DSBs has recently advanced in yeast, mammals and plants. DNA DSBs are created by the enzymatic activity of the early recombinosome, a topoisomerase-like complex containing SPO11. This opinion paper reviews recent insights on the regulation of the SPO11 cofactors necessary for the introduction of temporally and spatially controlled DSBs. We propose that a 'multi-key-lock' model for each subunit of the early recombinosome complex is required to secure the formation of DSBs. We also discuss the hypothetical implications that the established topoisomerase-like nature of the SPO11 core-complex can have in creating DSB in only one of the two replicated chromatids of early prophase I meiotic chromosomes. This hypothetical 'one per pair of chromatids' DSB formation model could optimize the faithful repair of the self-inflicted DSBs. Each DSB could use three potential intact homologous DNA sequences as repair template: one from the sister chromatid and the two others from the homologous chromosomes.
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Affiliation(s)
- Nahid Rafiei
- Department of Plant Molecular Biology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Arnaud Ronceret
- Department of Plant Molecular Biology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México.
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16
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Abdollahi Sisi N, Herzog E, Abbadi A, Snowdon RJ, Golicz AA. Analysis of the winter oilseed rape recombination landscape suggests maternal-paternal bias. Genome 2024; 67:445-453. [PMID: 39431738 DOI: 10.1139/gen-2023-0110] [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: 10/22/2024]
Abstract
Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers between homologous chromosomes generate new combinations of alleles and maintain genetic diversity. Due to genetic, epigenetic, and environmental factors, the recombination landscape is highly heterogeneous along the chromosomes and it also differs between populations and between sexes. Here, we investigated recombination characteristics across the 19 chromosomes of the model allopolyploid crop species oilseed rape (Brassica napus L.), using two unique multiparental populations derived from two genetically divergent founder pools, each of which comprised 50 genetically diverse founder accessions. A fully balanced, pairwise chain-crossing scheme was utilized to create each of the two populations. A total of 3213 individuals, spanning five successive generations, were genotyped using a 15K SNP array. We observed uneven distribution of recombination along chromosomes, with some genomic regions undergoing substantially more frequent recombination in both populations. In both populations, maternal recombination events were more frequent than paternal recombination. This study provides unique insight into the recombination landscape at chromosomal level and reveals a maternal-paternal bias for recombination number with implications for breeding.
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Affiliation(s)
- Nayyer Abdollahi Sisi
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392 Giessen, Germany
| | - Eva Herzog
- Department of Biometry and Population Genetics, Justus Liebig University, Giessen, 35392 Giessen, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392 Giessen, Germany
| | - Agnieszka A Golicz
- Department of Agrobioinformatics, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392 Giessen, Germany
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17
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Burgarella C, Brémaud MF, Von Hirschheydt G, Viader V, Ardisson M, Santoni S, Ranwez V, de Navascués M, David J, Glémin S. Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives. Evol Lett 2024; 8:866-880. [PMID: 39677571 PMCID: PMC11637685 DOI: 10.1093/evlett/qrae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/07/2024] [Accepted: 08/03/2024] [Indexed: 12/17/2024] Open
Abstract
How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome-wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used the Aegilops/Triticum grass species, a group characterized by contrasted mating systems (from obligate outcrossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome-wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and, more generally, for our understanding of the fundamental drivers of genetic diversity.
