Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).

BMC Genomics
Kevin StoffelAllen Van Deynze

Abstract

High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® a...Continue Reading

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Citations

Aug 21, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Laura D AtkinsonDavid A C Pink
Feb 6, 2013·Genome Génome / Conseil National De Recherches Canada·Shawn C YarnesAllen Van Deynze
Dec 8, 2015·Horticulture Research·Annabelle DamerumGail Taylor
Oct 8, 2013·Scientific Reports·Ivan SimkoRichard W Michelmore
Jul 14, 2016·The Plant Journal : for Cell and Molecular Biology·Heqiang HuoKent J Bradford
Apr 13, 2017·Nature Communications·Sebastian Reyes-Chin-WoRichard W Michelmore
Feb 10, 2018·Horticulture Research·Amanda M Hulse-KempAllen Van Deynze
Apr 4, 2013·G3 : Genes - Genomes - Genetics·Maria José TrucoRichard W Michelmore
Jan 24, 2017·Molecular Breeding : New Strategies in Plant Improvement·Peter G WalleyRosemary Collier
Oct 6, 2020·Postharvest Biology and Technology·Annabelle DamerumGail Taylor
Mar 28, 2021·G3 : Genes - Genomes - Genetics·Miguel Macias-GonzálezRichard W Michelmore

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Datasets Mentioned

BETA
SRP004854
SRP008310

Methods Mentioned

BETA
genotyping
chip
electrophoresis
chips
RNAseq
PCR
Assay

Software Mentioned

MySQL
PHP
SeqBoot
Bioconductor Affymetrix package
Linux
BLAST
PC
Affymetrix package
STAT®
BLASTn

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