A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

<p>An optimized, high-throughput and cost-effective genotyping method applicable to various crop breeding populations is very important in this genomic era. We have developed an optimized Nextera skim-sequencing (skim-seq) approach to genotype different populations that can be used for genetics studies and genomics-assisted breeding. We performed skim-seq on a variety of populations developed through doubled haploid (DH) technology, inter-specific recombinants developed through introgression, amphidiploid developed through wide crosses, and on known monosomic samples.</p> <p>1. A doubled haploid (DH) population consisting of 48 lines from the cross of spring wheat (<i>Triticum</i> <i>aestivum</i>) cultivars CDC Stanley and CDC Landmark developed by the Crop Development Centre at the University of Saskatchewan. We genotyped these DH with skim-seq and identified the genomic segments contributed by each of the two parental lines.</p> <p>2. A population of 335 back cross generation 1 (BC1) skim-seq samples for wheat-barley recombinants with group 7 translocations and 839 F1 wheat 5D monosomic lines (TA3059) along with 16 standard Chinese Spring lines as internal control.</p> <p>3. A panel of 144 <i>Thinopyrum</i> <i>intermedium</i> x <i>Triticum</i> <i>durum</i> (IWG--durum) lines and 141 <i>Thinopyrum</i> <i>intermedium</i> (IWG) lines were evaluated to assess skim-seq genome coverage as well as amphiploidy levels.</p> <p>The demultiplexed FASTQ files for all samples tested in the experiment are available at NCBI SRA public repository with respective BioProject accessions; DH lines [PRJNA729723], 5D monosomic line [PRJNA742385], wheat-barley recombinants [PRJNA738484], IWG-durum and IWG [PRJNA736976]. An example key file for the 5D monosomic line is also attached. </p> <p>This study indicated that skim-seq is an efficient approach for genomic evaluation of a range of different populations and applications. The scripts have been provided to implement skim-seq data for variant calling, identification of genomic segment dosage and alien introgression. Each step of the pipeline is described and implemented with similar sequencing data from skim-seq libraries.</p>