Development of genome-specific SSR markers for the identification of introgressed segments of in the background.

Unlabelled: L. (white mustard) is recognized for carrying host resistance against several biotic stresses including, , which is responsible for blight disease in cultivated Brassica. However, another cultivated has a dearth for genetic resistance for these stresses due to its narrow genetic base. Therefore, we performed introgression of the genomic regions of into backcross progenies of  +  somatic hybrids. These advanced generations with chromosomal segments are named - introgression lines (ILs). In the present study, we developed the genome-specific microsatellites from the draft genome to track the genome introgressions and responsible regions for resistance to . For developing these SSR markers, the unique contigs of draft genome were identified through BLASTN with , , , and reference genome assemblies, including mitochondrial and chloroplast genomes, and further used for marker development. Out of 403,423 contigs, we have identified 65,343 non-hit contigs of that yielded a total of 1231 genome-specific microsatellites, out of which 1107 were expected to produce a single allele upon amplification. Out of the total SSRs, 234 primer pairs were randomly picked from whole-genome and validated between and genomes for their specificity. In the validation experiment, these markers gave a single amplicon into , while they did not amplify in genome. Of these, 59 microsatellites were used to track introgressions in 80 BCF lines. To the best of our knowledge, this is the first time that these two genetic resources are developed in the form of ILs and -specific markers. Therefore, both the resources unlock a new avenue of breeding for biotic and abiotic stresses along with quality traits.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03402-0.