EST-SNP genotyping of citrus species using high-resolution melting curve analysis

Publication Overview
TitleEST-SNP genotyping of citrus species using high-resolution melting curve analysis
AuthorsDistefano G, La Malfa S, Gentile A, Wu S
TypeJournal Article
Journal NameTree genetics & genomes
Volume9
Issue5
Year2013
Page(s)1271-1281
CitationDistefano G, La Malfa S, Gentile A, Wu S. EST-SNP genotyping of citrus species using high-resolution melting curve analysis. Tree genetics & genomes. 2013; 9(5):1271-1281.

Abstract

Citrus taxonomy is very complex mainly due to specific aspects of its reproductive biology. A number of studies have been performed using various molecular markers in order to evaluate the level of genetic variability in Citrus. SNP markers have been used for genetic diversity assessment using a variety of different methods. Recently, the availability of EST database and whole genome sequences has made it possible to develop more markers such as SNPs. In the present study, the high-resolution melting curve analysis (HRM) was used to detect SNPs or INDELs in Citrus genus for the first time. We aimed to develop a panel of SNPs to differentiate Citrus genotypes which can also be applied to Citrus biodiversity studies. The results showed that 21 SNP containing markers produced distinct polymorphic melting curves among the Citrus spp. investigated through HRM analysis. It was proved that HRM is an efficient, cost-effective, and accurate method for discriminating citrus SNPs as well as a method to analyze more polymorphisms in a single PCR amplicon, representing a useful tool for genetic, biodiversity, and breeding studies. SNPs developed based on Citrus sinensis EST database showed a good transferability within the Citrus genus. Moreover, HRM analysis allowed the discrimination of citrus genotypes at specific level and the resulting genetic distance analysis clustered these genotypes into three main branches. The results suggested that the panel of SNP markers could be used in a variety of applications in citrus biodiversity assessment and breeding programs using HRM analysis.
Stocks
This publication contains information about 18 stocks:
Stock NameUniquenameType
AvanaAvanacultivar
ChislettChislettcultivar
ClemenrubiClemenrubicultivar
Comune clementineComune clementinecultivar
DeltaDeltacultivar
DuncanDuncancultivar
EtrogEtrogbreeding_research_material
Femminello siracusanoFemminello siracusanocultivar
HernandinaHernandinacultivar
MidknightMidknightcultivar
MiyagawaMiyagawacultivar
MoroMorocultivar
NovaNovacultivar
PrimosolePrimosolecultivar
Sha Tian YuSha Tian Yucultivar
Sour OrangeSour Orangecultivar
Tarocco GalloTarocco Gallocultivar
Washington NavelWashington Navelcultivar
Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2013
Published Location|||
Language Abbreng
Publication Model[electronic resource].
URLhttp://dx.doi.org/10.1007/s11295-013-0636-6
KeywordsCitrus sinensis, biodiversity, databases, expressed sequence tags, genetic distance, genetic markers, genetic variation, genotype, genotyping, melting, nucleotide sequences, polymerase chain reaction, single nucleotide polymorphism, taxonomy
Cross References
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DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4786197