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

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. 1. A doubled haploid (DH) population consisting of 48 lines from
the cross of spring wheat (Triticum aestivum) 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. 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. 3. A panel of 144 Thinopyrum intermedium x Triticum
durum (IWG--durum) lines and 141 Thinopyrum intermedium (IWG) lines were
evaluated to assess skim-seq genome coverage as well as amphiploidy
levels. 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.  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.