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Affiliation(s)
- Concetta Burgarella
- CNRS, Univ. Montpellier, ISEM – UMR 5554, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Department of Organismal Biology, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Marie-Fleur Brémaud
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Veronique Viader
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Morgane Ardisson
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sylvain Santoni
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Vincent Ranwez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Miguel de Navascués
- UMR CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jacques David
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sylvain Glémin
- CNRS, Univ. Rennes, ECOBIO – UMR 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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18
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Morgan AP, Payseur BA. Genetic background affects the strength of crossover interference in house mice. Genetics 2024; 228:iyae146. [PMID: 39241112 PMCID: PMC11538424 DOI: 10.1093/genetics/iyae146] [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: 07/29/2024] [Accepted: 08/22/2024] [Indexed: 09/08/2024] Open
Abstract
Meiotic recombination is required for faithful chromosome segregation in most sexually reproducing organisms and shapes the distribution of genetic variation in populations. Both the overall rate and the spatial distribution of crossovers vary within and between species. Adjacent crossovers on the same chromosome tend to be spaced more evenly than expected at random, a phenomenon known as crossover interference. Although interference has been observed in many taxa, the factors that influence the strength of interference are not well understood. We used house mice (Mus musculus), a well-established model system for understanding recombination, to study the effects of genetics and age on recombination rate and interference in the male germline. We analyzed crossover positions in 503 progeny from reciprocal F1 hybrids between inbred strains representing the three major subspecies of house mice. Consistent with previous studies, autosomal alleles from M. m. musculus tend to increase recombination rate, while inheriting a M. m. musculus X chromosome decreases recombination rate. Old males transmit an average of 0.6 more crossovers per meiosis (5.0%) than young males, though the effect varies across genetic backgrounds. We show that the strength of crossover interference depends on genotype, providing a rare demonstration that interference evolves over short timescales. Differences between reciprocal F1s suggest that X-linked factors modulate the strength of interference. Our findings motivate additional comparisons of interference among recently diverged species and further examination of the role of paternal age in determining the number and positioning of crossovers.
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Affiliation(s)
- Andrew P Morgan
- Department of Medicine, University of North Carolina, Campus Box #7085, Chapel Hill, NC 27599-7085, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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19
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Sakamoto T, Whiting JR, Yeaman S. Mutation potentiates migration swamping in polygenic local adaptation. Genetics 2024; 228:iyae165. [PMID: 39395190 PMCID: PMC11631501 DOI: 10.1093/genetics/iyae165] [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: 06/17/2024] [Accepted: 10/10/2024] [Indexed: 10/14/2024] Open
Abstract
Locally adapted traits can exhibit a wide range of genetic architectures, from pronounced divergence at a few loci to small frequency divergence at many loci. The type of architecture that evolves depends strongly on the migration rate, as weakly selected loci experience swamping and do not make lasting contributions to divergence. Simulations from previous studies showed that even when mutations are strongly selected and should resist migration swamping, the architecture of adaptation can collapse and become transient at high mutation rates. Here, we use an analytical two-population model to study how this transition in genetic architecture depends upon population size, strength of selection, and parameters describing the mutation process. To do this, we develop a mathematical theory based on the diffusion approximation to predict the threshold mutation rate above which the transition occurs. We find that this performs well across a wide range of parameter space, based on comparisons with individual-based simulations. The threshold mutation rate depends most strongly on the average effect size of mutations, weakly on the strength of selection, and marginally on the population size. Across a wide range of the parameter space, we observe that the transition to a transient architecture occurs when the trait-wide mutation rate is 10-3-10-2, suggesting that this phenomenon is potentially relevant to complex traits with a large mutational target. On the other hand, based on the apparent stability of genetic architecture in many classic examples of local adaptation, our theory suggests that per-trait mutation rates are often relatively low.
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Affiliation(s)
- Takahiro Sakamoto
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
- National Institute of Genetics 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
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20
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Boideau F, Huteau V, Maillet L, Brunet A, Coriton O, Deniot G, Trotoux G, Taburel-Lodé M, Eber F, Gilet M, Baron C, Boutte J, Richard G, Aury JM, Belser C, Labadie K, Morice J, Falentin C, Martin O, Falque M, Chèvre AM, Rousseau-Gueutin M. Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres. THE PLANT CELL 2024; 36:4472-4490. [PMID: 39121028 PMCID: PMC11449113 DOI: 10.1093/plcell/koae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/12/2024] [Indexed: 08/11/2024]
