Infections of banana and plantain by banana streak viruses (BSV) can occur in the absence of vector-mediated transmission, through the activation of infectious endogenous BSV sequences (eBSVs). Such infectious eBSVs are present in the genome of Musa balbisiana spp, which are important progenitors for breeding improved banana varieties. Once activated by biotic or abiotic stresses, these viral integrants cause spontaneous infection in both natural and synthetic interspecific hybrids harbouring the M. balbisiana (B) genome. Therefore, the presence of infectious eBSVs within B genomes is the main constraint for breeding banana and plantain interspecific hybrids and for exchanging Musa germplasm. The sequence and organization of eBSVs in the diploid M. balbisiana genitor Pisang Klutuk Wulung (PKW) was elucidated for BSV species Obino l'EwaI (BSOLV), Goldfinger (BSGFV) and ImovO (BSIMV). This work showed that integration of BSGFV and BSOLV is di-allelic, with one infectious and one non-infectious allele, whereas that of BSImV is monoallelic. Allele-specific molecular markers were developed and used to genotype M. balbisiana germplasm, unveiling important differences between accessions and the presence of modified eBSV alleles in several accessions. Breeding improved M. balbisiana progenitors devoid of infectious eBSGFV and/or eBSOLV alleles was achieved through self-pollination and chromosome doubling of haploid lines. Both approaches lead to M. balbisiana cultivars devoid of infectious eBSOLV and/or eBSGFV resulting from the segregation of eBSOLV and eBSGFV alleles. These results pave the way to the safe use of M. balbisiana in breeding programs, and open new perspectives for breeding improved banana and plantain hybrid varieties. (Texte intégral)