Good-bye banana streak virus

The banana streak virus (BSV) is integrated in the B genome of the plantain. So, if the plantain parents are used for breeding, the BSV genes are contained within the new variety. Recently, scientists have found a way to disable the virus in the plantain’s genome, allowing new opportunities to improve the hardy plantain and develop hybrids.

Plantains are resistant to major diseases and other stresses. They also have a good root structure. Plantains would be ideal to use in plant breeding, except for one problem; they can contain a pathogenic virus (BSV) inserted right into the B genome of the plantain.

Domesticated bananas come from two banana species: Musa accuminata (AA) and M. balbisiana (BB). Plantain varieties are AAB, that is, they have two sets of chromosomes from M. accuminata one set from M. balbisiana. The BSV virus is integrated as multiple copies at a single locus of the B genome of M. balbisiana and its derivatives, including plantains.

The virus is often latent, producing no symptoms, only to flare up under stresses such as drought or even while the banana plants are being reproduced by tissue culture (which is important for eliminating other types of virus). The BSV symptoms include yellow streaking of the plant leaves, stunting, dark blotches and splitting of the trunk (pseudostem). The bunches are smaller, and the plant can even die.

Because BSV is incorporated into the B genome, when the parents with B genome are used in crop breeding, they pass the virus along to the new varieties. This has been a major drawback for plantain breeding and for disseminating hybrids. A method was needed to disable the virus from the genome of parents used for plantain breeding.

In 2018, a team led by Leena Tripathi at IITA in Nairobi used gene editing technology (CRISPR/ Cas9) to disable the BSV virus from the plantain’s chromosome. “The breeding lines can be improved by inactivating the integrated BSV with genome editing and these breeding lines can then be used to develop plantain hybrids with no risk of activation of functional virus,” says Tripathi, principal scientist in plant biotechnology at IITA.

Leena Tripathi and team looking at the genome-edited banana plants in the laboratory. M. Adero/IITA – Kenya

The team grew eight edited plants in the glasshouse and subjected them to drought stress. Six of these plants showed no symptoms of BSV. Genetic analysis confirmed that all copies of the integrated BSV had been mutated into non- functional forms. The BSV virus on chromosome B was no longer pathogenic.

The edited plants still need to be tested in the field for a number of generations, to ensure that they do not become re-infected. Before these new plantains can be used, they will need to pass through the national biosafety committees which manage genetically modified and gene-edited crops.

This is the first report of the successful knockout of endogenous virus DNA from a host plant genome. This pioneering study paves the way for breeding programs to improve the plantain, and to allow the genes from this robust plant to be crossed with other types of bananas and the resulting hybrids shared and disseminated.