Genotypic Representation Analysis (GRA): A New Strategy for Identifying Molecular Markers Tightly Linked to a Target Gene

Molecular markers tightly linked to a gene (locus) of agronimic trait play an important role in crop genetics and breeding. The strategy of Genotype Representation Analysis (GRA) which is different from Bulked Segrenant Analysis (BSA) and Near Isogenic Lines (NIL) methods widely used these days, was put forward to identify the markers linked with an important agronomic trait locus. The primary step in GRA is constructing genotypic representation that contain 3~6 lines with different genetic backgrounds, while with the same target gene (locus). The primers were screened on the DNA samples of the genotype representations, and the one polymorphic marker that exhibiting the same pattern within the genotype representation and being different between the genotype representations is considered as a candidate marker. With this novel strategy two RAPD and three SSR markers tightly linked to the Rfl(＜1.0 cM) in cotton were detected, indicating that GRA is a highly efficient method of screening molecular marker(s) tightly linked to a gene (locus).