Comparative genetic mapping between clementine, pummelo and sweet orange and the interspecicic structure of the Clementine genome

Authors: OLLITRAULT, PATRICK - Cirad, France; TEROL, JAVIER - Valencian Institute For Agricultural Research; Chen, Chunxian; FEDERICI, CLAIRE - University Of California; LOTFY, SAMIA - Cirad, France; HIPPOLYTE, ISABELLE - Cirad, France; OLLITRAULT, FREDERIQUE - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; BERARD, AURELIE - Institut National De La Recherche Agronomique (INRA); CHAUVEAU, AURELIE - Institut National De La Recherche Agronomique (INRA); CUENCA, JOSE - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; COSTANTINO, GILLES - Institut National De La Recherche Agronomique (INRA); KACAR, YILDIZ - University Of Cukurova; MU, LISA - University Of California; GARCIA-LOR, ANDRES - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; CURK, FRANCK - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; FROELICHER, YANN - Cirad, France; ALEZA, PABLO - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; BOLAND, ANNE - Genomics Institute - Novartis; BILLOT, CLAIRE - Cirad, France; NAVARRO, LUIS - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; LURO, FRANCOIS - Institut National De La Recherche Agronomique (INRA); ROOSE, MIKEAL - University Of California; GMITTER JR., FRED - University Of Florida; TALON, MANUEL - Instituto De Investigaciones Agrarias Finca La Orden-Valdesequera; BRUNEL, DOMINIQUE - Institut National De La Recherche Agronomique (INRA)

Submitted to: Acta horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2014
Publication Date: 1/20/2015
Publication URL: http://www.actahort.org/books/1065/
Citation: Ollitrault, P., Terol, J., Chen, C., Federici, C., Lotfy, S., Hippolyte, I., Ollitrault, F., Berard, A., Chauveau, A., Cuenca, J., Costantino, G., Kacar, Y.A., Mu, L., Garcia-Lor, A., Curk, F., Froelicher, Y., Aleza, P., Boland, A., Billot, C., Navarro, L., Luro, F., Roose, M.L., Gmitter Jr., F.G., Talon, M., Brunel, D. 2015. Comparative genetic mapping between clementine, pummelo and sweet orange and the interspecicic structure of the Clementine genome. Acta Horticulturae. 1065:561-573.

Interpretive Summary: Citrus include tens of different fruit types, such as mandarin, pummelo, sweet orange, grapefruit, etc. Some may be true biological species, and others are likely natural hybrids. Comparative genomic mapping among these main types facilitate us to gain new insights into interspecific hybrids, and guide to assemble these genome sequences. Understanding of their genetic relation and origin will facilitate citrus genetics studies and breeding.

Technical Abstract: Comparative genetic mapping between clementine, pummelo and sweet orange and the interspecicic structure of the Clementine genome The availability of a saturated genetic map of Clementine was identified by the International Citrus Genome Consortium as an essential prerequisite to assist the assembly of the reference whole genome sequence based on a Clementine derived haploid. The primary goals of the present study were to establish a Clementine reference map, and to perform comparative mapping with pummelo and sweet orange. Five parental genetic maps were established with SNPs, SSRs and InDels. A medium density reference map (961 markers for 1084.1 cM) of Clementine was established and used by the ICGC to facilitate the chromosome assembly of the haploid genome sequence. Comparative mapping with pummelo and sweet orange revealed that the linear order of markers was highly conserved. Reasonable inferences of most citrus genomes should be obtained by mapping next-generation sequencing data against the haploid reference genome sequence. Skewed segregations were frequent and higher in the male than female Clementine potentially leading to false interpretation of the genetic determinism of phenotypic traits. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange and identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Introgression of pummelo genome fragments were identified in heterozygosity in each chromosome. Moreover, it appeared that the genome of the haploid Clementine used to establish the citrus reference genome sequence was inherited primarily from the ‘Mediterranean’ mandarin. The usefulness of this genetic map, anchored in the reference whole genome sequence, is discussed.