Deciphering the complex genomic structures of cultivated citrus

On 7 July 2014, the journal Nature Biotechnology published an article revealing the complex genomic structures of some modern citrus varieties arising from reticulate evolution. Four researchers from AGAP are co-authors of the results of this International Citrus Genomics Consortium (ICGC) project which AGAP helped to draw up, coordinate and implement.

The article, entitled “Sequencing of diverse mandarin, pummelo and orange genomes reveals a complex history of admixture during citrus domestication”, presents the high-quality reference sequence for citrus established by Sanger sequencing of a clementine haploid primarily undertaken by the ANR Citrusseq project (Genoscope, CIRAD, INRA and IVIA). On that occasion, AGAP coordinated the establishment of the first reference genetic map for citrus (Ollitrault et al., 2012) used for the assembly into pseudomolecules (chromosomes). The reference sequence for clementine and its annotation can be found on-line (http://www.phytozome.net/clementine.php). The re-sequencing data for eight citrus varieties, produced by ICGC and for 4 varieties released by a Chinese consortium (Xu et al., 2013) have been aligned on the reference sequence in order to analyse the phylogenetic structures. This work shows that the modern mandarin varieties analysed, generally considered to be representative of the species Citrus reticulata, are in fact introgressed at different sites by genomic fragments of the species C. maxima (grapefruit). The results also show once and for all that the species C. aurantium (Seville orange, “Bouquetier” bitter orange) results from direct interspecific hybridization between C. maxima and C. reticulata while C. sinensis (orange) displays a more complex genomic structure implying that its two parents were of interspecific origin between C. maxima and C. reticulata. The study also reveals along the whole length of the genome the phylogenetic origin of the chromosomal fragments in the different varieties.

The establishment of the reference sequence for citrus and deciphering of the interspecific structures of the genomes of modern varieties as described in the article published by Nature Biotechnology are two key stages that will make it easier to guide citrus breeding more effectively, particularly integration of the biodiversity of the species complex in improved varieties. It is thus likely that the introgressions of C. maxima in the mandarin genome are one of the major sources of the high phenotypic variability of this horticultural group. In addition, at a time when world orange production is being very severely impacted by various diseases such as Huanglongbing, variegated chlorosis and citrus canker, knowledge of the interspecific mosaic structure of C. sinensis opens up possibilities of reconstructing genotypes close to the “orange” ideotype (whose genetic base is very narrow) from the germplasm of the ancestral species C. reticulata and C. maxima. Lastly, the advances in genomics described in this article will considerably speed up the acquisition of knowledge on the determinants of phenotypic variability and the development of powerful early selection tools (MAS, genomic selection).

These recent developments in genomics are particularly fuelling the research of the AGAP citrus team, which is working on an integrated citrus breeding project ranging from deciphering the structure of genomes up to the selection of high quality small citrus varieties (seedlessness, aromas, health related components, etc.) that are resistant to certain diseases, along with rootstocks adapted to biotic and abiotic constraints in the Mediterranean Basin and tropical zones. These varietal innovation projects bringing into play biodiversity are based on one of the largest citrus collections at international level jointly managed by INRA and CIRAD, and on multidisciplinary research regarding (i) the organization of genetic diversity and that of the useful traits within the species complex; (ii) reproductive biology and its effect on the recombination and segregation of traits at diploid and polyploid level; (iii) the genetic, physiological and molecular determinants of traits of interest; (iii) the creation and selection methodology. The overall ultimate target is to contribute, through  novel planting material, to the development of sustainable citrus growing systems in different production basins, and particularly in the Mediterranean Basin and in tropical regions. This planting material needs to meet the expectations of society (environment-friendly, organoleptic and nutritional quality, food security) and those of stakeholders in the supply chain (reduced inputs and labour costs, supplies to the fresh fruit market over longer periods, etc.).

Published: 17/07/2014