New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties.
Amandine Cornille,Amandine Cornille,Amandine Cornille,Pierre Gladieux,Pierre Gladieux,Pierre Gladieux,Marinus J. M. Smulders,Isabel Roldán-Ruiz,François Laurens,François Laurens,François Laurens,Bruno Le Cam,Bruno Le Cam,Bruno Le Cam,Anush Nersesyan,Joanne Clavel,Joanne Clavel,Joanne Clavel,Marina V. Olonova,Laurence Feugey,Laurence Feugey,Laurence Feugey,Ivan Gabrielyan,Xiu-Guo Zhang,Maud I. Tenaillon,Tatiana Giraud,Tatiana Giraud,Tatiana Giraud +27 more
TLDR
It is shown that the evolution of domesticated apples occurred over a long time period and involved more than one wild species, supporting the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication.Abstract:
The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.read more
Citations
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Evolution of crop species: genetics of domestication and diversification
TL;DR: Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations That occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations.
Journal ArticleDOI
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
Nicolas Daccord,Jean-Marc Celton,Gareth Linsmith,Claude Becker,Nathalie Choisne,Elio Schijlen,Henri van de Geest,Luca Bianco,Diego Micheletti,Riccardo Velasco,Erica A. Di Pierro,Jérôme Gouzy,D. Jasper G. Rees,Philippe Guérif,Helene Muranty,Charles-Eric Durel,François Laurens,Yves Lespinasse,Sylvain Gaillard,Sébastien Aubourg,Hadi Quesneville,Detlef Weigel,Eric van de Weg,Michela Troggio,Etienne Bucher +24 more
TL;DR: High-quality de novo assembly of the apple genome is produced and genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
Journal ArticleDOI
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
G Albert Wu,Simon E. Prochnik,Jerry Jenkins,Jérôme Salse,Uffe Hellsten,Florent Murat,Xavier Perrier,Manuel Ruiz,Simone Scalabrin,Javier Terol,Marco Aurélio Takita,Karine Labadie,Julie Poulain,Arnaud Couloux,Kamel Jabbari,Federica Cattonaro,Cristian Del Fabbro,Sara Pinosio,Andrea Zuccolo,Jarrod Chapman,Jane Grimwood,Francisco R. Tadeo,Leandro H. Estornell,Juan V. Munoz-Sanz,Victoria Ibanez,Amparo Herrero-Ortega,Pablo Aleza,Julián Pérez-Pérez,Daniel Ramón,Dominique Brunel,François Luro,Chunxian Chen,William G. Farmerie,Brian Desany,Chinnappa D. Kodira,Mohammed Mohiuddin,Tim Harkins,Karin M. Fredrikson,Paul Burns,Alexandre Lomsadze,Mark Borodovsky,Giuseppe Reforgiato,Juliana Freitas-Astúa,Francis Quetier,Luis Navarro,Mikeal L. Roose,Patrick Wincker,Jeremy Schmutz,Michele Morgante,Marcos A. Machado,Manuel Talon,Olivier Jaillon,Patrick Ollitrault,Frederick G. Gmitter,Daniel S. Rokhsar +54 more
TL;DR: This work sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and shows that cultivated types derive from two progenitor species.
Journal ArticleDOI
Genomics of the origin and evolution of Citrus
Guohong Albert Wu,Javier Terol,Victoria Ibanez,Antonio López-García,Estela Pérez-Román,Carles Borredá,Concha Domingo,Francisco R. Tadeo,José Carbonell-Caballero,Roberto Alonso,Franck Curk,Dongliang Du,Patrick Ollitrault,Mikeal L. Roose,Joaquín Dopazo,Frederick G. Gmitter,Daniel S. Rokhsar,Daniel S. Rokhsar,Daniel S. Rokhsar,Manuel Talon +19 more
TL;DR: Ten natural citrus species are described, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and it is proposed that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons.
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The Evolution of Animal Domestication
Greger Larson,Dorian Q. Fuller +1 more
TL;DR: A framework for understanding how unconscious selection characterized the earliest steps of animal domestication and the role of introgression and the importance of relaxed and positive selection in shaping modern domestic phenotypes and genomes is presented.
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