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Aliphatic glucosinolates are the predominant sulfur-rich plant secondary metabolites in economically important  Brassica  crops. Glucosinolates and their hydrolysis products are involved in plant–microbe, plant–insect, plant–animal, and plant–human interactions. It is, therefore, important to manipulate glucosinolate profiles and contents in  Brassica  species. In this study, aliphatic glucosinolates were genetically manipulated through homoeologous recombination in backcross lines followed by marker assisted selection in  B. rapa . A resynthesized  B. napus  line, from a cross between  B. rapa  and  B. oleracea , was backcrossed with Chinese cabbage doubled haploid line, RI16. Marker assisted selection for non-functional gene was performed in each backcross generations. Advanced backcross progenies (BC 3 F 2 ) were developed to identify homoeologous gene replacement and/or introgression. Reduction in 5C aliphatic glucosinolates (gluconapoleiferin, glucoalyssin, and glucobrassicanapin) was observed in BC 3 F 2  progenies of the recurrent parent that carried the  GSL-ELONG  -  gene. The  GSL-ELONG  -  positive backcross progenies were also screened by the A-genome and  BraGSL-ELONG  gene specific marker, which linked with 5C aliphatic glucosinolates. The A-genome specific marker was absent in the plants of advanced backcross progenies which showed reduction in 5C aliphatic glucosinolates. The results suggest that the functional allele had been replaced by the non-functional  GSL-ELONG  -  allele from  B. oleracea . Some advanced backcross progenies (BC 3 F 2 ) positive for the  GSL-ELONG  -  allele and the A-genome specific SCAR marker BraMAM1-1 did not show reduction in 5C aliphatic glucosinolates, suggesting that  GSL-ELONG  -  allele is recessive. Replacement of the functional locus in the A-genome by non-functional counterpart in the C-genome reduced the content of 5C aliphatic glucosinolates in  B. rapa  seeds with 20 μmol/g.

Homoeologous GSL-ELONG gene replacement for manipulation of aliphatic glucosinolates in Brassica rapa L. by marker assisted selection