Abstract
Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Anael Brunet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | | | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Cécile Baron
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Julien Boutte
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, 91057 Evry, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Olivier Martin
- Institute of Plant Sciences Paris-Saclay, Université de Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, 91192 Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, 91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, 91190 Gif-sur-Yvette, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
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21
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Oyundelger K, Großmann L, Herklotz V, Harpke D, Batlai O, Wesche K, Ritz C. Relationship Between Genetic and Phenotypic Variations in Natural Populations of Perennial and Biennial Sagebrush. Ecol Evol 2024; 14:e70419. [PMID: 39429795 PMCID: PMC11486663 DOI: 10.1002/ece3.70419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 09/17/2024] [Accepted: 09/23/2024] [Indexed: 10/22/2024] Open
Abstract
Plant responses to environmental heterogeneity depend on life-history traits, which could relate to phenotypical and genetic characteristics. To elucidate this relationship, we examined the variation in population genetics and functional traits of short- and long-lived Artemisia species that are co-occurring in the steppes of Mongolia. Mongolian steppes represent stressful and water-limited habitats, demanding phenotypic modifications in the short term and/or genetic adaptation in the long term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation, and their interrelationships in temperate grasslands. Here, we investigated 21 populations of the widely distributed subshrub Artemisia frigida and the herbaceous biennial Artemisia scoparia. Genetic variation was assessed with newly developed simple sequence repeats (SSRs) markers. Functional trait data were collected from each individual, and data on environmental variables was collected for each population. We detected significantly higher genetic diversity in the biennial species (H E = 0.86) compared with the perennial (H E = 0.79). For both species, the largest share of genetic variation was partitioned within populations (96%). Population genetic structure in the biennial A. scoparia was weak, while the perennial A. frigida showed some spatial genetic structure, which was impacted by geographical factors, soil nutrients, and precipitation amount. Morphology-related functional traits (i.e., plant height) were predominantly associated with environmental variables rather than with genetic variation, whereas physiology-related trait (i.e., specific leaf area [SLA]) was partly genetically determined.
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Affiliation(s)
| | - Lisa Großmann
- General Botany, Insitute of Biochemistry and Biology, University of PotsdamPotsdamGermany
| | - Veit Herklotz
- Department of BotanySenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Dörte Harpke
- Leibniz Institute of Plant Genetics and Crop Plant ResearchSeelandGermany
| | - Oyuntsetseg Batlai
- Department of Biology, School of Arts and SciencesNational University of MongoliaUlaanbaatarMongolia
| | - Karsten Wesche
- Department of BotanySenckenberg Museum of Natural History GörlitzGörlitzGermany
- Chair of Biodiversity of Higher Plants, International Institute ZittauTechnische Universität DresdenZittauGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Christiane M. Ritz
- Department of BotanySenckenberg Museum of Natural History GörlitzGörlitzGermany
- Chair of Biodiversity of Higher Plants, International Institute ZittauTechnische Universität DresdenZittauGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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22
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Brazier T, Glémin S. Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes. Mol Biol Evol 2024; 41:msae183. [PMID: 39302634 DOI: 10.1093/molbev/msae183] [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: 06/27/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024] Open
Abstract
During the meiosis of many eukaryote species, crossovers tend to occur within narrow regions called recombination hotspots. In plants, it is generally thought that gene regulatory sequences, especially promoters and 5' to 3' untranslated regions, are enriched in hotspots, but this has been characterized in a handful of species only. We also lack a clear description of fine-scale variation in recombination rates within genic regions and little is known about hotspot position and intensity in plants. To address this question, we constructed fine-scale recombination maps from genetic polymorphism data and inferred recombination hotspots in 11 plant species. We detected gradients of recombination in genic regions in most species, yet gradients varied in intensity and shape depending on specific hotspot locations and gene structure. To further characterize recombination gradients, we decomposed them according to gene structure by rank and number of exons. We generalized the previously observed pattern that recombination hotspots are organized around the boundaries of coding sequences, especially 5' promoters. However, our results also provided new insight into the relative importance of the 3' end of genes in some species and the possible location of hotspots away from genic regions in some species. Variation among species seemed driven more by hotspot location among and within genes than by differences in size or intensity among species. Our results shed light on the variation in recombination rates at a very fine scale, revealing the diversity and complexity of genic recombination gradients emerging from the interaction between hotspot location and gene structure.
