Data Sets - Updates Coming Soon!

The majority of our published DNA sequence datasets are available through the "PopSet" archive at NCBI (GenBank). Unfortunately, the PopSet archive does not preserve original alignments. Links to PopSet data sets are below, and original alignments will be added. There are also links to a couple of datasets (e.g., wild barley Adh1 and Adh3, SNP genotyping data from maize and teosinte) that we did not generate but have used in analyses.

Kono et al. (in preparation). BioRxiv. Barley SNPs from Illumina resequencing, genotyping platforms, and prior Sanger sequencing in VCF format.

Poets et al. (in review). G3: Genes | Genomes | Genetics. SNP genotyping data from the Barley CAP project.

Poets et al. 2015. Genome Biology. SNP calls for barley landraces based on machine-scored data using Alchemy.

Fang et al. 2014. G3: Genes | Genomes | Genetics. SNP genotyping from barley oligo pool assay 1 & 2 (BOPA1 & BOPA2) and SSR from the Wild Barley Diversity Collection. SNP calls are based on machine-scored data using Alchemy.

McCoy et al. 2014. J of Heredity. GYS1 diversity in horses.

Morrell et al 2014. J. of Heredity. Resequencing from barley additional barley landraces. Loci are the same as those from Morrell et al. 2007 (see below).
Cbf3, Dhn4, Dhn9, Faldh, G3pdh, ORF1, Stk
Hordeum bulbosum sequences for these loci are below.

 Data sets for additional loci from individual barley cultivars.
alpha-amylase type B, Dhn5, Dhn7, 5'Pepc, Pepc, Waxy

Fang et al. 2014. G3: Genes | Genomes | Genetics. Examination of a barley experimental population subject to introgression for Fusarium head blight resistance. Genotypic and phenotypic data for individual lines are available for download from T3 by selecting populations labeled “MN Reopened” and “MN Closed” under “select lines by properties.”

Kono et al. 2013. Mol Ecol Resour. SNP annotation from barley Illumina assays and genotype by sequencing (GBS).
Barley Annotations from Illumina Data: BOPA1, BOPA2, POPAs, Barley9K

Mascher et al. 2013. Plant J. Illumina resequencing of barley exome capture. Links to the NCBI Short Read Archive (SRA) are below. PRJEB1810, PRJEB1811, PRJEB1812, PRJEB3403, PRJEB3404 

Fang et al. 2013. J of Heredity. Resequencing data from Ipomoea purpurea from naturalized populations in the Southeastern U.S. Loci are the same as those from Gonzales et al. 2012 (see below). The additional samples in this study are included in the following links ALS, CHS-D, CHS-E, DFR-B, F3H, FLS, HLH1-like, MYB1, WDR1, MYB4, UF3GT  

Cavanagh et al. 2013. Proc Natl Acad Sci USA. SNP genotyping data from wheat 9K iSelect Illumina design.

Fang et al. 2012. Genetics. SNP genotyping data from maize and teosinte. SNP data

Gonzales et al. 2012. J of Heredity. Resequencing data from 30 accessions of Ipomoea purpurea from wild populations in Mexico from ALS, CHS-D, CHS-E, DFR-BF3H, FLS, IpHLH1, IpMyb2, IpMyb4, IpWDR1, UF3GT

Akhunov et al. 2010. BMC Genomics. Resequencing data from 2,114 wheat genes.

Aguilar-Meléndez et al. 2009. Am J Bot. Resequencing data from 80 accessions of chile pepper for Dhn, G3pdh, and Waxy.

Chen et al. 2009. J of Heredity. Resequencing data from 33 cultivated avocado accessions for Cellulase, CHS, F3H, and Stk. Aligned fasta files

Chen et al. 2008. J of Heredity. Resequencing data from 21 wild avocado accessions for Cellulase, CHS, F3H, and Stk.

Morrell et al. 2007. Proc Natl Acad Sci USA. Resequencing data for 20 additional accessions of wild barley for Cbf3, Dhn9, and ORF1, and for 32 cultivated barley accessions for Cbf3, Dhn4, Dhn9, Faldh, G3pdh, ORF1, and Stk.

Morrell et al. 2006. Genetics. Corrected haplotypes after error detection.
Fasta alignments for 18 loci and 25 wild barley accessions

Morrell et al. 2005. Proc Natl Acad Sci USA. Resequencing data for 25 wild barley 5'Pepc, Cbf3, Dhn1, Dhn4, Dhn7, Faldh, ORF1, Stk, Vrn1.

Morrell, Lundy, & Clegg 2003. Proc Natl Acad Sci USA. Resequencing data for 25 wild barley accessions for alpha-amylase type B, Dhn5, Dhn9, G3pdh, Pepc, Waxy.

Lin, Morrell, & Clegg 2002. Genetics. Resequencing data for 25 wild barley accessions for Adh2.

Lin, Brown & Clegg 2001. Proc Natl Acad Sci USA. Resequencing data for 25 wild barley accessions for Adh3.

Cummings & Clegg 1998. Proc Natl Acad Sci USA. Resequencing data for 25 wild barley accessions for Adh1.

Morrell et al. 2000. Plant Syst Evol. Phylogenetic and resequencing data for 28 Gilia accessions for ITS and trnL.

Morrell & Rieseberg 1998. Am J Bot. Phylogenetic and resequencing data for 33 Gilia accessions for ITS and trnL.

Page Updated: 18 November 2015