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:
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ACO-PACO-Pgenetic_marker
ADCM421ADCM421genetic_marker
AocM250.1AocM250.1genetic_marker
AocM503.1AocM503.1genetic_marker
AocP256.1AocP256.1genetic_marker
ATGGcM155ATGGcM155genetic_marker
C07E05C07E05genetic_marker
C10H05C10H05genetic_marker
CAID5628CAID5628genetic_marker
Cax1P460.1Cax1P460.1genetic_marker
Cax4M386Cax4M386genetic_marker
Cax4P116Cax4P116genetic_marker
CF-1T07CF-1T07genetic_marker
CF-AAG04CF-AAG04genetic_marker
CF-ACA01CF-ACA01genetic_marker
CF-AG04CF-AG04genetic_marker
CF-AG05CF-AG05genetic_marker
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CF-CA05CF-CA05genetic_marker
CF-CA14.1CF-CA14.1genetic_marker
CF-CA16CF-CA16genetic_marker
CF-CA19CF-CA19genetic_marker

Pages

Stocks
This publication contains information about 16 stocks:
Stock NameUniquenameType
ChandlerChandlercultivar
NulesNulescultivar
PinkPinkcultivar
Sweet OrangeSweet Orangebreeding_research_material
Trifoliate orangeTrifoliate orangecultivar
SanfordSanfordbreeding_research_material
ArgentinaArgentinabreeding_research_material
FiwickeFiwickecultivar
flying dragonflying dragoncultivar
Ridge PineappleRidge Pineapplebreeding_research_material
RubyRubybreeding_research_material
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
Journal AbbreviationBMC Genomics
Year2012
Keywordsbreeding, chromosome mapping, Citrus, molecular evolution, genetic markers, genotypes, haplotypes, genetic hybridization, SSR, SNP
Cross References
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DatabaseAccession
PMID: PubMedPMID:23126659