Wen-Wu Guo, Marcos Antonio Machado, Luis Navarro, Chunxian Chen, Kevin Kwok, Manuel Talon, Gilles Costantino, Benedetta Chiancone, Xiuxin Deng, Esther Carrera, Yann Froelicher, Claire T. Federici, Maria Germana, Mikeal L. Roose, Dominique Dambier, Patrick Ollitrault, Gabino Ríos, Miguel A. Naranjo, Pablo Aleza, François Luro, Qiang Xu, Jose Juarez, Victoria Ibanez, Frederick G. Gmitter, Università degli Studi di Palermo, Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research (IVIA), University of Florida [Gainesville] (UF), SE Fruit & Tree Nut Res Lab, United States Department of Agriculture, Station de recherches agronomiques de San Giuliano, Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Huazhong Agricultural University, University of California [Riverside] (UCR), University of California, Universidade Estadual de Campinas (UNICAMP), Spanish Ministerio de Ciencia e Innovacion-FEDER [PSE-060000-2009-008, IPT-010000-2010-43], Ministry of 'Econom a y Competivida-Fondo Europeo de Desarrollo Regional (FEDER)' [AGL2011-26490], Generalitat Valenciana, Spain [PrometeoII/2013/008], Florida Citrus Production Research Advisory Council, Citrus Research and Development Foundation, on behalf of the Florida citrus growers, French Genomic ANR CITRUSSEQ project, INCT Citrus by FAPESP, CNPq, GERMANÀ, M, ALEZA, P, CARRERA, E, CHEN, C, CHIANCONE, B, COSTANTINO, G, DAMBIER, D, DENG, X, FEDERICI, TC, FROELICHER, Y, GUO, W, IBÁÑEZ, V, JUÁREZ, J, KWOK, K, LURO, F, MACHADO, AM, NARANJO, AM, NAVARRO, L, OLLITRAULT, P, RÍOS, G, ROOSE, LM, TALON, M, XU, Q, and GMITTER, GF
Background Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). Results Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a single peak (allele), were observed among the three plants at almost all SSR loci distributed across the entire diploid donor genome. Those few loci with extra peaks visualized as output from automated sequencing runs, generally low or ambiguous, might result from amplicons of paralogous members at the locus, non-specific sites, or unexpected recombinant alleles. No new alleles were found, suggesting the genomes remained stable and intact during gametogenesis and regeneration. The integrity of the haploid genome also was supported by array-CGH studies, in which genomic profiles were comparable to the diploid control. Conclusions The presence of few gene hybridization abnormalities, corroborated by gene dosage measurements, were hypothetically due to the segregation of hemizygous alleles and minor genomic rearrangements occurring during the haploidization procedure. In conclusion, these plants that are valuable genetic and breeding materials contain completely homozygous and essentially intact genomes.