A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species

Publication Overview
TitleA nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species
AuthorsGarcia-Lor A, Curk F, Snoussi-Trifa H, Morillon R, Ancillo G, Luro F, Navarro L, Ollitrault P
TypeJournal Article
Journal NameAnnals of botany
Volume111
Issue1
Year2013
Page(s)1-19
CitationGarcia-Lor A, Curk F, Snoussi-Trifa H, Morillon R, Ancillo G, Luro F, Navarro L, Ollitrault P. A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species. Annals of botany. 2013 Jan; 111(1):1-19.

Abstract

BACKGROUND AND AIMS
Despite differences in morphology, the genera representing 'true citrus fruit trees' are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial 'species' of Citrus are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between 'true citrus fruit trees' were clarified.

METHODS
Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of Citrus and relatives of Citrus to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed.

KEY RESULTS
A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that Citrus reticulata and Fortunella form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha). These results confirm the taxonomic subdivision between the subgenera Metacitrus and Archicitrus. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial Citrus spp.

CONCLUSIONS
Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for Citrus and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of C. sinensis.

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Pages

Stocks
This publication contains information about 35 stocks:
Stock NameUniquenameType
EurekaEurekacultivar
Willow leafWillow leafcultivar
ArizonaArizonacultivar
ArrufatinaArrufatinacultivar
Avana apirenoAvana apirenocultivar
Bouquet de fleursBouquet de fleurscultivar
Buddha's HandBuddha's Handcultivar
ChandlerChandlercultivar
ClausellinaClausellinacultivar
ClemenulesClemenulescultivar
CleopatraCleopatracultivar
CorsicanCorsicancultivar
DancyDancycultivar
DiamanteDiamantecultivar
Ichang papedaIchang papedacultivar
KingKingcultivar
MarshMarshcultivar
Mauritius PapedaMauritius Papedacultivar
Melanesian papedaMelanesian papedabreeding_research_material
MexicanMexicancultivar
Nam roiNam roicultivar
OrlandoOrlandocultivar
PinkPinkcultivar
Poncire CommunPoncire Communcultivar
PonkanPonkancultivar

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1095-8290
eISSN1095-8290
Publication Date2013 Jan
Journal AbbreviationAnn. Bot.
DOI10.1093/aob/mcs227
Elocation10.1093/aob/mcs227
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
LanguageEnglish
Publication TypeResearch Support, Non-U.S. Gov't
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:23104641