Durum wheat gene annotation and selection signature detection in the tetraploid wheat germplasm from wild emmer to modern durum wheat

The domestication of the wild emmer wheat nearly 10,000 years ago in the Fertile Crescent lead to the evolution of the free-threshing and easy to harvest tetraploid Triticum durum wheat. We annotated the gene models and assessed the gene expression pattern of a 10.45-gigabase assembly of durum wheat cultivar Svevo and predicted 66,559 high-confidence genes with 95.8% expression evidence. 75.0, 70.5 and 74.5% of high-confidence genes were expressed in grain, leaf and root tissues, respectively, of the 13 elite worldwide durum wheat varieties. Additionally, we annotated 1,487 loci associated with NBS-LRR genes that are prominently involved in signaling and plant disease resistance. Using the Global Tetraploid wheat Collection composed of 1,856 accessions representing the four principal germplasm groups involved in the tetraploid domestication and selection history, we detected the genetic diversity and selection signature regions associated with wild emmer domestication and durum wheat evolution on the pericentromeric regions of chromosome groups 2, 4, 6 and on chromosomes 1A, 7B. Several diversity reduction and selection signature peaks overlapped with loci associated with domestication, disease resistance, yellow pigment content and seed dormancy. Population structure of the tetraploid diversity panel assessed by ADMIXTURE subdivided wild emmer (WEW) in two main populations, domesticated emmer (DEW) and durum landraces (DWL) in six populations each, and durum cultivars (DWC) in five subpopulations. The modern durum wheat germplasm showed the highest relationship to the North African and Turkey to Transcaucasia DWL populations, while the Ethiopian and T. turanicum populations were the most differentiated with a minimal contribution to the modern durum germplasm. The selection signature detection provided an insight into the dynamics of tetraploid wheat domestication and selection. The reference assembly of durum wheat is a valuable resource directed to accelerate the progress and accuracy of genome-assisted advancement of modern wheat.