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Comparative Genomics Yields Clues to African Crop Virus

NEW YORK (GenomeWeb News) – Researchers are using comparative genomics to understand the evolution and epidemiology of a destructive plant virus affecting African maize crops — and to develop resistance strategies against the virus.
In a paper scheduled to appear in the September issue of the Journal of General Virology, an international team of researchers sequenced more than 80 maize streak viruses in an effort to understand the evolution of MSV-A — a strain that damages maize crops in sub-Saharan Africa. The research uncovered a handful of new grass-adapted MSV strains and provided new insights into the emergence of the disease-causing strain. Now, researchers say, this information is being applied to develop maize resistance strategies.
“Given the frailty of African agriculture and perpetual famine risks with millions of lives at stake, MSV is actually one of the most important plant pathogens worldwide,” senior author Darren Martin, an infectious disease researcher at the University of Cape Town, said in a statement. “We wanted to learn more about how the virus emerged and spread so we can develop new ways to fight the diseases it causes.”
Maize streak disease, caused by the MSV-A strain, is transmitted by leafhoppers and leads to yellowing and severe disease in African maize crops. In contrast, four grass-adapted MSV strains — MSV -B to -E — mainly infect crops such as wheat, rye, barley, and oats, causing only mild damage in maize.
The researchers suspected that understanding the genetics of these grass-adapted strains could improve their understanding of MSV-A’s biology and evolution as well. They sequenced the genomes of 83 MSVs from African grasses in South Africa, Zimbabwe, Mozambique, Nigeria, Uganda, Burundi, Rwanda, Mali, and La Reunion. In the process, they uncovered six new strains, dubbed MSV-F to –K.
By combining their own data along with publicly available sequence data for MSV and non-MSV streak viruses, the team began pinpointing recombination hotspots in the MSV genome. They found that more than 90 percent of the MSVs appear to be recombinant, with the most pathogenic MSV-A strain representing a combination of two apparently harmless grass-adapted strains.
“[E]very MSV that causes severe disease in maize has descended from an ancestral virus that was the recombinant offspring of two relatively harmless wild grass infecting viruses,” Martin noted in a statement. “This chance recombination event could be the reason MSV has become such a serious problem.”
Even so, Martin told GenomeWeb Daily News, there are limitations to MSV recombination, with MSV strains apparently undergoing conserved gene swapping events. “The patterns are evolutionarily constrained,” Martin said. “In the design of resistance strategies, we are specifically taking that into account.”
The patterns of MSV infection were also telling. Overall, the researchers found significant MSV strain differences in southern Africa, East Africa, West Africa, and La Reunion. In contrast, the MSV-A strains were relatively similar in each of these regions. The team’s conclusion: the MSV-A strain may be moving across Africa more quickly than other, less damaging MSV strains.
That, in turn, may be due to the strain’s ability to infect numerous plant species. Indeed, based on their data, the researchers speculated that MSV-A might be more promiscuous than anticipated, infecting a greater variety of grasses than any of the other MSV strains.
Together, that convergence of recombination events, broad host range, and increased transmission speed appear to have contributed to the emergence of increasingly pathogenic MSV-A viruses, Martin said. 
By collecting and sequencing MSVs from additional parts of Africa, the researchers hope to learn even more about the nature of MSV recombination, evolution, and the emergence of pathogenic strains such as MSV-A.
In addition, using their knowledge of MSV recombination traits and host resistance factors, the researchers are developing new tactics to combat maize streak disease and curb its spread. “There’s very little you can do to stop a virus from emerging,” Martin said. “You can just prepare for it to emerge.”
For instance, Martin said, co-author Dionne Shepherd, a virologist and plant biotechnologist at the University of Cape Town, is spearheading an effort to create transgenic maize lines with MSV resistance strategies. Those lines, which are being developed in conjunction with the South African company Pannar Seed, are currently being tested and are predicted to be on the market within three years or so, Martin said.
And although there are regulatory hurdles, he added, genetically modified crops generally face less opposition in Africa than in other parts of the world. “Starvation and malnutrition are by far the biggest killer in Africa,” Martin said. “Being a bit squeamish about GM plants and things is not something that African governments are going to do.”

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