Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies

Publication Overview
TitleComparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies
AuthorsGarcía-Lor A, Luro F, Navarro L, Ollitrault P
TypeJournal Article
Journal NameMolecular genetics and genomics
Volume287
Issue1
Year2012
Page(s)77-94
CitationGarcía-Lor A, Luro F, Navarro L, Ollitrault P. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Molecular genetics and genomics. 2012; 287(1):77-94.

Abstract

Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion–deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata.
Stocks
This publication contains information about 6 stocks:
Stock NameUniquenameType
Willow leafWillow leafcultivar
Buddha's HandBuddha's Handcultivar
ChandlerChandlercultivar
CleopatraCleopatracultivar
CorsicanCorsicancultivar
PinkPinkcultivar
Features
This publication contains information about 31 features:
Feature NameUniquenameType
1-Deoxyxylulose5-phosphate synthase1-Deoxyxylulose5-phosphate synthasegenetic_marker
b-Carotene hydroxylaseb-Carotene hydroxylasegenetic_marker
Cation/H+ membrane antiporterCation/H+ membrane antiportergenetic_marker
Chalcone isomeraseChalcone isomerasegenetic_marker
Chalcone synthaseChalcone synthasegenetic_marker
Flavonol synthaseFlavonol synthasegenetic_marker
IDAPVIDAPVgenetic_marker
IDAtGRCIDAtGRCgenetic_marker
IDCAXIDCAXgenetic_marker
IDCHIIDCHIgenetic_marker
IDEMAIDEMAgenetic_marker
IDHYB1IDHYB1genetic_marker
IDHYB2IDHYB2genetic_marker
IDLCY2IDLCY2genetic_marker
IDPEPC1IDPEPC1genetic_marker
IDPEPC2IDPEPC2genetic_marker
IDPSYIDPSYgenetic_marker
ISTRPAISTRPAgenetic_marker
Lycopene b-cyclaseLycopene b-cyclasegenetic_marker
Lycopene b-cyclase 2Lycopene b-cyclase 2genetic_marker
Malate dehydrogenaseMalate dehydrogenasegenetic_marker
Malic enzymeMalic enzymegenetic_marker
Phosphoenolpyruvate carboxylasePhosphoenolpyruvate carboxylasegenetic_marker
PhosphofructokinasePhosphofructokinasegenetic_marker
Phytoene synthasePhytoene synthasegenetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2012
Published Location|||
Language Abbreng
Publication Model[electronic resource].
URLhttp://dx.doi.org/10.1007/s00438-011-0658-4
KeywordsCitrus aurantium, Citrus limon, Citrus maxima, Citrus medica, Citrus paradisi, Citrus reticulata, Citrus sinensis, cultivars, genes, genetic markers, genetic recombination, genetic variation, grapefruits, hybrids, interspecific hybridization, lemons, linkage disequilibrium, mandarins, microsatellite repeats, oranges, pummelos
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4650149
PMID: PubMedPMID:22160318