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Chen X, Avia K, Forler A, Remoué C, Venon A, Rousselet A, Lucas G, Kwarteng AO, Rover R, Le Guilloux M, Belcram H, Combes V, Corti H, Olverà-Vazquez S, Falque M, Alins G, Kirisits T, Ursu TM, Roman A, Volk GM, Bazot S, Cornille A. Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple. Ann Bot 2023; 131:1025-1037. [PMID: 37148364 PMCID: PMC10332392 DOI: 10.1093/aob/mcad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations. METHODS Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested. KEY RESULTS A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates. CONCLUSIONS This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.
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Affiliation(s)
- X Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - K Avia
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France
| | - A Forler
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - C Remoué
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Venon
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Rousselet
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Lucas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - A O Kwarteng
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - R Rover
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Le Guilloux
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Belcram
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - V Combes
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Corti
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - S Olverà-Vazquez
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Falque
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Alins
- Institut de Recerca i Tecnologia Agroalimentàries, IRTA-Fruit Production, PCiTAL, Parc 21 de Gardeny, edifici Fruitcentre, 25003 Lleida, Spain
| | - T Kirisits
- Institute of Forest Entomology, Forest Pathology and Forest Protection (IFFF), Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Peter-Jordan-Straße 82 (Franz Schwackhöfer-Haus), A-1190 Vienna, Austria
| | - T M Ursu
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - A Roman
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - G M Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
| | - S Bazot
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris‐Saclay, Orsay, France
| | - A Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
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Falque M, Mercier R, Mézard C, de Vienne D, Martin OC. Patterns of recombination and MLH1 foci density along mouse chromosomes: modeling effects of interference and obligate chiasma. Genetics 2007; 176:1453-67. [PMID: 17483430 PMCID: PMC1931555 DOI: 10.1534/genetics.106.070235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crossover interference in meiosis is often modeled via stationary renewal processes. Here we consider a new model to incorporate the known biological feature of "obligate chiasma" whereby in most organisms each bivalent almost always has at least one crossover. The initial crossover is modeled as uniformly distributed along the chromosome, and starting from its position, subsequent crossovers are placed with forward and backward stationary renewal processes using a chi-square distribution of intercrossover distances. We used our model as well as the standard chi-square model to simulate the patterns of crossover densities along bivalents or chromatids for those having zero, one, two, or three or more crossovers; indeed, such patterns depend on the number of crossovers. With both models, simulated patterns compare very well to those found experimentally in mice, both for MLH1 foci on bivalents and for crossovers on genetic maps. However, our model provides a better fit to experimental data as compared to the standard chi-square model, particularly regarding the distribution of numbers of crossovers per chromosome. Finally, our model predicts an enhancement of the recombination rate near the extremities, which, however, explains only a part of the pattern observed in mouse.
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Affiliation(s)
- M Falque
- UMR de Génétique Végétale, INRA, Université Paris-Sud, CNRS, Gif-sur-Yvette, France.
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Manicacci D, Falque M, Le Guillou S, Piégu B, Henry AM, Le Guilloux M, Damerval C, De Vienne D. Maize Sh2 gene is constrained by natural selection but escaped domestication. J Evol Biol 2007; 20:503-16. [PMID: 17305816 DOI: 10.1111/j.1420-9101.2006.01264.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Zea mays L., we studied the molecular evolution of Shrunken2 (Sh2), a gene that encodes the large subunits of a major enzyme in endosperm starch biosynthesis, ADP-glucose pyrophosphorylase. We compared 4669 bp of the Sh2 coding region on 50 accessions of maize and teosinte. Very few nucleotide polymorphisms were found when compared with other genes in Z. mays, revealing an effect of purifying selection in the whole species that predates domestication. Additionally, the comparison of Sh2 sequences in all Z. mays subspecies and outgroups Z. diploperennis and Tripsacum dactyloides suggests the occurrence of an ancient selective sweep in the Sh2 3' region. The amount and nature of nucleotide diversity are similar in both maize and teosinte, confirming previous results that suggested that Sh2 has not been involved in maize domestication. The very low level of nucleotide diversity as well as the highly conserved protein sequence suggest that natural selection retained effective Sh2 allele(s) long before agriculture started, making human selection inefficient on this gene.
