High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

BMC Genomics
Cristina EsterasBelén Picó

Abstract

Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along ...Continue Reading

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Citations

Aug 10, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Katherine SandlinCecilia McGregor
Feb 6, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Cristina EsterasBelén Picó
Jun 19, 2013·Journal of Agricultural and Food Chemistry·Ángeles ObreroBelén Román
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Apr 15, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Shahid Ali KhanWeijian Zhuang
Dec 23, 2015·Journal of Genetics·Biplab Kumar Bhowmick, Sumita Jha
Oct 17, 2018·International Journal of Molecular Sciences·Chenggang XiangChanglin Wang
Jan 4, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Gregory VogelChristine D Smart

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Methods Mentioned

BETA
genotyping
Assay
for
PCR
RAPD

Software Mentioned

EXP
Python
GenomeStudio
GoldenGate
Joinmap
MAPMAKER
ICUGI
Illumina Assay Design Tool ( ADT )
Scallop
Qgene

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