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ARS Home » Midwest Area » West Lafayette, Indiana » Crop Production and Pest Control Research » Research » Publications at this Location » Publication #231337

Title: Development of VNTR Markers to Assess Genetic Diversity of Mycosphaerella Fijiensis, the Causal Agent of Black Leaf Streak Disease in Bananas (Musa spp.)

item VAN DER LEE, T.A.J.
item QUIROS, Q
item Goodwin, Stephen - Steve
item GUZMAN, M
item SOUZA, JR., M
item KEMA, G.H.J.

Submitted to: Symposium Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 7/26/2008
Publication Date: 8/18/2008
Citation: Fereira, C.F., Van Der Lee, T., Quiros, Q., Te Lintel, H.B., Zapater, M.F., Carlier, J., Goodwin, S.B., Guzman, M., Souza, Jr., M.T., Kema, G. 2008. Development of VNTR Markers to Assess Genetic Diversity of Mycosphaerella Fijiensis, the Causal Agent of Black Leaf Streak Disease in Bananas (Musa spp.). Symposium Proceedings. Available:

Interpretive Summary: Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana, commonly known as Black Sigatoka, is one of the most devastating plant pathogens. Black leaf streak was first discovered in Fiji during the 1960s and the pathogen still actively colonizes new areas where bananas are grown. Using the genome sequence of M. fijiensis isolate CIRAD86 (, we identified Variable Number of Tandem Repeat (VNTR) markers using a bioinformatics pipeline. The VNTR screening resulted in 1528 candidate VNTR loci of which many were imperfect mono-, di-, or tri-nucleotide repeats. Sixteen VNTR markers were selected based on repeat type, repeat length and the number of units of the repeat. Primers for these 16 VNTR markers were tested on a set of M. fijiensis isolates and five VNTR markers that showed multiple alleles were tested on M. fijiensis field isolates and on progeny of the cross between isolates CIRAD86 and CIRAD 139a. Numbers of alleles identified varied from 2 to 5 per locus. The markers allowed high throughput and robust scoring on agarose gels and proved useful for genetic diversity and population genetic studies using basic molecular instrumentation. We envisage that this set will enable more detailed analyses of the large-scale migration pattern of this important pathogen as well as small-scale effects of fungicide treatments on the population diversity in banana plantations.

Technical Abstract: Mycosphaerella fijiensis is the causal agent of black leaf streak (BLS) disease in bananas. This pathogen threatens global banana production as the main export cultivars are highly susceptible. As a consequence, commercial banana plantations must be protected chemically with fungicides; up to 40 applications are per year representing >40% of total production costs. Ascospores are the major drivers of BLS epidemics and M. fijiensis is currently still colonizing new banana-growing areas, which has a huge economic impact on banana producers. The frequent fungicide applications exert a strong selection pressure on M. fijiensis populations resulting in abrupt resistance development to strobilurins and a gradual increase of resistance to azole fungicides. To provide the community with necessary genetic tools we developed a genetic linkage map of M. fijiensis. One-hundred and thirty-six F1 individuals from the CIRAD086 (Cameroon, Mat1-1) x CIRAD 139A (Colombia, Mat1-2) cross were evaluated. Eighty-seven Simple-Sequence Repeat (SSR) markers, 3 Variable Number of Tandem Repeat (VNTR) markers, the mating type locus and 235 Diversity Arrays Technology (DArT) markers were positioned in 19 linkage groups covering 1417 cM of the genome. The arrays containing individual fragments of the M. fijiensis genome generated DArT markers with a 90% genotype call rate and 98.8% reliability score. In total, 87% of the markers could be positioned reliably with LOD scores <10. The map is the first high-quality genetic linkage map of M. fijiensis with SSR and Dart markers. Due to its excellent genome coverage we decided to sequence the DArT markers to align this genetic map with the genome sequence of CIRAD086, which will considerably assist the genome assembly of this important fungus.