Genome stability assessment in new diverse <em>Brassica</em> allohexaploid crop types (AABBCC) using molecular karyotyping

Interspecific hybridization and polyploidization processes are known to confer advantages, such as hybrid vigor and increased environmental tolerances. Although cultivated diploid and allotetraploid Brassica species which contain different combinations of the A, B, and C genomes exist, there is no naturally occurring allohexaploid containing all three genomes (AABBCC). Despite this, there are traits in each of the Brassica species, that if combined, can potentially produce a new species with many advantageous features. Although hexaploids can be produced via human intervention, these neo-polyploids have quite unstable genomes and usually suffer from severe genome reshuffling. Whether these genome rearrangements continue in later generations and follow similar, reproducible patterns between different lines, is still unknown. This thesis aims to investigate genomic stability, chromosomes inheritance, seed fertility, and crossability between and within four Brassica allohexaploid types (2n = AABBCC = 54): naponigra (B. napus × B. nigra), carirapa (B. carinata × B. rapa), junleracea (B. juncea × B. oleracea), and NCJ (B. napus × B. carinata × B. juncea). Genomic stability was investigated using the Illumina Infinium Brassica 90K SNP array genotyping. Karyotype stability varied between genotypes. Although some genomic regions were more likely to be duplicated, deleted or rearranged, a consensus pattern was not shared between genotypes. Significant differences between genotypes and within lineages were found for frequencies of euploids and rearrangements, with one NCJ line showing relatively high karyotype stability. Only 3.2% of allohexaploid plants investigated were euploids. Hybridization between different allohexaploids was mostly achievable, with 0 - 4.6 seeds per flower bud on average, and strong maternal genotype effects were also found. Novel F1 hybrids between allohexaploid lineages showed similar fertility and stability to their parents. Meiosis analysis of the new F1 hybrids showed the production of on average 8.6 new rearrangements, with no improvement in genome stability, despite increased heterozygosity. According to the findings in this thesis, synthetic Brassica allohexaploids can develop genomic stability in a few generations, but this occurs at very low frequencies and may not always be under selective pressure, due to the unforeseeable link between fertility and karyotype constitution in these hybrid types