10.5061/DRYAD.FXPNVX0SN
Adhikari, Laxman
0000-0001-9507-5117
Kansas State University
Poland, Jesse
Kansas State University
Shrestha, Sandesh
Kansas State University
Wu, Shuanyge
Kansas State University
Crain, Jared
Kansas State University
Gao, Lianglian
Kansas State University
Evers, Byron
Kansas State University
Wilson, Duane
Kansas State University
Ju, Yoonha
Kansas State University
Koo, Dal-Hoe
Kansas State University
Hulc, Pierre
University of Saskatchewan
Pozniak, Curtis
University of Saskatchewan
Walkowiak, Sean
University of Saskatchewan
Wang, Xiaoyun
Cornell University
Wu, Jing
Cornell University
Glaubitz, Jeffrey
Cornell University
DeHaan, Lee
The Land Institute
Friebe, Bernd
Kansas State University
A high-throughput skim-sequencing approach for genotyping, dosage
estimation and identifying translocations
Dryad
dataset
2021
FOS: Biological sciences
2021-10-09T00:00:00Z
2021-10-09T00:00:00Z
en
https://doi.org/10.5281/zenodo.5831961
85040 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Skim-sequencing data of different populations described in the manuscript
were generated using Nextera library preparation method. The data
processing steps were illustrated in the attached pipeline script.
We have Readme.pdf file which describes about the dataset.