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Root depth, as an important component of root architecture, plays a significant role in growth, grain yield determination and abiotic stress tolerance in crop plants, but its genetic basis remains poorly elucidated. In this study, a panel composed of 323 wheat ( Triticum aestivum  L.) accessions was assessed for variation in root depth and genotyped with the Wheat 660K SNP Array. GWAS (genome‐wide association study) detected significant association between a 125 bp miniature inverted‐repeat transposable element (MITE) in the promoter of the  TaVSR1‐B  gene with root depth at the booting stage. We showed that the MITE repressed  TaVSR1‐B  expression by DNA methylation and H3K27 tri‐methylation. The roles of  TaVSR1‐B  in root growth were verified by altered expression of the gene in transgenic wheat, rice and a  tavsr1  TILLING mutant. Increased  TaVSR1‐B  expression made the root elongation zone shorter and the differentiation zone longer, leading to deeper root. This work provides novel insight into the genetic basis of variation in root depth and a promising target for genetic improvement of root architecture in wheat.

A transposon in the vacuolar sorting receptor gene TaVSR1‐B promoter region is associated with wheat root depth at booting stage