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  T3 Barley Sandbox

Genotyping experiment Ethiopia_Eritrea_9K

Description

Experiment Short NameETH_ERI_9K
PlatformInfinium 9K
Data ProgramUniversity of Minnesota - Agronomy (MN)
Breeding ProgramUniversity of Minnesota - Agronomy (MN)
OPA Namen/a
Processing Date4/16/13
SoftwareIllumina Genome Studio
Software version2010.3
CommentsDNA was extracted from leaves harvested from two weeks-old third selfed generation (S3) of each landrace. Leaf samples were frozen in liquid nitrogen and stored at -20 degrees C until freeze-drying using general purpose freeze dryer (Model 24DX48, Virtis Company, Gardiner, NY) according to the specifications of the manufacturer. The lyophilized tissue was subjected to tissue lysis for total genomic DNA isolation. DNA extraction was conducted using the high-throughput BioSprint 96 DNA-liquid handling workstation and the BioSprint 96 DNA Plant Kit (Qiagen) according to the manufacturer\'s instructions. DNA yield and purity were determined by measuring absorbance at 260 nm (A260) and the ratio of absorbance at 260 nm and 280 nm (A260/A280), respectively. DNA concentration of each sample was then adjusted to 50 ng/ul with 0.1X TE Buffer. The quality of DNA was confirmed by running 20 ul of the normalized DNA on a 1% agarose gel. Twenty microliters of normalized DNA was shipped to the USDA-ARS Biosciences Research Laboratory (Fargo, ND) for genotyping. Five microliters of 50 ng/ul DNA stock sample was used to run the genotyping assay. The samples were genotyped with the barley iSelect SNP chip of the expanded barley SNP marker platform using the Illumina Infinium II assay (Steemers et al. 2006). The barley iSelect SNP chip contains a total of 7,842 SNPs that comprise 2,832 of the existing barley oligonucleotide pooled assay (BOPA1 and BOPA2) SNPs discovered and mapped previously (Close et al. 2009; Munoz-Amatriai­n et al. 2011), plus 5,010 new SNPs developed from next generation sequencing data (Comadran et al. 2012). The mapping information for the barley iSelect SNPs was from the consensus map by Munoz-Amatriain et al. (in preparation). The data generated by the Infinium assay were visualized and analyzed with the genotyping module of GenomeStudio data analysis software GSGT, version 1.8.4 (Illumina, San Diego, CA). After quality evaluations, genotype calls were generated using the GenCall algorithm (version 6.3.0) implemented in the GenomeStudio software.rnReferencesrnClose T. et al. (2009BMC Genomics 10:582, Comadran J. et al. (2012). Nat Genet 44:1388-1392, Munoz-Amatriain M. et al (2011) The Plant Genome 4:238-249, Steemers FJ et al (2006). Nature methods 3:31

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6702 markers were assayed for 298 lines.
(lines and markers)

Removed by filteringRemaining
637 markers have a minor allele frequency (MAF) less than 5%
47 markers are missing more than 10% of data
682 markers removed
6020 markers

Maximum Missing Data: %     Minimum MAF: %    



Additional files available

Samples (germplasm lines)
Manifest (markers used)
Cluster File
Raw data

In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement

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