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Affiliation(s)
- D Manicacci
- UMR de Génétique Végétale (8120), Ferme du Moulon, F91 190 Gif sur Yvette, France.
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Van Der Hulst RGM, Mes THM, Falque M, Stam P, Den Nijs JCM, Bachmann K. Genetic structure of a population sample of apomictic dandelions. Heredity (Edinb) 2003; 90:326-35. [PMID: 12692586 DOI: 10.1038/sj.hdy.6800248] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In Northern Europe, dandelion populations consist solely of triploid or higher polyploid apomicts. Without a regular sexual cycle or lateral gene transmission, a clonal structure is expected for Taraxacum apomicts, although this was not found by compatibility analysis. In this study, we investigate whether this observation could be suported by performing independent tests based on data from hypervariable microsatellite markers as well as more conservative data based on allozymes and matrilinear cpDNA markers. In addition, population genetic methods were used to test departure from panmictic expectations, which is expected for clonal populations. Results indicated that many data sets, again, did not agree with expectations from clonal evolution because only small groups of genotypes exhibit no marker incompatibility. Population genetic analysis revealed that virtually all genotypes, but not individuals, agreed with random segregation and genotypic equilibria. Exceptions were genotypes with rare allozyme alleles or nearly identical microsatellite genotypes. Consequently, a population sample of apomictic dandelions essentially harbours genotypes that resulted from segregation and/or recombination and only a few genotypes that may have differentiated by somatic mutations.
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Affiliation(s)
- R G M Van Der Hulst
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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Hirel B, Bertin P, Quilleré I, Bourdoncle W, Attagnant C, Dellay C, Gouy A, Cadiou S, Retailliau C, Falque M, Gallais A. Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize. Plant Physiol 2001; 125:1258-70. [PMID: 11244107 PMCID: PMC65606 DOI: 10.1104/pp.125.3.1258] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2000] [Accepted: 12/20/2000] [Indexed: 05/18/2023]
Abstract
To enhance our understanding of the genetic basis of nitrogen use efficiency in maize (Zea mays), we have developed a quantitative genetic approach by associating metabolic functions and agronomic traits to DNA markers. In this study, leaves of vegetative recombinant inbred lines of maize, already assessed for their agronomic performance, were analyzed for physiological traits such as nitrate content, nitrate reductase (NR), and glutamine synthetase (GS) activities. A significant genotypic variation was found for these traits and a positive correlation was observed between nitrate content, GS activity and yield, and its components. NR activity, on the other hand, was negatively correlated. These results suggest that increased productivity in maize genotypes was due to their ability to accumulate nitrate in their leaves during vegetative growth and to efficiently remobilize this stored nitrogen during grain filling. Quantitative trait loci (QTL) for various agronomic and physiological traits were searched for and located on the genetic map of maize. Coincidences of QTL for yield and its components with genes encoding cytosolic GS and the corresponding enzyme activity were detected. In particular, it appears that the GS locus on chromosome 5 is a good candidate gene that can, at least partially, explain variations in yield or kernel weight. Because at this locus coincidences of QTLs for grain yield, GS, NR activity, and nitrate content were also observed, we hypothesize that leaf nitrate accumulation and the reactions catalyzed by NR and GS are coregulated and represent key elements controlling nitrogen use efficiency in maize.
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Affiliation(s)
- B Hirel
- Unité de Nutrition Azotée des Plantes, Institut National de la Recherche Agronomique, Route de St-Cyr 78026, Versailles cedex, France.