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Affiliation(s)
- Thomas Brazier
- Unité Mixte de Recherche (UMR) 6553 - ECOBIO (Ecosystems, Biodiversity, Evolution), University of Rennes, CNRS, Rennes, France
| | - Sylvain Glémin
- Unité Mixte de Recherche (UMR) 6553 - ECOBIO (Ecosystems, Biodiversity, Evolution), University of Rennes, CNRS, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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23
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Morgan AP, Payseur BA. Genetic background affects the strength of crossover interference in house mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596233. [PMID: 38854148 PMCID: PMC11160618 DOI: 10.1101/2024.05.28.596233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Meiotic recombination is required for faithful chromosome segregation in most sexually reproducing organisms and shapes the distribution of genetic variation in populations. Both the overall rate and the spatial distribution of crossovers vary within and between species. Adjacent crossovers on the same chromosome tend to be spaced more evenly than expected at random, a phenomenon known as crossover interference. Although interference has been observed in many taxa, the factors that influence the strength of interference are not well understood. We used house mice (Mus musculus), a well-established model system for understanding recombination, to study the effects of genetics and age on recombination rate and interference in the male germline. We analyzed crossover positions in 503 progeny from reciprocal F1 hybrids between inbred strains representing the three major subspecies of house mice. Consistent with previous studies, autosomal alleles from M. m. musculus tend to increase recombination rate, while inheriting a M. m. musculus X chromosome decreases recombination rate. Old males transmit an average of 0.6 more crossovers per meiosis (5.0%) than young males, though the effect varies across genetic backgrounds. We show that the strength of crossover interference depends on genotype, providing a rare demonstration that interference evolves over short timescales. Differences between reciprocal F1s suggest that X-linked factors modulate the strength of interference. Our findings motivate additional comparisons of interference among recently diverged species and further examination of the role of paternal age in determining the number and positioning of crossovers.
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Affiliation(s)
- Andrew P Morgan
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
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24
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Johnston SE. Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future. Mol Biol Evol 2024; 41:msae112. [PMID: 38959451 PMCID: PMC11221659 DOI: 10.1093/molbev/msae112] [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: 04/17/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/05/2024] Open
Abstract
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms of recombination are remarkably conserved across eukaryotes, yet meiotic genes and proteins show substantial variation in their sequence and function, even between closely related species. Furthermore, the rate and distribution of recombination shows a huge diversity within and between chromosomes, individuals, sexes, populations, and species. This variation has implications for many molecular and evolutionary processes, yet how and why this diversity has evolved is not well understood. A key step in understanding trait evolution is to determine its genetic basis-that is, the number, effect sizes, and distribution of loci underpinning variation. In this perspective, I discuss past and current knowledge on the genetic basis of variation in recombination rate and distribution, explore its evolutionary implications, and present open questions for future research.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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25
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She H, Liu Z, Xu Z, Zhang H, Wu J, Wang X, Cheng F, Charlesworth D, Qian W. Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra. THE NEW PHYTOLOGIST 2024; 243:477-494. [PMID: 38715078 DOI: 10.1111/nph.19799] [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: 02/12/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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26
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Kawaguchi K, Ohki T, Ishikawa G, Sayama M, Terasawa Y, Oda S, Fujita M, Ito M, Hatta K. Identification of a major QTL conferring resistance to wheat yellow mosaic virus derived from the winter wheat 'Hokkai 240' on chromosome 2AS. BREEDING SCIENCE 2024; 74:232-239. [PMID: 39555005 PMCID: PMC11561412 DOI: 10.1270/jsbbs.23079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/04/2024] [Indexed: 11/19/2024]
Abstract
Wheat yellow mosaic disease is a soilborne disease caused by wheat yellow mosaic virus (WYMV). Symptoms include yellow mosaic coloring of leaves, stunting, and growth inhibition. Here we conducted a detailed analysis of resistance to this virus in winter wheat 'Hokkai 240' by carrying out inoculation tests of WYMV and conducting field tests. The resistance level observed in 'Hokkai 240' was compared with those in varieties harboring known resistance genes. In the inoculation tests, 'Hokkai 240' showed resistance to WYMV Pathotypes I and II and partial resistance to Pathotype III. This result was contrary to the sensitive responses to the three pathotypes exhibited by the variety harboring resistance gene on chromosome 2DL. In fields infected with WYMV Pathotypes II and III, 'Hokkai 240' plants exhibited few disease symptoms and little proliferation of the virus. By analyzing the quantitative trait loci (QTLs) in recombinant inbred lines from a cross between 'Hokkai 240' and 'Nanbukomugi', a single major QTL, Q.Ymhk, from 'Hokkai 240', which had significant effects on Pathotypes II and III of the virus, was detected in the proximity of snp4212 and snp4215 mapped on chromosome 2AS. These results indicate that Q.Ymhk may be useful for developing broad resistance to WYMV in wheat breeding programs.
