Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus

Publication Overview
TitleIdentification and analysis of single nucleotide polymorphisms (SNPs) in citrus
AuthorsNovelli V, Takita M, Machado M
TypeJournal Article
Journal NameEuphytica : international journal of plant breeding
Volume138
Issue3
Year2004
Page(s)227-237
CitationNovelli V, Takita M, Machado M. Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus. Euphytica : international journal of plant breeding. 2004; 138(3):227-237.

Abstract

Most of the cultivated species of citrus have narrow genetic basis. Relationships among species and cultivars are obscured by sexual compatibility, polyembryony, apomixis and a high incidence of somatic mutations. DNA analysis is crucial in genetic studies not only for citrus breeding programs but also for characterization of hybrids and species. In this paper, single nucleotide polymorphisms (SNPs) were investigated in 58 accessions of Citrus, hybrids and related genera. Genomic sequences of ‘Pˆera IAC’ sweet orange (Citrus sinensis L. Osbeck) were used for primer design and selection of sequence tagged sites (STSs) for identification of SNPs. Analysis of 36 STSs showed identical sequences among 40 of the 41 sweet orange accessions studied. However, these accessions were heterozygous for many SNPs. Ten selected STSs were analyzed in 17 additional accessions from 13 species and hybrids. Comparing to the ‘Pˆera IAC’ sweet orange accession, a total of 150 polymorphic nucleotides were identified and most of the alterations were transitions (52.7%). The greatest number of SNPs was observed in Poncirus trifoliata (L.) Raf. and the smallest in ‘Ponkan’ mandarin (Citrus reticulata Blanco). At the intra-specific level, ‘Ba´ıa Gigante’ (Citrus sinensis L. Osbeck) was the only sweet orange accession with a divergent SNPs genotype, which corroborates the hypothesis of a hybrid origin for this accession. Although the STSs analyzed represent randomly sampled genomic sequences, they provided consistent information about the level of polymorphism and showed the potential of SNPs markers for characterization and phylogenetic studies.
Features
This publication contains information about 10 features:
Feature NameUniquenameType
CCSM-SNP_03CCSM-SNP_03genetic_marker
CCSM-SNP_13CCSM-SNP_13genetic_marker
CCSM-SNP_22CCSM-SNP_22genetic_marker
CCSM-SNP_26CCSM-SNP_26genetic_marker
CCSM-SNP_27CCSM-SNP_27genetic_marker
CCSM-SNP_28CCSM-SNP_28genetic_marker
CCSM-SNP_31CCSM-SNP_31genetic_marker
CCSM-SNP_35CCSM-SNP_35genetic_marker
CCSM-SNP_36CCSM-SNP_36genetic_marker
CCSM-SNP_53CCSM-SNP_53genetic_marker
Properties
Additional details for this publication include:
Property NameValue
URLhttps://link.springer.com/article/10.1023/B:EUPH.0000047086.47988.82
Publication Date2004
Language Abbreng
Publication Model[electronic resource]
Published Location|||
Publication TypeJournal Article
KeywordsCitrus, Poncirus trifoliata, single nucleotide polymorphism, germplasm, plant genetic resources, genetic markers, nucleotide sequences, sequence tagged sites, molecular sequence data