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Van Dijk PJ, Tas IC, Falque M, Bakx-Schotman T. Crosses between sexual and apomictic dandelions (Taraxacum). II. The breakdown of apomixis. Heredity (Edinb) 1999; 83 ( Pt 6):715-21. [PMID: 10651916 DOI: 10.1046/j.1365-2540.1999.00620.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some dandelions are diplosporous gametophytic apomicts. In order to study the inheritance and breakdown of apomixis, crosses were made between diploid sexuals and triploid apomicts. To investigate their breeding system, four nonapomictic diploid and 10 nonapomictic triploid hybrids were pollinated with diploids and the progenies were analysed. Seed fertility was significantly reduced in two diploid hybrids. Nine triploid hybrids were fertile and could be classified into three types, with respect to the composition of their progenies. Type A produced n+n hybrids. Type B produced either a mixture of n + n and 2n + n hybrids, or a mixture of pseudogamous 2n + 0 apomicts and 2n + n hybrids. Type C produced exclusively 2n + n hybrids. Inheritance of a microsatellite marker strongly suggested that 2n egg cells in type C plants were produced by a first division restitution mechanism. As in apomicts, microsporogenesis in type C plants was reductional. This suggests that type C plants are diplosporous plants that lack parthenogenesis. Such plants are very rare in other apomictic plant species. It is concluded that 'elements of apomixis', diplospory and parthenogenesis, can be uncoupled. This is inconsistent with the single-locus model for apomixis in Taraxacum as suggested by Mogie (1992). Instead, our results suggest that several loci are involved in the genetic control of apomixis in Taraxacum.
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Affiliation(s)
- P J Van Dijk
- Department of Plant Population Biology, Netherlands Institute of Ecology, Center for Terrestrial Ecology (NIOO-CTO), PO Box 40, 6666 ZG Heteren, The Netherlands.
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Van Dijk PJ, Tas IC, Falque M, Bakx-Schotman T. Crosses between sexual and apomictic dandelions (Taraxacum). II. The breakdown of apomixis. Heredity (Edinb) 1999. [PMID: 10651916 DOI: 10.1038/sj.hdy.6886200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Some dandelions are diplosporous gametophytic apomicts. In order to study the inheritance and breakdown of apomixis, crosses were made between diploid sexuals and triploid apomicts. To investigate their breeding system, four nonapomictic diploid and 10 nonapomictic triploid hybrids were pollinated with diploids and the progenies were analysed. Seed fertility was significantly reduced in two diploid hybrids. Nine triploid hybrids were fertile and could be classified into three types, with respect to the composition of their progenies. Type A produced n+n hybrids. Type B produced either a mixture of n + n and 2n + n hybrids, or a mixture of pseudogamous 2n + 0 apomicts and 2n + n hybrids. Type C produced exclusively 2n + n hybrids. Inheritance of a microsatellite marker strongly suggested that 2n egg cells in type C plants were produced by a first division restitution mechanism. As in apomicts, microsporogenesis in type C plants was reductional. This suggests that type C plants are diplosporous plants that lack parthenogenesis. Such plants are very rare in other apomictic plant species. It is concluded that 'elements of apomixis', diplospory and parthenogenesis, can be uncoupled. This is inconsistent with the single-locus model for apomixis in Taraxacum as suggested by Mogie (1992). Instead, our results suggest that several loci are involved in the genetic control of apomixis in Taraxacum.
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Affiliation(s)
- P J Van Dijk
- Department of Plant Population Biology, Netherlands Institute of Ecology, Center for Terrestrial Ecology (NIOO-CTO), PO Box 40, 6666 ZG Heteren, The Netherlands.
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Lanaud C, Risterucci AM, N'goran AK, Clement D, Flament MH, Laurent V, Falque M. A genetic linkage map of Theobroma cacao L. Theor Appl Genet 1995; 91:987-93. [PMID: 24169987 DOI: 10.1007/bf00223910] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/1995] [Accepted: 05/12/1995] [Indexed: 05/08/2023]
Abstract
A linkage map of the cocoa genome comprising 193 loci has been constructed. These loci consist of 5 isozymes, 101 cDNA/RFLPs, 4 loci from genes of known function, 55 genomic DNA/RFLPs and 28 RAPDs. A population of 100 individuals derived from a cross between two heterozygous genotypes was used. Segregation analyses were performed with the JoinMap program. Ten linkage groups, which putatively correspond to the ten gametic chromosomes of cocoa, were identified. The map covers a total length of 759 cM with a 3.9 cM average distance between 2 markers. A small fraction (9%) of the markers deviated significantly from the expected Mendelian ratios.
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Affiliation(s)
- C Lanaud
- CIRAD-Biotrop, BP 5035, F-34032, Montpellier Cedex, France
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