Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley

C.B. Hill; D. Wong; J. Tibbits; K. Forrest; M. Hayden; X-Q Zhang; S. Westcott; T.T. Angessa; C. Li

doi:10.1038/s41597-019-0011-z

Back

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley

Journal article

Open access

Peer reviewed

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley

C.B. Hill, D. Wong, J. Tibbits, K. Forrest, M. Hayden, X-Q Zhang, S. Westcott, T.T. Angessa and C. Li

Scientific Data, Vol.6, Article number: 12

2019

DOI: https://doi.org/10.1038/s41597-019-0011-z

Files and links (2)

pdf

variants in barley.pdfDownload View

Published (Version of Record) Open Access

url

Free to Read *No subscription requiredView

Abstract

In barley and other cereal crops, phenological diversity drives adaptation to different cultivation areas. Improvement of barley yield and quality traits requires adaptation to specific production areas with introgression of favorable alleles dependent upon precise identification of the underlying genes. Combining targeted sequence capture systems with next-generation sequencing provides an efficient approach to explore target genetic regions at high resolution, and allows rapid discovery of thousands of genetic polymorphisms. Here, we apply a versatile target-capture method to detect genome-wide polymorphisms in 174 flowering time-related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Sequences were generated across a phenologically diverse panel of 895 barley varieties, resulting a high mean depth coverage of ~25x allowing reliable discovery and calling of insertion-deletion (InDel) and single nucleotide polymorphisms (SNPs). Sequences of InDel and SNPs from the targeted enrichment were utilized to develop 67 Kompetitive Allele Specific PCR (KASP) markers for validation. This work provides researchers and breeders a comprehensive molecular toolkit for the selection of phenology-related traits in barley.

Details

Title: Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley
Authors/Creators: C.B. Hill (Author/Creator) - Murdoch University
D. Wong (Author/Creator) - Agriculture Victoria
J. Tibbits (Author/Creator) - Agriculture Victoria
K. Forrest (Author/Creator) - Agriculture Victoria
M. Hayden (Author/Creator) - La Trobe University
X-Q Zhang (Author/Creator) - Murdoch University
S. Westcott (Author/Creator) - Department of Primary Industries and Regional Development
T.T. Angessa (Author/Creator) - Murdoch University
C. Li (Author/Creator) - Department of Primary Industries and Regional Development
Publication Details: Scientific Data, Vol.6, Article number: 12
Publisher: Nature Publishing Group
Identifiers: 991005541973307891
Murdoch Affiliation: Western Barley Genetics Alliance; School of Veterinary and Life Sciences; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

#12 Responsible Consumption & Production

Metrics

155 File views/ downloads

42 Record Views

23 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Multidisciplinary Sciences
ESI research areas: Molecular Biology & Genetics