Karyotype instability varies by species and genotype combination in allohexaploid Brassica

Synthetic Brassica allohexaploids (2n = AABBCC) do not exist naturally but can be produced between six different parent species combinations, and can be used to investigate processes of polyploid formation and genome stabilization. In this study, we investigated hybridization potential, accumulation and frequency of copy number variants (CNVs), fertility, and karyotype stability in advanced generations of diverse allohexaploid genotypes belonging to different Brassica allohexaploid species combinations (NCJ types: B. napus x B. carinata x B. juncea; junleracea types: B. juncea x B. oleracea; naponigra types: B. napus x B. nigra; and carirapa types: B. rapa x B. carinata). Only 3.2% of allohexaploid plants investigated were euploids, with high frequencies of rearrangements. Significant differences between genotypes and between lineages within parent genotype combinations were found for frequencies of euploids and rearrangements, with one NCJ line showing relatively high karyotype stability. Hybridization between different allohexaploids was mostly achievable, with 0 - 4.6 seeds per flower bud on average, and with strong effects of maternal genotype. Novel hybrids between allohexaploid lineages showed similar fertility and stability to their parents. In the novel hybrid population, a significant correlation was observed between the inheritance of A-genome chromosome fragments (relative to C-genome fragments) and the total number of seeds produced per plant (r = 0.24). Our results suggest that synthetic Brassica allohexaploids can develop genomic stability, but that this occurs at very low frequencies, and may not always be under selective pressure due to the unpredictable relationship between fertility and genome composition in these hybrid types. Article SummaryBrassica plants with three sets of chromosomes (allohexaploids) do not exist in nature, but can be made from combinations between six different species. Here, we compared different combinations to see which are the most genomically stable and fertile, and found major differences between all allohexaploid types as well as one putatively stable line. Crosses between allohexaploid types could also be achieved in most cases, although hybrids were not more stable or fertile than their parents.