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Seed colour inheritance in Brassicajuncea was studied in F1, F2 and BC1 populations.Seed colour was found under the control of the maternal genotype and the brown-seeded trait was dominant over the yellow-seeded trait.Segregation analysis revealed one pair of major genes controlled the seed colour.To develop markers linked to the seed colour gene, AFLP (amplified fragments length polymorphism) combined with BSA (bulk segregant analysis) technologyique was used to screen the parents and bulks selected randomly from an F2 population (Wuqi yellow-mustard × Wugong mustard) consisting of 346 individuals.From a survey of 512 AFLP primer combinatons, 15 AFLP markers located on either side of the gene were identified and the average distance between markers was 2.59cM.P11MG15 was a co-segregated marker and the closest markers (P03MC08, P16MC02 and P11MG01) were at a distance of 0.3, 0.3 and 0.7cM from the target gene, respectively.In order to utilize the markers for breeding of yellow-seeded varieties, four AFLP markers, P11MG01, P15MG15, P09MC12 and P16MC02 were successfully converted into SCAR (sequence characterized amplified region) markers.The seed colour trait controlled by the single gene together with the available molecular markers will greatly facilitate the future breeding of yellow-seeded varieties.The markers found in the present study could accelerate the step of map -based cloning of the target gene.