Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping

Publication Overview
TitleTransferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping
AuthorsLuro F, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, and Morillon R
TypeJournal Article
Journal NameBMC Genomics
Volume9
Issue1
Year2008
Page(s)287
CitationLuro F, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, and Morillon R. (2008). Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics. 2008. 9(1):287.

Abstract

BACKGROUND:During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences.RESULTS:Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis.CONCLUSION:Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus.
Stocks
This publication contains information about 14 stocks:
Stock NameUniquenameType
Willow leafWillow leafaccession
Brazil sweetBrazil sweetaccession
CleopatraCleopatraaccession
CorsicanCorsicanaccession
KindiaKindiaaccession
Lisbon foothillLisbon foothillaccession
MarshMarshaccession
MexicanMexicanaccession
MorrocoMorrocoaccession
NulesNulesaccession
PinkPinkaccession
Sans pepinSans pepinaccession
Washington NavelWashington Navelaccession
RubidouxRubidouxaccession
Features
This publication contains information about 42 features:
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Ci01H05.2Ci01H05.2genetic_marker
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10.110.1genetic_marker
16.116.1genetic_marker
20.120.1genetic_marker
21.121.1genetic_marker
25.125.1genetic_marker
26.126.1genetic_marker
32.132.1genetic_marker
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43.143.1genetic_marker
67.167.1genetic_marker
92.192.1genetic_marker
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121.1121.1genetic_marker
137.1137.1genetic_marker
154.1154.1genetic_marker
159.1159.1genetic_marker

Pages

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Property NameValue
DOI10.1186/1471-2164-9-287
TitleBMC Genomics
URLhttp://www.biomedcentral.com/1471-2164/9/287
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DatabaseAccession
PMID: PubMedPMID:18558001