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Yellow mustard, cultivated in northern Shaanxi of China, is a valuable germplasm of Brassica juncea with low erucic acid content. Its yellow seed colour is controlled by a recessive allele of a single gene, whose dominant allele conditions brown seed colour. To map the yellow seed colour allele, amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) technologies were used to identify markers linked to the recessive allele. The analysis was done on 386 F 2 plants, segregating for seed colour, from the cross Wuqi yellow mustard × Wugong mustard. The plants were selfed to determine their seed colour genotype. Twenty AFLP markers and eight SSR markers were identified from 256 AFLP primer combinations and 624 pairs of SSR primers, respectively. Blast analysis indicated that the sequences of four closely linked AFLP and SSR markers showed good collinearity with those of Arabidopsis chromosome 3, and the homologue of the yellow seed col - our allele was located between At3g14190 and At3g32130 . Sequence information of the region between the two genes of Arabidopsis could be used to develop more closely linked markers to narrow down the homologue of the yellow seed colour allele. These results would accelerate the procedure of yellow seed colour gene cloning and marker-assisted selection for yellow mustard

AFLP and SSR markers linked to the yellow seed colour gene in Brassica juncea L.