SNP Calling Between Two Genotypes of Brassica napus

Brassica napus (AACC), an economically important crop, is a tetraploid species that resulted from hybridization between two diploid species B. rapa (AA) and B. olereacea (CC) followed by chromosome doubling. We have synthesized two new B. napus genotypes Da-Ae (AACC) and Da-Ol-1 (AACC). These strains differ in fatty acid content and the level of drought tolerance. While Da-Ae was selected from the synthetic allopolyploid F2 population created by hybridizing B.rapa with B.olereacea, Da-Ol-1 was made by crossing B.napus with B.juncea (AABB) and then backcrossing to B.napus. Over 250,000 SNPs were identified between Da-Ae and Da-Ol-1 by analyzing the RNA-seq data generated from different stages of these two genotypes, 2/3 of which are localized to subgenome A of B.napus. The higher divergence between subgenome A of the two genotypes reflected the breeding history of these two genotypes. SNP data identified from this study can be used for future genetic map construction and QTL analysis.