Location: Genomics and Bioinformatics ResearchTitle: Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species) Author
Submitted to: Mycologia
Publication Type: Peer reviewed journal
Publication Acceptance Date: 2/24/2013
Publication Date: 5/25/2013
Publication URL: http://handle.nal.usda.gov/10113/61104
Citation: Fajolu, O.L., Wadl, P.A., Vu, A.L., Gwinn, K.D., Scheffler, B.E., Trigiano, R.N., Ownley, B.H. 2013. Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species. Mycologia. 105(5):1164-1173. DOI: 10.3852/12-210. Interpretive Summary: Switchgrass has the potential as a cellulose based biofuel system suitable for U.S.A. agricultural systems. However it is susceptible to a pathogen that causes spot blotch and root rot that is caused by a mitosporic (imperfect) fungal pathogen (Bipolaris sorokiniana). In order to study the relationship of the pathogen and its host switchgrass, it is important to be able to characterize fungal isolates found at different locations and in plants. The best system to accomplish this is the use of DNA markers. In this research effort DNA markers were developed, characterized and validated for Bipolaris sorokinian. These DNA markers were tested on other Bipolaris species and should be useful as a diagnostic tool for pathogen studies on switchgrass.
Technical Abstract: Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n=384) harbored various SSR motifs. After eliminating the redundant sequences, 196 SSR loci were identified, of which 84.7% were dinucleotide repeats, and 9.7% and 5.6% were tri- and tetra-nucleotide repeats, respectively. Primer pairs were designed for 105 loci, and 85 successfully amplified loci. Sixteen polymorphic loci were characterized using fifteen B. sorokiniana isolates obtained from infected switchgrass plant materials collected from five states in the United States. These loci successfully cross amplified isolates from at least one related species including Bipolaris oryzae, Bipolaris spicifera and Bipolaris victoriae that cause leaf spot on switchgrass. Haploid gene diversity per locus across all isolates studied varied from 0.633 to 0.861. Cluster analysis by unweighted paired group method with the arithmetic mean and principal component analysis of SSR data grouped isolates according to their respective species. These SSR markers will be a valuable tool for genetic variability and population studies of B. sorokiniana and related species that are pathogenic on switchgrass and other host plants. Additionally, these markers are potential diagnostic tools for species in the genus Bipolaris.