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Characterization of Expressed Sequence Tag–Derived Simple Sequence Repeat Markers for Aspergillus flavus: Emphasis on Variability of Isolates from the Southern United States

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Abstract

Simple sequence repeat (SSR) markers were developed from Aspergillus flavus expressed sequence tag (EST) database to conduct an analysis of genetic relationships of Aspergillus isolates from numerous host species and geographical regions, but primarily from the United States. Twenty-nine primers were designed from 362 tri-nucleotide EST-SSR sequences. Eighteen polymorphic loci were used to genotype 96 Aspergillus species isolates. The number of alleles detected per locus ranged from 2 to 24 with a mean of 8.2 alleles. Haploid diversity ranged from 0.28 to 0.91. Genetic distance matrix was used to perform principal coordinates analysis (PCA) and to generate dendrograms using unweighted pair group method with arithmetic mean (UPGMA). Two principal coordinates explained more than 75 % of the total variation among the isolates. One clade was identified for A. flavus isolates (n = 87) with the other Aspergillus species (n = 7) using PCA, but five distinct clusters were present when the others taxa were excluded from the analysis. Six groups were noted when the EST-SSR data were compared using UPGMA. However, the latter PCA or UPGMA comparison resulted in no direct associations with host species, geographical region or aflatoxin production. Furthermore, there was no direct correlation to visible morphological features such as sclerotial types. The isolates from Mississippi Delta region, which contained the largest percentage of isolates, did not show any unusual clustering except for isolates K32, K55, and 199. Further studies of these three isolates are warranted to evaluate their pathogenicity, aflatoxin production potential, additional gene sequences (e.g., RPB2), and morphological comparisons.

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Acknowledgments

This work was supported by the United States Department of Agriculture Grant # 58-6404-7-213. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by Mississippi State University, Texas A&M University, the University of Tennessee, or the United States Department of Agriculture.

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Correspondence to Xinwang Wang or Richard Baird.

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Xinwang Wang, Phillip A. Wadl, and Alicia Wood-Jones contributed equally to this project.

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Wang, X., Wadl, P.A., Wood-Jones, A. et al. Characterization of Expressed Sequence Tag–Derived Simple Sequence Repeat Markers for Aspergillus flavus: Emphasis on Variability of Isolates from the Southern United States. Mycopathologia 174, 371–382 (2012). https://doi.org/10.1007/s11046-012-9573-4

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