The Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome

Burridge, Amanda J, Winfield, Mark O, Wilkinson, Paul A ORCID: 0000-0002-8836-5439, Przewieslik-Allen, Alexandra M, Edwards, Keith J and Barker, Gary LA (2022) The Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome. FRONTIERS IN PLANT SCIENCE, 13. 841855-.

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Abstract

The bread wheat (<i>Triticum aestivum</i>) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite <i>T. aestivum</i> cultivars and two <i>T. aestivum</i> landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented.

Item Type:	Article
Uncontrolled Keywords:	exome capture, exome capture sequencing, introgression, sequence variation, Triticum aestivum, wheat
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	20 May 2022 10:03
Last Modified:	18 Jan 2023 21:01
DOI:	10.3389/fpls.2022.841855
Open Access URL:	https://doi.org/10.3389/fpls.2022.841855
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3155198