Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication-related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.

BGI Genomics BGI Shenzhen Shenzhen China

BGI Institute of Applied Agriculture BGI Shenzhen Shenzhen China

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Olomouc Czech Republic

College of Bioscience and Engineering Jiangxi Agricultural University Nanchang Jiangxi China

College of Horticulture and Forestry Sciences Hubei Engineering Technology Research Center for Forestry Information Huazhong Agricultural University Wuhan China

Department of Plant Sciences University of California Davis CA USA

Key Laboratory of Crop Gene Resources and Germplasm Enhancement Ministry of Agriculture The National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China

School of Biological Sciences and Institute of Agriculture The University of Western Australia Perth WA Australia

State Agriculture Biotechnology Centre School of Veterinary and Life Sciences Australia Export Grains Innovation Centre Murdoch University Perth WA Australia

State Key Laboratory of Crop Stress Biology for Arid Areas College of Plant Protection Northwest A and F University Yangling Shaanxi China

State Key Laboratory of Crop Stress Biology in Arid Areas College of Agronomy and Yangling Branch of China Wheat Improvement Center Northwest A and F University Yangling Shaanxi China

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