High-throughput genotyping in citrus accessions using an SNP genotyping array

Publication Overview
TitleHigh-throughput genotyping in citrus accessions using an SNP genotyping array
AuthorsFujii H, Shimada T, Nonaka K, Kita M, Kuniga T, Endo T, Ikoma Y, Omura M
TypeJournal Article
Journal NameTree genetics & genomes
Volume9
Issue1
Year2013
Page(s)145-153
CitationFujii H, Shimada T, Nonaka K, Kita M, Kuniga T, Endo T, Ikoma Y, Omura M. High-throughput genotyping in citrus accessions using an SNP genotyping array. Tree genetics & genomes. 2013; 9(1):145-153.

Abstract

We developed a 384 multiplexed SNP array, named CitSGA-1, for the genotyping of Citrus cultivars, and evaluated the performance and reliability of the genotyping. SNPs were surveyed by direct sequence comparison of the sequence tagged site (STS) fragment amplified from genomic DNA of cultivars representing the genetic diversity of citrus breeding in Japan. Among 1497 SNPs candidates, 384 SNPs for a high-throughput genotyping array were selected based on physical parameters of Illumina’s bead array criteria. The assay using CitSGA-1 was applied to a hybrid population of 88 progeny and 103 citrus accessions for breeding in Japan, which resulted in 73,726 SNP calls. A total of 351 SNPs (91 %) could call different genotypes among the DNA samples, resulting in a success rate for the assay comparable to previously reported rates for other plant species. To confirm the reliability of SNP genotype calls, parentage analysis was applied, and it indicated that the number of reliable SNPs and corresponding STSs were 276 and 213, respectively. The multiplexed SNP genotyping array reported here will be useful for the efficient construction of linkage map, for the detection of markers for marker-assisted breeding, and for the identification of cultivars.
Features
This publication contains information about 277 features:
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SI001SI001genetic_marker
SI002SI002genetic_marker
SI003SI003genetic_marker
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SI006SI006genetic_marker
SI007SI007genetic_marker
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SI032SI032genetic_marker
SI033SI033genetic_marker

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Stocks
This publication contains information about 98 stocks:
Stock NameUniquenameType
Okitsu 57 GouOkitsu 57 Gouaccession
Okitsu 58 GouOkitsu 58 Gouaccession
Okitsu 60 GouOkitsu 60 Gouaccession
OrlandoOrlandoaccession
OsceolaOsceolaaccession
Otani-iyokanOtani-iyokanaccession
PagePageaccession
PixiePixieaccession
PonkanPonkanaccession
ReikouReikouaccession
RobinsonRobinsonaccession
Seminole tangeloSeminole tangeloaccession
SetokaSetokaaccession
SetomiSetomiaccession
ShikaikanShikaikanaccession
ShiranuiShiranuiaccession
Southern RedSouthern Redaccession
Sweet SpringSweet Springaccession
TamamiTamamiaccession
Tankan-T132Tankan-T132accession
TempleTempleaccession
Trovita orangeTrovita orangeaccession
YoukouYoukouaccession

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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/s11295-012-0542-3
KeywordsCitrus, DNA, chromosome mapping, cultivars, genetic variation, genotype, genotyping, marker-assisted selection, parentage, progeny, sequence analysis, single nucleotide polymorphism