We developed an integrated genetic linkage map of Brassica carinata(Ethiopian mustard,2n=34)using high-throughput markers based on genotyping by sequencing approach.These markers were merged into the first genetic linkage map composed of 212 PCR-based markers.The new map consisted of 1366 unique loci including 639 bins containing a total of 4032 markers covering 2048cM.We identified 136 blocks and islands(small blocks)conserved in Brassicaceae,which showed a feature of hexaploidisation representing the ancestral karyotype of Arabidopsis.The genome of B.carinata shared 85%of common conserved blocks with the B genome of B.nigra/B.juncea and 80%of common blocks with the C genome of B.napus.Comparative analyses of the genomic structure of B.napus,B.carinata,A.thaliana,B.juncea and B.nigra showed that insertions and inversions at block level were frequently detected in B/C genomes of B.carinata.Up to 24 QTL for flowering and budding time were identified in the DH population.One consistent QTL for flowering time was identified in all of environments on J block of B4 linkage group where a group of genes for flowering time in Arabidopsis were aligned.Another major QTL for flowering time at winter-cropped environment was detected at E block of C6 where FT gene was localized in B.napus previously.A total of 36 and 14 QTL separately referring to six yield related attributes and three seed quality traits had been also identified in different linkage groups.The high density map of B carinata provides an opportunity for molecular-based genetic improvement of B.carinata and related species worldwide,and markers linked to the QTL we have reported should be useful for marker assisted breeding for flowering time and yield related attributes.Genetic map would also be suitable for comparative analysis of the structural variation in Brassica subgenomes and for identifying functional geneswhich have been transferred to other Brassica crops,e.g.B.napus,by breeding efforts.