A 5-bp deletion in exon 3 of a Brassica rapa ortholog of GLABRA1 (BrGL1) was previously thought to be responsible for the hairless trait of a doubled haploid line. In this study, the sequence variation of Brassica GL1 was characterized. The DNA-binding domain of GL1 in Arabidopsis thaliana was found to be highly conserved in Brassica species, while in hairless B. oleracea lines, frameshifts and nonsynonymous substitutions were detected in the coding sequences of BoGL1. Phylogenetic analysis showed that BnGL1 in hairless B. napus lines is closely related to BiGL1 in a hairy B. incana line. In 11 lines of B. rapa germplasm, nucleotide polymorphisms were only detected in exon 3 of BrGL1. Regarding the nucleotide polymorphisms in the DNA-binding domain of BrGL1, four alleles were identified, and corresponding dot-blot single nucleotide polymorphism (SNP) markers were developed and used for genotyping of 63 lines of B. rapa. The genotyping results showed that nucleotide polymorphisms in the DNA-binding domain of BrGL1 are associated with leaf hairiness. Reverse-transcription PCR analysis indicated that different BrGL1 alleles are all expressed normally. These findings reveal the key nucleotide polymorphisms of BrGL1 affecting leaf hairiness in the natural B. rapa population.
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