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Structure variation of chromosomes,e.g.reversion,translocation,insertion and deletion of segments,among close related species has been demonstrated in various organisms.Three tetraploid specie of Brassica,i.e.,B.napus(AnAnCnCn),B.juncea(AjAjBjBj)and B.carinata(BcBcCcCc),share one set of genomes each other which are divergent into subgenomes during evolution process.To reveal the structure variation between each set of subgemomes not only help on understanding the history of evolution but also facilitate the usages of valuable genetic resources of one subgenome in other tetraploid specie of Brassica.Assisted with the high through-put SNP markers and DArT GBS markers,we genotyped three mapping populations for each of the three tetraploid species and established high density genetic maps,respectively.The chromosomal structure variation among the different A,B and C subgenomes will be reported at the meeting,and the structure variation of individual genomes within the same crop,B.napus,will also be discussed.Available and new phenotypic data referring to the yield and seed quality traits for the three populations will be integrated and analyzed for discussing the impacts of genome variation within and among three tetraploid Brassica species on important agronomic traits.