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Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity

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Abstract

Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93 % of the samples analyzed but the vast majority of these were Ia. The remaining 7 % represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7 % of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here.

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Acknowledgments

We thank Dr Bekele Kassa (Plant Pathology Department, Holeta Agricultural Research Centre, Ethiopia) for help with part of sample collection in 2011. We would like to express our thanks to Department of Forest Mycology and Plant Pathology, Swedish University of Agriculture Sciences (SLU) for help with molecular laboratory facility. A Swedish Government Initiative, the SLU Africa Food Security Research Program supports this work.

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Authors and Affiliations

  1. School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia

    Daniel Shimelash, Temam Hussien & Chemeda Fininsa

  2. CIP-China Center for Asia Pacific, Pan Pacific Plaza A12 Zhongguancun Nandajie, Beijing, 100081, China

    Greg Forbes

  3. Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07, Uppsala, Sweden

    Jonathan Yuen

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  1. Daniel Shimelash
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  2. Temam Hussien
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Correspondence to Daniel Shimelash.

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Communicated by M. Kupiec.

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Shimelash, D., Hussien, T., Fininsa, C. et al. Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity. Curr Genet 62, 657–667 (2016). https://doi.org/10.1007/s00294-016-0572-8

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  • DOI: https://doi.org/10.1007/s00294-016-0572-8

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