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Background  Mustard ( Brassica juncea ) is an important economic vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not been well studied.    Result  In this study, free-hand sections and metabolomics showed that the purple leaves of mustard accumulated more anthocyanins than green ones. The gene controlling purple leaves in mustard,  Mustard Purple Leaves  ( MPL ), was genetically mapped and a  MYB113-like  homolog was identified as the candidate gene. We identified three alleles of the  MYB113-like  gene,  BjMYB113a  from a purple cultivar,  BjMYB113b  and  BjMYB113c  from green cultivars. A total of 45 single nucleotide polymorphisms (SNPs) and 8 InDels were found between the promoter sequences of the purple allele  BjMYB113a  and the green allele  BjMYB113b . On the other hand, the only sequence variation between the purple allele  BjMYB113a  and the green allele  BjMYB113c  is an insertion of 1,033-bp fragment in the 3’region of  BjMYB113c . Transgenic assay and promoter activity studies showed that the polymorphism in the promoter region was responsible for the up-regulation of the purple allele  BjMYB113a  and high accumulation of anthocyanin in the purple cultivar. The up-regulation of  BjMYB113a  increased the expression of genes in the anthocyanin biosynthesis pathway including  BjCHS ,  BjF3H ,  BjF3’H ,  BjDFR ,  BjANS  and  BjUGFT , and consequently led to high accumulation of anthocyanin. However, the up-regulation of  BjMYB113  was compromised by the insertion of 1,033-bp in 3’region of the allele  BjMYB113c .    Conclusions  Our results contribute to a better understanding of the genetics and evolution of the  BjMYB113  gene controlling purple leaves and provide useful information for further breeding programs of mustard.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03084-5.

Frequent gain- and loss-of-function mutations of the BjMYB113 gene accounted for leaf color variation in Brassica juncea