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Affiliation(s)
- Kenji Kawaguchi
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido 082-0081, Japan
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Takehiro Ohki
- NARO Hokkaido Agricultural Research Center, Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Goro Ishikawa
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| | - Mitsuru Sayama
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido 082-0081, Japan
| | - Yohei Terasawa
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido 082-0081, Japan
| | - Shunsuke Oda
- NARO Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Masaya Fujita
- NARO Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Miwako Ito
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido 082-0081, Japan
| | - Koichi Hatta
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido 082-0081, Japan
- NARO Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
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27
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Hockens C, Lorenzi H, Wang TT, Lei EP, Rosin LF. Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species. PLoS Genet 2024; 20:e1011329. [PMID: 38913752 PMCID: PMC11226059 DOI: 10.1371/journal.pgen.1011329] [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: 10/13/2023] [Revised: 07/05/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events such as homolog pairing and chromosome segregation are not fully understood in many species. Here, we employ Oligopaint DNA FISH to investigate mechanisms of meiotic homolog pairing and chromosome segregation in the holocentric pantry moth, Plodia interpunctella, and compare our findings to new and previous studies in the silkworm moth, Bombyx mori, which diverged from P. interpunctella over 100 million years ago. We find that pairing in both Bombyx and Plodia spermatogenesis is initiated at gene-rich chromosome ends. Additionally, both species form rod shaped cruciform-like bivalents at metaphase I. However, unlike the telomere-oriented chromosome segregation mechanism observed in Bombyx, Plodia can orient bivalents in multiple different ways at metaphase I. Surprisingly, in both species we find that kinetochores consistently assemble at non-telomeric loci toward the center of chromosomes regardless of where chromosome centers are located in the bivalent. Additionally, sister kinetochores do not seem to be paired in these species. Instead, four distinct kinetochores are easily observed at metaphase I. Despite this, we find clear end-on microtubule attachments and not lateral microtubule attachments co-orienting these separated kinetochores. These findings challenge the classical view of segregation where paired, poleward-facing kinetochores are required for accurate homolog separation in meiosis I. Our studies here highlight the importance of exploring fundamental processes in non-model systems, as employing novel organisms can lead to the discovery of novel biology.
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Affiliation(s)
- Clio Hockens
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hernan Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tricia T. Wang
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leah F. Rosin
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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28
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Charlesworth D, Harkess A. Why should we study plant sex chromosomes? THE PLANT CELL 2024; 36:1242-1256. [PMID: 38163640 PMCID: PMC11062472 DOI: 10.1093/plcell/koad278] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/10/2023] [Indexed: 01/03/2024]
Abstract
Understanding plant sex chromosomes involves studying interactions between developmental and physiological genetics, genome evolution, and evolutionary ecology. We focus on areas of overlap between these. Ideas about how species with separate sexes (dioecious species, in plant terminology) can evolve are even more relevant to plants than to most animal taxa because dioecy has evolved many times from ancestral functionally hermaphroditic populations, often recently. One aim of studying plant sex chromosomes is to discover how separate males and females evolved from ancestors with no such genetic sex-determining polymorphism, and the diversity in the genetic control of maleness vs femaleness. Different systems share some interesting features, and their differences help to understand why completely sex-linked regions may evolve. In some dioecious plants, the sex-determining genome regions are physically small. In others, regions without crossing over have evolved sometimes extensive regions with properties very similar to those of the familiar animal sex chromosomes. The differences also affect the evolutionary changes possible when the environment (or pollination environment, for angiosperms) changes, as dioecy is an ecologically risky strategy for sessile organisms. Dioecious plants have repeatedly reverted to cosexuality, and hermaphroditic strains of fruit crops such as papaya and grapes are desired by plant breeders. Sex-linked regions are predicted to become enriched in genes with sex differences in expression, especially when higher expression benefits one sex function but harms the other. Such trade-offs may be important for understanding other plant developmental and physiological processes and have direct applications in plant breeding.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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29
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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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30
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Parée T, Noble L, Ferreira Gonçalves J, Teotónio H. rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers. Genetics 2024; 226:iyad205. [PMID: 38001364 DOI: 10.1093/genetics/iyad205] [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: 10/03/2023] [Revised: 10/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Meiotic control of crossover (CO) number and position is critical for homologous chromosome segregation and organismal fertility, recombination of parental genotypes, and the generation of novel genetic combinations. We here characterize the recombination rate landscape of a rec-1 loss of function modifier of CO position in Caenorhabditis elegans, one of the first ever modifiers discovered. By averaging CO position across hermaphrodite and male meioses and by genotyping 203 single-nucleotide variants covering about 95% of the genome, we find that the characteristic chromosomal arm-center recombination rate domain structure is lost in the loss of function rec-1 mutant. The rec-1 loss of function mutant smooths the recombination rate landscape but is insufficient to eliminate the nonuniform position of CO. Lower recombination rates in the rec-1 mutant are particularly found in the autosomal arm domains containing the pairing centers. We further find that the rec-1 mutant is of little consequence for organismal fertility and egg viability and thus for rates of autosomal nondisjunction. It nonetheless increases X chromosome nondisjunction rates and thus male appearance. Our findings question the maintenance of recombination rate heritability and genetic diversity among C. elegans natural populations, and they further suggest that manipulating genetic modifiers of CO position will help find quantitative trait loci located in low-recombining genomic regions normally refractory to discovery.
