Abstract
We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth ≥3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbour-joining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution.
Highlights
Tetraploid emmer wheat (Triticum turgidum L. subsp. dicoccum [Schrank ex Schubl.] Thell.), the cultivated form of T. turgidum L. subsp. dicoccoides (Korn. ex Asch. & Graebn.) Thell., was among the first plant species to be domesticated in the Fertile Crescent of southwest Asia [1]
The study material consisted of 189 tetraploid wheat accessions (S1 Table) which, according to the germplasm identifications, comprised eleven Triticum timopheevii subsp. armeniacum, eight T. timopheevii subsp. timopheevii, 76 wild emmer (T. turgidum subsp. dicoccoides), 42 domesticated emmer (T. turgidum subsp. dicoccum) including one described as T. ispahanicum Heslot and 52 naked tetraploid wheats (27 durum wheats [T. turgidum subsp. durum], eleven rivet wheats [T. turgidum subsp. turgidum], six Khorasan wheats [T. turgidum L. subsp. turanicum (Jakubz) A . & D
40.3% mapped to unique positions in the T. aestivum reference genome, 48.1% mapped to multiple positions and 11.7% were unmapped
Summary
Tetraploid emmer wheat (Triticum turgidum L. subsp. dicoccum [Schrank ex Schubl.] Thell.), the cultivated form of T. turgidum L. subsp. dicoccoides (Korn. ex Asch. & Graebn.) Thell., was among the first plant species to be domesticated in the Fertile Crescent of southwest Asia [1]. But from it evolved the naked tetraploid wheats such as durum All of the naked wheats are fully domesticated but they have different ear characteristics and environmental requirements. It is not known if they emerged independently from domesticated emmer or if there was a common naked wheat ancestor: some molecular studies indicate genetic uniformity between different naked subspecies and other studies report regional or taxonomic differences [2,3,4]. The domestication of wild emmer was a critical stage in the transition from a hunting-gathering mode of subsistence to one based on agriculture
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