9k snp chip

Fifty wild barley ILs of the S42IL library (83 lines) and the recipient parent Scarlett were selected for the experiment. The S42IL library was developed from the advanced backcross population S42 and described in detail by Schmalenbach [47 (link),63 (link)]. In brief, the S42ILs were originated from the cross between the German spring cultivar Scarlett (Hordeum vulgare ssp. vulgare) and the wild barley accession ISR42-8 (H. vulgare ssp. spontaneum, Koch), followed by three rounds of backcrossing to Scarlett as a recurrent parent and several rounds of self-pollination, combined with marker-assisted selection to produce a BC₃S₄ population (83 lines). Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8, meanwhile the remaining part of the genome is derived from the elite barley cultivar Scarlett. The introgression lines were genotyped with Illumina 9K SNP chip and genetic map of the S42ILs library was created by Comadran et al. [64 (link)], where more details can be found. The genetic characterization of position and extent of Hsp introgressions of the complete set based on the Infinium 9k iSelect assay has been published by Honsdorf et al. [39 (link)].

DNA samples were extracted from young leaves (2- to 3-wk-old) taken from each line, using Wizard Genomic DNA purification (Promega) following the manufacturer’s protocol. DNA samples were genotyped using an Illumina 9K SNP chip with 8632 SNPs (Cavanagh et al. 2013 ). For a given marker, the genotype for the ith line was coded as the number of copies of a designated marker-specific allele carried by the ith line (absences equal to zero, and presents equal to one). SNP markers with unexpected genotype AB (heterozygous) were recoded as either AA or BB, based on the graphical interface visualization tool of GenomeStudio (Illumina) software. SNP markers that did not show clear clustering patterns were excluded. In addition, 66 simple sequence repeat (SSR) markers were screened. After filtering the markers for 0.05 minor allele frequency (MAF), and deleting markers with more than 10% of no calls, the final set of SNPs was 1635 SNPs.

DNA samples were extracted from young leaves 2–3 weeks old, taken from each line, using Wizard Genomic DNA purification (Promega) and following the manufacturer’s protocol. DNA samples were genotyped using an Illumina 9K SNP chip with 8632 single nucleotide polymorphisms (SNPs) (Cavanagh et al., 2013). For a given marker, the genotype for the ith line was coded as the number of copies of a designated marker-specific allele carried by the ith line (absence = zero and presence = one). SNP markers with unexpected AB (heterozygous) genotype were recoded as either AA or BB, based on the graphical interface visualization tool of GenomeStudio (Illumina) software. SNP markers that did not show clear clustering patterns were excluded. In addition, 66 simple sequence repeat markers were screened. After filtering the markers for 0.05 minor allele frequency and deleting markers with 0.10% of no calls, the final set of SNPs included 1635 SNPs.