title: Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.
abstract: Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.
authors.affiliation: Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (Inra), Centre Inra de Corse, F-20230, San Giuliano, Corsica, France; Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113, Moncada, Valencia, Spain.
authors.forename: Franck
authors.initials: F
authors.lastname: Curk
authors.affiliation: Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113, Moncada, Valencia, Spain.
authors.forename: Gema
authors.initials: G
authors.lastname: Ancillo
authors.affiliation: Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113, Moncada, Valencia, Spain.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Ollitrault
authors.affiliation: Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de coopération Internationale en Recherche Agronomique pour le Développement (Cirad), TA A-108/02, 34398, Montpellier, Cedex 5, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Perrier
authors.affiliation: Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de coopération Internationale en Recherche Agronomique pour le Développement (Cirad), TA A-108/02, 34398, Montpellier, Cedex 5, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Jacquemoud-Collet
authors.affiliation: Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113, Moncada, Valencia, Spain.
authors.forename: Andres
authors.initials: A
authors.lastname: Garcia-Lor
authors.affiliation: Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113, Moncada, Valencia, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Navarro
authors.affiliation: Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113, Moncada, Valencia, Spain; Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Station de Roujol, 97170, Petit-Bourg, Guadeloupe, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Ollitrault
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D002957:Citrus / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D013045:Species Specificity