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Background  Plant architecture, which is mostly determined by shoot branching, plays an important role in plant growth and development. Thus, it is essential to explore the regulatory molecular mechanism of branching patterns based on the economic and ecological importance. In our previous work, a multiple-branches birch mutant  br  was identified from 19  CINNAMOYL-COENZYME A REDUCTASE 1  ( CCR1 )-overexpressed transgenic lines, and the expression patterns of differentially expressed genes in  br  were analyzed. In this study, we further explored some other characteristics of  br , including plant architecture, wood properties, photosynthetic characteristics, and IAA and Zeatin contents. Meanwhile, the T-DNA insertion sites caused by the insertion of exogenous  BpCCR1  in  br  were identified to explain the causes of the mutation phenotypes.    Results  The mutant  br  exhibited slower growth, more abundant and weaker branches, and lower wood basic density and lignin content than  BpCCR1  transgenic line (OE2) and wild type (WT). Compared to WT and OE2,  br  had high stomatal conductance (Gs), transpiration rate (Tr), but a low non-photochemical quenching coefficient (NPQ) and chlorophyll content. In addition,  br  displayed an equal IAA and Zeatin content ratio of main branches’ apical buds to lateral branches’ apical buds and high ratio of Zeatin to IAA content. Two T-DNA insertion sites caused by the insertion of exogenous  BpCCR1  in  br  genome were found. On one site, chromosome 2 (Chr2), no known gene was detected on the flanking sequence. The other site was on Chr5, with an insertion of 388 bp T-DNA sequence, resulting in deletion of 107 bp 5′ untranslated region (UTR) and 264 bp coding sequence (CDS) on  CORONATINE INSENSITIVE 1  ( BpCOII ). In comparison with OE2 and WT,  BpCOI1  was down-regulated in  br , and the sensitivity of  br  to Methyl Jasmonate (MeJA) was abnormal.    Conclusions  Plant architecture, wood properties, photosynthetic characteristics, and IAA and Zeatin contents in main and lateral branches’ apical buds changed in  br  over the study’s time period. One T-DNA insertion was identified on the first exon of  BpCOI1 , which resulted in the reduction of  BpCOI1  expression and abnormal perception to MeJA in  br . These mutation phenotypes might be associated with a partial loss of  BpCOI1  in birch.

Characterization and T-DNA insertion sites identification of a multiple-branches mutant br in Betula platyphylla × Betula pendula