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
CiC0004CiC0004genetic_marker
CiC0019CiC0019genetic_marker
CiC0021CiC0021genetic_marker
CiC0023CiC0023genetic_marker
CiC0025CiC0025genetic_marker
CiC0046CiC0046genetic_marker
CiC0054CiC0054genetic_marker
CiC0094CiC0094genetic_marker
CiC0096CiC0096genetic_marker
CiC0100CiC0100genetic_marker
CiC0145CiC0145genetic_marker
CiC0158CiC0158genetic_marker
CiC0181CiC0181genetic_marker
CiC0202CiC0202genetic_marker
CiC0204CiC0204genetic_marker
CiC0208CiC0208genetic_marker
CiC0215CiC0215genetic_marker
CiC0234CiC0234genetic_marker
CiC0245CiC0245genetic_marker
CiC0251CiC0251genetic_marker
CiC0257CiC0257genetic_marker
CiC0264CiC0264genetic_marker
CiC0265CiC0265genetic_marker
CiC0277CiC0277genetic_marker
CiC0279CiC0279genetic_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