A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

Publication Overview
TitleA reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping
AuthorsOllitrault P, Terol J, Chen C, Federici CT, Lotfy S, Hippolyte I, Ollitrault F, Bérard A, Chauveau A, Cuenca J, Costantino G, Kacar Y, Mu L, Garcia-Lor A, Froelicher Y, Aleza P, Boland A, Billot C, Navarro L, Luro F, Roose ML, Gmitter FG, Talon M, Brunel D
TypeJournal Article
Journal NameBMC Genomics
Volume13
Year2012
Page(s)593
CitationOllitrault, P, Terol, J, Chen, C, Federici, CT, Lotfy, S, Hippolyte, I, Ollitrault, F, Bérard, A, Chauveau, A, Cuenca, J, Costantino, G, Kacar, Y, Mu, L, Garcia-Lor, A, Froelicher, Y, Aleza, P, Boland, A, Billot, C, Navarro, L, Luro, F, Roose, ML, Gmitter, FG, Talon, M, and Brunel, D. A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genomics. 2012. 13:593.

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.
Features
This publication contains information about 944 features:
Feature NameUniquenameType
CiC2573CiC2573genetic_marker
CiC2579CiC2579genetic_marker
CiC2590CiC2590genetic_marker
CiC2612CiC2612genetic_marker
CiC2625CiC2625genetic_marker
CiC2635CiC2635genetic_marker
CiC2644CiC2644genetic_marker
CiC2647CiC2647genetic_marker
CiC2648CiC2648genetic_marker
CiC2672CiC2672genetic_marker
CiC2689CiC2689genetic_marker
CiC2693CiC2693genetic_marker
CiC2699CiC2699genetic_marker
CiC2700CiC2700genetic_marker
CiC2708CiC2708genetic_marker
CiC2709CiC2709genetic_marker
CiC2768CiC2768genetic_marker
CiC2788CiC2788genetic_marker
CiC2790CiC2790genetic_marker
CiC2797CiC2797genetic_marker
CiC2804CiC2804genetic_marker
CiC2809CiC2809genetic_marker
CiC2810CiC2810genetic_marker
CiC2815CiC2815genetic_marker
CiC2824CiC2824genetic_marker

Pages

Stocks
This publication contains information about 16 stocks:
Stock NameUniquenameType
ChandlerChandleraccession
NulesNulesaccession
PinkPinkaccession
Sweet OrangeSweet Orangeaccession
Trifoliate orangeTrifoliate orangeaccession
SanfordSanfordaccession
ArgentinaArgentinaaccession
FiwickeFiwickeaccession
flying dragonflying dragonaccession
Ridge PineappleRidge Pineappleaccession
RubyRubyaccession
Citrus-SweetOrange-Ref-F1Citrus-SweetOrange-Ref-F1population
Citrus-Chandler-Ref-F1Citrus-Chandler-Ref-F1population
Citrus-Clementine-Ref-F1Citrus-Clementine-Ref-F1population
Citrus-Pink-Ref-F1Citrus-Pink-Ref-F1population
Poncirus/Citrus-SynthesisMap-Ref-F1Poncirus/Citrus-SynthesisMap-Ref-F1population
Properties
Additional details for this publication include:
Property NameValue
Year2012
Journal AbbreviationBMC Genomics
Keywordsbreeding, chromosome mapping, Citrus, molecular evolution, genetic markers, genotypes, haplotypes, genetic hybridization, SSR, SNP