Spelt wheat is an old crop that has recently been re-established, accompanied by a continuing increase in acreage to satisfy current consumer trends for novel and interesting products. Here, we employed a diversity panel of 123 old and new spelt accessions to molecularly characterize them and to investigate the genetic architecture underlying eight agronomic, morphological and disease resistance traits. We show that there is no major population structure and no grouping according to the age of the accessions, in line with the short breeding history and the intensive use of old cultivars in the re-establishment of spelt. Nevertheless, allele frequency differences between old and new accessions indicate a potential effect of breeding and selection on some genomic regions. Linkage disequilibrium was found to stretch approximately 5–10 cM. Genomewide association mapping identified putative QTL for all eight traits, but indicates different genetic architectures. Taken together, our results may assist future breeding of this ancient crop, towards sustainable product chains and a further diversification of our food basket.
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