1. Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus
- Author
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Ahmed, Dalel, Comte, Aurore, Curk, Franck, Costantino, Gilles, Luro, François, Dereeper, Alexis, Mournet, Pierre, Froelicher, Yann, Ollitrault, Patrick, Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), European Union (EU), Instituto de Salud Carlos III, Agropolis Fondation : 1504-006, Labex Agro:ANR-10-LABX-0001-01, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
- Subjects
citrus ,reticulate evolution ,genome ,GBS ,polyploids ,SNPs ,phylogenomic karyotype ,Phylogénie ,Citrus ,Genotype ,reticulate evolution,genome ,Lime ,Évolution ,F30 - Génétique et amélioration des plantes ,Pool de gènes ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Caryotype ,Phylogeny ,amélioration génétique ,Vegetal Biology ,phylogenomic ,fungi ,food and beverages ,Original Articles ,Gene Pool ,Diploidy ,karyotype ,mosaic genome ,Biologie végétale ,Génotype - Abstract
International audience; Background and Aims Reticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly to be used for large populations. The aim of this work was to develop an approach to infer phylogenomic structures in diploid, triploid and tetraploid individuals from sequencing data in reduced genome complexity libraries. The approach was applied to the cultivated Citrus gene pool resulting from reticulate evolution involving four ancestral taxa, C. maxima, C. medico, C. micrantha and C. reticulara. Methods A genotyping, by sequencing library was established with the restriction enzyme ApeK.1 applying one base (A) selection. Diagnostic single nucleotide polymorphisms (DSNPs) for the four ancestral taxa were mined in 29 representative varieties. A generic pipeline based on a maximum likelihood analysis of the number of read data was established to infer ancestral contributions along the genome of diploid, triploid and tetraploid individuals. The pipeline was applied to 48 diploid, four triploid and one tetraploid citrus accessions. Key Results Among 43 598 mined SNPs, we identified a set of 15 946 DSNPs covering the whole genome with a distribution similar to that of gene sequences. The set efficiently inferred the phylogenomic karyotype of the 53 analysed accessions, providing patterns for common accessions very close to that previously established using WGS data. The complex phylogenomic karyotypes of 21 cultivated citrus, including bergamot, triploid and tetraploid limes, were revealed for the first time. Conclusions The pipeline, available online, efficiently inferred the phylogenomic structures of diploid, triploid and tetraploid citrus. it will be useful for any species whose reproductive behaviour resulted in an interspecific mosaic of large genomie fragments. It can also be used for the first generations of interspecific breeding scheme
- Published
- 2019
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