Abstract
Background and AimsBanana cultivars are derived from hybridizations involving Musa acuminata subspecies. The latter diverged following geographical isolation in distinct South-east Asian continental regions and islands. Observation of chromosome pairing irregularities in meiosis of hybrids between these subspecies suggested the presence of large chromosomal structural variations. The aim of this study was to characterize such rearrangements.MethodsMarker (single nucleotide polymorphism) segregation in a self-progeny of the ‘Calcutta 4’ accession and mate-pair sequencing were used to search for chromosomal rearrangements in comparison with the M. acuminata ssp. malaccensis genome reference sequence. Signature segment junctions of the revealed chromosome structures were identified and searched in whole-genome sequencing data from 123 wild and cultivated Musa accessions.Key ResultsTwo large reciprocal translocations were characterized in the seedy banana M. acuminata ssp. burmannicoides ‘Calcutta 4’ accession. One consisted of an exchange of a 240 kb distal region of chromosome 2 with a 7.2 Mb distal region of chromosome 8. The other involved an exchange of a 20.8 Mb distal region of chromosome 1 with a 11.6 Mb distal region of chromosome 9. Both translocations were found only in wild accessions belonging to the burmannicoides/burmannica/siamea subspecies. Only two of the 87 cultivars analysed displayed the 2/8 translocation, while none displayed the 1/9 translocation.ConclusionTwo large reciprocal translocations were identified that probably originated in the burmannica genetic group. Accurate characterization of these translocations should enhance the use of this disease resistance-rich burmannica group in breeding programmes.
Highlights
Bananas (Musa genus) provide staple food for millions of people in Asia, Africa, Latin America and Oceania, and represent a major cash crop around the world
Pairwise associations between ‘Calcutta 4’ markers projected on the 11 M. acuminata reference chromosome sequence showed, for most markers physically close on the reference sequence, strong genetic linkage, as expected (Supplementary data Fig. S2A, B)
To increase the chance of detecting signature segment junction (SSJ) corresponding to chromosome 8, we accurately identified their positions on the ‘Maia’Oa’ preliminary assembly and the ‘Banksii’ corrected assembly, and aligned paired-end data from the 123 accessions using these assemblies as additional references (Supplementary data Table S1)
Summary
Bananas (Musa genus) provide staple food for millions of people in Asia, Africa, Latin America and Oceania, and represent a major cash crop around the world. Musa acuminata diverged following the Pliocene geographical isolation in distinct South-east Asian continental regions and islands (Daniells et al, 2001; Perrier et al, 2009; Janssens et al, 2016; Rouard et al, 2018). It has been divided into 6–9 partially interfertile subspecies The current domestication scenario suggests that plants were transported during human migrations, leading to hybridization between Musa species and subspecies (Perrier et al, 2011) This resulted in the emergence of inter(sub)specific hybrids with reduced fertility (Dodds and Simmonds, 1948; Shepherd, 1999). These large-scale monocultures have favoured the emergence of diseases and extensive pesticide use (Lescot et al, 2008)
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