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Affiliation(s)
- Tom Parée
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
| | - Luke Noble
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
- EnviroDNA, 95 Albert St., Brunswick, Victoria 3065, Australia
| | - João Ferreira Gonçalves
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
| | - Henrique Teotónio
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
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31
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Fu L, Gu C, Mochizuki K, Xiong J, Miao W, Wang G. The genome-wide meiotic recombination landscape in ciliates and its implications for crossover regulation and genome evolution. J Genet Genomics 2024; 51:302-312. [PMID: 37797835 DOI: 10.1016/j.jgg.2023.09.013] [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: 08/12/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa. However, genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates: the synaptonemal complex (SC)-independent meiosis and the nuclear dimorphism. Here, we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny. We detect 1021 crossover (CO) events (35.8 per meiosis), corresponding to an overall CO rate of 9.9 cM/Mb. However, gene conversion by non-crossover is rare (1.03 per meiosis) and not biased towards G or C alleles. Consistent with the reported roles of SC in CO interference, we find no obvious sign of CO interference. CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions. Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes. We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.
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Affiliation(s)
- Lu Fu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Gu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of Montpellier, 34396 Montpellier, France
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China.
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.
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32
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Castellani M, Zhang M, Thangavel G, Mata-Sucre Y, Lux T, Campoy JA, Marek M, Huettel B, Sun H, Mayer KFX, Schneeberger K, Marques A. Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning. NATURE PLANTS 2024; 10:423-438. [PMID: 38337039 PMCID: PMC10954556 DOI: 10.1038/s41477-024-01625-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/15/2024] [Indexed: 02/12/2024]
Abstract
Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics, influencing the overall distribution and frequency of crossovers. Here we show how recombination is regulated and distributed in the holocentric plant Rhynchospora breviuscula, a species with diffused centromeres. Combining immunocytochemistry, chromatin analysis and high-throughput single-pollen sequencing, we discovered that crossover frequency is distally biased, in sharp contrast to the diffused distribution of hundreds of centromeric units and (epi)genomic features. Remarkably, we found that crossovers were abolished inside centromeric units but not in their proximity, indicating the absence of a canonical centromere effect. We further propose that telomere-led synapsis of homologues is the feature that best explains the observed recombination landscape. Our results hint at the primary influence of mechanistic features of meiotic pairing and synapsis rather than (epi)genomic features and centromere organization in determining the distally biased crossover distribution in R. breviuscula, whereas centromeres and (epi)genetic properties only affect crossover positioning locally.
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Affiliation(s)
- Marco Castellani
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Meng Zhang
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gokilavani Thangavel
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yennifer Mata-Sucre
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Centre of Biosciences, Federal University of Pernambuco, Recife, Brazil
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Centre for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - José A Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Pomology, Estación Experimental de Aula Dei (EEAD), Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Magdalena Marek
- Max Planck Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hequan Sun
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Centre for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany.
