Previously we identified a major quantitative trait locus qTaLRO-B1 for primary root length (PRL) in wheat. Here we compared proteomics in the roots of the qTaLRO-B1 QTL isolines 178A with short PRL and small meristem size, and 178B with long PRL and large meristem size. Totally 16 differentially expressed proteins were identified, one TGF-beta receptor-interacting protein-1 (TaTRIP1) was enriched in 178A, while various peroxidases (PODs) were more abundantly expressed in 178B. The 178A roots showed higher TaTRIP1 expression, and lower levels in the unphosphorylated form of the brassinosteroid (BR) signaling component BZR1, the expression of POD genes, POD activity and O2 (.-) accumulation in root elongation zone than did the 178B roots. Low level of 24-epibrassinolide increased POD gene expression and root meristem size, and rescued the short PRL phenotype of 178A. TaTRIP1 directly interacted with BR receptor TaBRI1 of wheat. Moreover, overexpressing TaTRIP1 in Arabidopsis reduced the unphosphorylated BZR1 protein abundance, altered expression of BR-responsive genes, and inhibited POD activity, O2 (.-) accumulation in the root tip, and root meristem size. Our data suggested TaTRIP1 involved in BR signaling, and inhibited root meristem size possibly by reducing POD activity and O2 (.-) accumulation in root rip. We further demonstrated a negative correlation between TaTRIP1 mRNA level and PRL of landraces and modern wheat varieties, providing a valuable cue for better understanding the molecular mechanism underlying the genotypic difference in root morphology of wheat in the future. This article is protected by copyright. All rights reserved.