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
CX6F24CX6F24genetic_marker
CX6F32CX6F32genetic_marker
CXF06CXF06genetic_marker
DxsDxsgenetic_marker
FLSFLSgenetic_marker
HKT1c800F141.1HKT1c800F141.1genetic_marker
IDCAXIDCAXgenetic_marker
JI-AAG01JI-AAG01genetic_marker
JI-AAG03JI-AAG03genetic_marker
JI-AC03JI-AC03genetic_marker
JI-AT03JI-AT03genetic_marker
JI-AT04JI-AT04genetic_marker
JI-CA0JI-CA0genetic_marker
JI-CA01JI-CA01genetic_marker
JI-GA01.1JI-GA01.1genetic_marker
JI-GAA03JI-GAA03genetic_marker
JI-TA05JI-TA05genetic_marker
JI-TA06JI-TA06genetic_marker
JI-TAT01JI-TAT01genetic_marker
JI-TC01JI-TC01genetic_marker
JI-TC04JI-TC04genetic_marker
JI-TCT01JI-TCT01genetic_marker
JI-TG01JI-TG01genetic_marker
JK-CAC15JK-CAC15genetic_marker
JK-TAA1JK-TAA1genetic_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