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Filatov DA. Evolution of a plant sex chromosome driven by expanding pericentromeric recombination suppression. Sci Rep 2024; 14:1373. [PMID: 38228625 DOI: 10.1038/s41598-024-51153-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Recombination suppression around sex-determining gene(s) is a key step in evolution of sex chromosomes, but it is not well understood how it evolves. Recently evolved sex-linked regions offer an opportunity to understand the mechanisms of recombination cessation. This paper analyses such a region on Silene latifolia (Caryophyllaceae) sex chromosomes, where recombination was suppressed in the last 120 thousand years ("stratum 3"). Locating the boundaries of the stratum 3 in S. latifolia genome sequence revealed that this region is far larger than assumed previously-it is about 14 Mb long and includes 202 annotated genes. A gradient of X:Y divergence detected in the stratum 3, with divergence increasing proximally, indicates gradual recombination cessation, possibly caused by expansion of pericentromeric recombination suppression (PRS) into the pseudoautosomal region. Expansion of PRS was also the likely cause for the formation of the older stratum 2 on S. latifolia sex chromosomes. The role of PRS in sex chromosome evolution has been underappreciated, but it may be a significant factor, especially in the species with large chromosomes where PRS is often extensive.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
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34
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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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35
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Chowdary KVSKA, Saini R, Singh AK. Epigenetic regulation during meiosis and crossover. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1945-1958. [PMID: 38222277 PMCID: PMC10784443 DOI: 10.1007/s12298-023-01390-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 01/16/2024]
Abstract
Meiosis is a distinctive type of cell division that reorganizes genetic material between generations. The initial stages of meiosis consist of several crucial steps which include double strand break, homologous chromosome pairing, break repair and crossover. Crossover frequency varies depending on the position on the chromosome, higher at euchromatin region and rare at heterochromatin, centromeres, telomeres and ribosomal DNA. Crossover positioning is dependent on various factors, especially epigenetic modifications. DNA methylation, histone post-translational modifications, histone variants and non-coding RNAs are most probably playing an important role in positioning of crossovers on a chromosomal level as well as hotspot level. DNA methylation negatively regulates crossover frequency and its effect is visible in centromeres, pericentromeres and heterochromatin regions. Pericentromeric chromatin and heterochromatin mark studies have been a centre of attraction in meiosis. Crossover hotspots are associated with euchromatin regions having specific chromatin modifications such as H3K4me3, H2A.Z. and H3 acetylation. This review will provide the current understanding of the epigenetic role in plants during meiotic recombination, chromosome synapsis, double strand break and hotspots with special attention to euchromatin and heterochromatin marks. Further, the role of epigenetic modifications in regulating meiosis and crossover in other organisms is also discussed.
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Affiliation(s)
- K. V. S. K. Arjun Chowdary
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Ramswaroop Saini
- Department of Biotechnology, Joy University, Vadakangulam, Tirunelveli, Tamil Nadu 627116 India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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Lian Q, Maestroni L, Gaudin M, Llorente B, Mercier R. Meiotic recombination is confirmed to be unusually high in the fission yeast Schizosaccharomyces pombe. iScience 2023; 26:107614. [PMID: 37664590 PMCID: PMC10474467 DOI: 10.1016/j.isci.2023.107614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
In most eukaryotes, meiotic crossovers (COs) are limited to 1-3 per chromosome, and are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to these general rules, was reported to have the highest CO number per chromosome and no or weak interference. However, global CO frequency was indirectly estimated, calling for confirmation. Here, we used an innovative strategy to determine COs genome-wide in S. pombe. We confirmed weak CO interference, acting at physical distances compatible with the patterning of recombination precursors. We revealed a slight co-variation in CO number between chromosomes, suggesting that a limiting pro-CO factor varies between meiocytes. CO number per chromosome varies proportionally with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This reinforces S. pombe's status as the eukaryote with the highest CO number per chromosome described to date.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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Huang HR, Liu X, Arshad R, Wang X, Li WM, Zhou Y, Ge XJ. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. HORTICULTURE RESEARCH 2023; 10:uhad153. [PMID: 37701454 PMCID: PMC10493638 DOI: 10.1093/hr/uhad153] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 09/14/2023]
Abstract
Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome was still undecoded for banana cultivars. Here, we reported the telomere-to-telomere (T2T) and haplotype-resolved reference genome of 'Baxijiao' (Cavendish) consisting of three haploid assemblies. The sizes of the three haploid assemblies were estimated to be 477.16 Mb, 477.18 Mb, and 469.57 Mb, respectively. Although with monospecific origins, the three haploid assemblies showed great differences with low levels of sequence collinearity. Several large reciprocal translocations were identified among chromosomes 1, 4, and 7. An expansion of gene families that might affect fruit quality and aroma was detected, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process. Besides, an expansion of gene families related to anther and pollen development was observed, which could be associated with parthenocarpy and sterility of the Cavendish cultivar. Finally, much fewer resistance genes were identified in 'Baxijiao' than in M. acuminata, particularly in the gene clusters in chromosomes 3 and 10, providing potential targets to explore for molecular analysis of disease resistance in banana. This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding, and genetic improvement of banana.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xin Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rida Arshad
- State 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 518120, China
| | - Xu Wang
- State 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 518120, China
| | - Wei-Ming Li
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China
| | - Yongfeng Zhou
- State 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 518120, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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38
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Näsvall K, Boman J, Höök L, Vila R, Wiklund C, Backström N. Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements. PLoS Genet 2023; 19:e1010717. [PMID: 37549188 PMCID: PMC10434929 DOI: 10.1371/journal.pgen.1010717] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/17/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
Reshuffling of genetic variation occurs both by independent assortment of chromosomes and by homologous recombination. Such reshuffling can generate novel allele combinations and break linkage between advantageous and deleterious variants which increases both the potential and the efficacy of natural selection. Here we used high-density linkage maps to characterize global and regional recombination rate variation in two populations of the wood white butterfly (Leptidea sinapis) that differ considerably in their karyotype as a consequence of at least 27 chromosome fissions and fusions. The recombination data were compared to estimates of genetic diversity and measures of selection to assess the relationship between chromosomal rearrangements, crossing over, maintenance of genetic diversity and adaptation. Our data show that the recombination rate is influenced by both chromosome size and number, but that the difference in the number of crossovers between karyotypes is reduced as a consequence of a higher frequency of double crossovers in larger chromosomes. As expected from effects of selection on linked sites, we observed an overall positive association between recombination rate and genetic diversity in both populations. Our results also revealed a significant effect of chromosomal rearrangements on the rate of intergenic diversity change between populations, but limited effects on polymorphisms in coding sequence. We conclude that chromosomal rearrangements can have considerable effects on the recombination landscape and consequently influence both maintenance of genetic diversity and efficiency of selection in natural populations.
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Affiliation(s)
- Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Roger Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Christer Wiklund
- Department of Zoology: Division of Ecology, Stockholm University, Stockholm, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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40
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. THE NEW PHYTOLOGIST 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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41
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Huang K, Jahani M, Gouzy J, Legendre A, Carrere S, Lázaro-Guevara JM, González Segovia EG, Todesco M, Mayjonade B, Rodde N, Cauet S, Dufau I, Staton SE, Pouilly N, Boniface MC, Tapy C, Mangin B, Duhnen A, Gautier V, Poncet C, Donnadieu C, Mandel T, Hübner S, Burke JM, Vautrin S, Bellec A, Owens GL, Langlade N, Muños S, Rieseberg LH. The genomics of linkage drag in inbred lines of sunflower. Proc Natl Acad Sci U S A 2023; 120:e2205783119. [PMID: 36972449 PMCID: PMC10083583 DOI: 10.1073/pnas.2205783119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/18/2022] [Indexed: 03/29/2023] Open
Abstract
Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
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Affiliation(s)
- Kaichi Huang
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Alexandra Legendre
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - José Miguel Lázaro-Guevara
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Eric Gerardo González Segovia
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Nathalie Rodde
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Isabelle Dufau
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - S. Evan Staton
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Research and Development Department, NRGene Canada Inc., Saskatoon, SKS7N 3R3, Canada
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Camille Tapy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Brigitte Mangin
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Alexandra Duhnen
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Véronique Gautier
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000France
| | - Charles Poncet
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000France
| | - Cécile Donnadieu
- Plateforme Génome et Transcriptome (GeT-PlaGe), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Tali Mandel
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016Israel
| | - Sariel Hübner
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016Israel
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, GA30602
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Nicolas Langlade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
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