M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations on meiosis in inter-subspecies hybrids..

These differences in chromosomal structure are assumed to impact chromosome segregation, hence some traits of agronomic interest, as well as fertility. However, very little is known about their precise nature, their distribution within banana diversity and the size of the zones involved.

The production of a reference sequence for banana, combined with new sequencing technologies, has provided access to a new level of resolution for characterizing these structural differences. In this context, we have developed an approach combining genetic mapping data from genotyping by sequencing, comparative genomics based on end sequences of large DNA fragments, BAC-FISH and targeted PCR.

We thus identified a reciprocal translocation involving a 3 Mb fragment at the end of chromosome 1 and a 10 Mb fragment at the end of chromosome 4 in a diploid accession belonging to the M. a.malaccensis  subspecies, in the heterozygous state.

This heterozygous structure was associated with a large reduction in recombination on the whole of chromosome 1. In addition, the ratios of gametes passed on to the progeny were distorted and this new structure was preferentially transmitted to the progenies.

The distribution of this new structure in the diversity of the tested bananas suggests that it emerged in the subspecies malaccensis. Its existence in half of the triploid banana cultivars tested suggests a role of this structure in the domestication process through mechanisms that remain to be determined (reduced fertility, increase in the production of non-reduced gametes, hence the formation of triploids, etc.).

The characterization of these structural variations and of their impact on chromosome segregation and recombination will now make it possible to take them into account for the genetic analysis of traits of agronomic interest (QTL, GWAS) and, ultimately, for the choice of crosses in breeding programmes.