Genome Dominance in Allium Hybrids (A. cepa × A. roylei).

Genome dominance is a phenomenon in wide hybrids when one of the parental genomes becomes "dominant," while the other genome turns to be "submissive." This dominance may express itself in several ways including homoeologous gene expression bias and modified epigenetic regulation. Moreover, some wide hybrids display unequal retention of parental chromosomes in successive generations. This may hamper employment of wide hybridization in practical breeding due to the potential elimination of introgressed segments from progeny. In onion breeding, Allium roylei (A. roylei) Stearn has been frequently used as a source of resistance to downy mildew for cultivars of bulb onion, Allium cepa (A. cepa) L. This study demonstrates that in A. cepa × A. roylei hybrids, chromosomes of A. cepa are frequently substituted by those of A. roylei and in just one generation, the genomic constitution shifts from 8 A. cepa + 8 A. roylei chromosomes in the F1 generation to the average of 6.7 A. cepa + 9.3 A. roylei chromosomes in the F2 generation. Screening of the backcross generation A. cepa × (A. cepa × A. roylei) revealed that this shift does not appear during male meiosis, which is perfectly regular and results with balanced segregation of parental chromosomes, which are equally transmitted to the next generation. This indicates that female meiotic drive is the key factor underlying A. roylei genome dominance. Single nucleotide polymorphism (SNP) genotyping further suggested that the drive has different strength across the genome, with some chromosome segments displaying Mendelian segregation, while others exhibiting statistically significant deviation from it.

Insights from the first genome assembly of Onion (Allium cepa).

Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.