Assessment of haplotype and allelic diversity of SSR markers in canola

To study the haplotype and allelic diversity and to identify the informative markers of morphologic characteristics of 41 canola lines and genotypes under drought stress, 36 microsatellite markers linked to the QTLs located on the chromosome A1, C3, C5 and C6 controlling morphologic characteristics under drought stress were used. Thirteen seven selected primers produced 166 discernible bands, with 157 (94.58%) being polymorphic, indicating considerable genetic diversity among lines and genotypes. The results showed that average of marker index including Nei’s gene diversity, Shannon’s information index, the effective number of alleles were 1.508, 0.449 and 0.298 respectively in line and genotypes of rapeseed. The haplotype diversity was characterized with SSR markers associated using the QTLs associated with the two traits (shoot dry weight and total dry weight) on chromosome A1, C3, C5 and C6. The results showed that forty one rapeseed lines and genotypes divided into 9 and 5 different haplotypes based on total dry weight QTL located on chromosome A1 and C3, respectively using SLM046 cultivar as the reference. The haplotypes possessing Ol2-F11, BRMS-096 and BARS041 markers on chromosome A1 and Na10-E02, FITO133 and Na12-A08 markers on chromosome C1 could discriminate the tolerant genotypes and hence could be useful for marker-assisted selection of QTL associated with drought tolerance.