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Title: Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species

item PERUMAL, RAMASAMY - Texas A&M University
item NIMMAKAYALA, P. - West Virginia State University
item ERATTAIMUTHU, S. - Texas A&M University
item NO, E. - Texas A&M University
item REDDY, U - West Virginia State University
item Prom, Louis
item ODVODY, G. - Texas A&M University
item Luster, Douglas - Doug
item MAGILL, C. - Texas A&M University

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2008
Publication Date: 11/29/2008
Citation: Perumal, R., Nimmakayala, P., Erattaimuthu, S., No, E.G., Reddy, U.K., Prom, L.K., Odvody, G.N., Luster, D.G., Magill, C. 2008. Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species. BMC Genetics. 9:77.

Interpretive Summary: A recent outbreak of sorghum downy mildew in Texas has led to the discovery of both metalaxyl fungicide resistance and a new type of the causal organism, Peronosclerospora sorghi. These observations and the difficulty in separating similar closely-related downy mildew pathogens require the need for simple molecular markers in order to differentiate among isolates and species. In this study, we presented the results of newly developed molecular microsatellites markers to detect the differences of sorghum downy mildew isolates and other related downy mildew isolates of corn, sugarcane, pearl millet and rose at the DNA level.

Technical Abstract: Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55%) with dinucleotide repeats and 6 (11%) with trinucleotide repeats. A total of 22 microsatellites with CA/AC or GT/TG repeats were the most abundant (40%) and GA/AG or CT/TC types contribute 15% in our collection. When used to amplify DNA from 19 isolates from P. sorghi, as well as from 5 related species that causes downy mildew on other hosts, the number of different bands detected for each SSR primer pair using a LI-COR- DNA Analyzer ranged from two to eight. Successful cross-amplification for 12 primer pairs studied in detail using DNA from downy mildews that attack maize (P. maydis & P. philippinensis), sugar cane (P. sacchari), pearl millet (Sclerospora graminicola) and rose (Peronospora sparsa) indicates that the flanking regions are conserved in all these species. A total of 15 SSR amplicons unique to P. philippinensis (one of the potential threats to US maize production) were detected, and these have potential for development of diagnostic tests. A total of 260 alleles were obtained using 54 microsatellites primer combinations, with an average of 4.8 polymorphic markers per SSR across 34 Peronosclerospora, Peronospora and Sclerospora spp isolates studied. Cluster analysis by UPGMA as well as principal coordinate analysis (PCA) grouped the 34 isolates into three distinct groups (all 19 isolates of Peronosclerospora sorghi in cluster I, five isolates of P. maydis and three isolates of P. sacchari in cluster II and five isolates of Sclerospora graminicola in cluster III). To our knowledge, this is the first attempt to extensively develop SSR markers from Peronosclerospora genomic DNA. The newly developed SSR markers can be readily used to distinguish isolates within several species of the oomycetes that cause downy mildew diseases in sorghum, maize, sugarcane, pearl millet and rose.