Genotypic data from the Hi-AM association mapping on Barley - SNPs (Hi-AM_SNPs)
Genotypic data from the Hi-AM association mapping panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program. Out of the 261 genotypes, 124 were from ICARDA's barley breeding program (50 two-row and 74 six-row type), 32 from Europe (28 two-row and 4 six-row type), 34 North America (28 two-row and 6 six-row type), 67 from South America (62 two-row and 5 six-row type) and 4 from Australia (only two-row type). Total genomic DNA extraction was performed on a single plant from each genotype from the HI-AM panel using a Biosprint 96 DNA Plant Kit (Qiagen, Hilden, Germany). DNA sample were processed for DaRT-Seq (Diversity Array Technology Pty Ltd, DaRT P/L) by a series of digestion/ligation reactions (Cruz et al., 2013; Ames et al., 2015). The system combines complexity reduction methods with next-generation sequencing platforms, targeting primarily genic regions (Carling et al., 2015). It produces two types of markers, SilicoDaRT markers characterized by presence/absence variation (PAVs) and classical SNPs present in the sequenced fragments (http://www.diversityarrays.com/dartapplication-dartseq-data-types). The PAV/SNP markers were subsequently aligned by using sequence information available at ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/anchoring. The Thresholds for minimum base id of 90% and E-value of 5−10 were imposed to declare positive matches against the available datasets of the physical map (ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/). The dataset contains data about SNPs markers.
| Main Authors: | , , |
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| Language: | English |
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MELDATA
2020
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| Subjects: | Agricultural Sciences, pre-breeding, disease resistance, genome-wide association study (gwas), genotypic data, qtl (quantitative trait loci), |
| Online Access: | https://hdl.handle.net/20.500.11766.1/FK2/R2AW6A |
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