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ARS Home » Midwest Area » West Lafayette, Indiana » Crop Production and Pest Control Research » Research » Publications at this Location » Publication #161425
Title: MINING MICROSATELLITES IN AN EST DATABASE OF MYCOSPHAERELLA GRAMINICOLA

Author
item Goodwin, Stephen - Steve
item Cavaletto, Jessica
item LEE, THEO - PLANT RES INTL, W. NL
item HEKKERT, BAS - PLANT RES INTL, W. NL
item KEMA, GERT - PLANT RES INTL, W. NL

Submitted to: Fungal Genetics Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/19/2004
Publication Date: 4/17/2004
Citation: Goodwin, S.B., Cavaletto, J.R., Lee, T.V., Hekkert, B.T., Kema, G.H. 2004. Mining microsatellites in an EST database of Mycoshpaerella graminicola. 7th European Conference on Fungal Genetics, Copenhagen, Denmark. Abstract IXp-26:223.

Interpretive Summary:

Technical Abstract: Mycosphaerella graminicola, the cause of septoria tritici blotch of wheat, is developing rapidly as a model for fungi in the order Dothideales. Genetic analyses of this fungus are aided by extensive sets of molecular markers, including RFLP, AFLP, and RAPD. Each of these marker systems has particular limitations, many of which are overcome by microsatellite or simple-sequence repeat (SSR) markers. However, only nine microsatellite loci have been identified so far in M. graminicola, and none has been mapped. To identify additional polymorphic SSR loci, a database of EST data from M. graminicola was scanned for di- and trinucleotide units repeated six or more times. Among more than 30,000 EST sequences screened, 104 possible SSR loci were identified and primers flanking these SSRs were developed using an automated software pipeline. To test whether these SSRs are informative for population studies, 38 primer pairs have been tested on six isolates of M. graminicola and four isolates of the closely related barley pathogen Septoria passerinii. Thirty-one of the 38 primer pairs (82%) generated a single amplicon and 24 (63%) showed polymorphism among the six isolates of M. graminicola. Among these 24 microsatellites, 18 were polymorphic between the parents of the M. graminicola mapping population and can be incorporated easily into the existing genetic map. Most primer pairs also amplified bands in S. passerinii, but they usually had a different size and were less variable than those amplified with the same primers in M. graminicola. The EST database provided a rich source of new microsatellites, which were selected efficiently. These microsatellite markers will facilitate integration of the different types of genetic analyses performed on this important plant pathogen.