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Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.

Circular RNAs (circRNAs) are a kind of non-coding RNAs; they were first found over 35 years ago but have only become a research hotspot in recent years. CircRNAs are covalently closed loops derived from precursor mRNAs by non-sequential back-splicing. Based on their genomic location, circRNAs can be classified into exonic, intronic, intergenic, and exon-intronic circRNAs (Chen, 2016). By taking advantages of recent advances in bioinformatics algorithms, a large number of circRNAs have been detected among diverse organisms, including plants such as Arabidopsis thaliana and Oryza sativa (Memczak et al., 2013; Ye et al., 2015; Chen, 2016).