Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
Highlights
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants
As a result of rapid advances in sequencing technologies combined with decreasing costs, the first complete wheat genome has been s equenced[7] and the first step towards a wheat pan-genome sequence has been made[8]
We have shown for the first time that introgressions and their putative donor species can be identified without prior knowledge of the pedigree
Summary
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Interspecific hybridisation, known as interspecies crossing, wide hybridisation, or distant hybridisation, allows the transfer of DNA from a donor species into a crop plant This strategy has been used in breeding to add desired traits to crop plants, for example, resistance or tolerance to biotic or abiotic stress[10,11,12]. The methods mentioned above do not identify putative donor species, which is especially interesting for elite lines with multiple introgressions from different donors or for old landraces For such wheat accessions, the origin of a genomic region that might influence an important trait is often unknown. We describe a method for identifying introgressions and predicting putative donor species and demonstrate its applicability using 10 RQAs of wheat
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