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

Hill, C.B.ORCID: 0000-0002-6754-5553, Wong, D., Tibbits, J., Forrest, K., Hayden, M., Zhang, X-Q, Westcott, S., Angessa, T.T. and Li, C. (2019) Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley. Scientific Data, 6 (1).

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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.

Item Type: Journal Article
Murdoch Affiliation: Western Australian State Agricultural Biotechnology Centre
Western Barley Genetics Alliance
School of Veterinary and Life Sciences
Publisher: Nature Publishing Group
United Nations SDGs: Goal 12: Responsible Consumption and Production
URI: http://researchrepository.murdoch.edu.au/id/eprint/44802
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