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
CiC6193CiC6193genetic_marker
CiC6213CiC6213genetic_marker
CiC6233CiC6233genetic_marker
CiC6235CiC6235genetic_marker
CiC6243CiC6243genetic_marker
CiC6249CiC6249genetic_marker
CiC6259CiC6259genetic_marker
CiC6260CiC6260genetic_marker
CiC6278CiC6278genetic_marker
CiC6288CiC6288genetic_marker
CiC6294CiC6294genetic_marker
CiC6306CiC6306genetic_marker
CiC6314CiC6314genetic_marker
CiC6315CiC6315genetic_marker
CiC6320CiC6320genetic_marker
CiC6324CiC6324genetic_marker
CiC6325CiC6325genetic_marker
CiC6337CiC6337genetic_marker
CiC6339CiC6339genetic_marker
CiC6363CiC6363genetic_marker
CiC6367CiC6367genetic_marker
CiC6391CiC6391genetic_marker
CiC6417CiC6417genetic_marker
CiC6423CiC6423genetic_marker
CiC6441CiC6441genetic_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