Brassica juncea is an important vegetable and oil crop cultivated worldwide. To increase its genetic variation, we introgressed the A genome of Brassica rapa into B. juncea. We used three each of heading and semi-heading B. juncea accessions as recipient parents and a B. rapa line, B9008, as the donor parent. We obtained 101 BC₁S₁ lines in total with expanded phenotypic variations such as leafy head shapes. We developed 132 single-nucleotide polymorphism (SNP) markers that could distinguish the A genome of B. juncea from the B. rapa genome, and tracked the introgression of B. rapa segments in the new B. juncea germplasm. On average, 59.2% of the B. juncea A genome in the B. juncea introgression lines was covered by the donor segments. We also identified three markers whose donor genotype frequencies were significantly lower than the theoretical value, suggesting strong selection of the recipient genotype during the introgression process. We provide an effective strategy to evaluate the diversity of the new germplasm based on the combination of parental resequencing data and marker genotyping results. Further genetic analysis of 1642 SNPs showed that the genetic diversity of the new B. juncea germplasm with the introgressed B. rapa genome was significantly increased. This study illustrates the potential for expanding the genetic diversity of B. juncea through the introgression of the B. rapa genome.

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