title: A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping.
abstract: BACKGROUND
  Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine.
  
  
  RESULTS
  Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome.
  
  
  CONCLUSIONS
  A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.
authors.affiliation: CIRAD, UMR AGAP, F-34398 Montpellier, France. patrick.ollitrault@cirad.fr
authors.forename: Patrick
authors.initials: P
authors.lastname: Ollitrault
authors.forename: Javier
authors.initials: J
authors.lastname: Terol
authors.forename: Chunxian
authors.initials: C
authors.lastname: Chen
authors.forename: Claire T
authors.initials: CT
authors.lastname: Federici
authors.forename: Samia
authors.initials: S
authors.lastname: Lotfy
authors.forename: Isabelle
authors.initials: I
authors.lastname: Hippolyte
authors.forename: Frédérique
authors.initials: F
authors.lastname: Ollitrault
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bérard
authors.forename: Aurélie
authors.initials: A
authors.lastname: Chauveau
authors.forename: Jose
authors.initials: J
authors.lastname: Cuenca
authors.forename: Gilles
authors.initials: G
authors.lastname: Costantino
authors.forename: Yildiz
authors.initials: Y
authors.lastname: Kacar
authors.forename: Lisa
authors.initials: L
authors.lastname: Mu
authors.forename: Andres
authors.initials: A
authors.lastname: Garcia-Lor
authors.forename: Yann
authors.initials: Y
authors.lastname: Froelicher
authors.forename: Pablo
authors.initials: P
authors.lastname: Aleza
authors.forename: Anne
authors.initials: A
authors.lastname: Boland
authors.forename: Claire
authors.initials: C
authors.lastname: Billot
authors.forename: Luis
authors.initials: L
authors.lastname: Navarro
authors.forename: François
authors.initials: F
authors.lastname: Luro
authors.forename: Mikeal L
authors.initials: ML
authors.lastname: Roose
authors.forename: Frederick G
authors.initials: FG
authors.lastname: Gmitter
authors.forename: Manuel
authors.initials: M
authors.lastname: Talon
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
mesh_terms: D001947:Breeding / Q000379:methods; D002874:Chromosome Mapping; D002957:Citrus / Q000235:genetics*; D019143:Evolution, Molecular; D005819:Genetic Markers; D005838:Genotype; D006239:Haplotypes / Q000235:genetics; D006824:Hybridization, Genetic; D008126:Lod Score; D018895:Microsatellite Repeats / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
chemical_list: D005819:Genetic Markers