Diversity and distribution of pathotypes of the soybean rust fungus Phakopsora pachyrhizi in East Africa

Harun M. Murithi, Rafael M. Soares, George Mahuku, Peter van Esse, Matthieu H.A.J. Joosten*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)


Phakopsora pachyrhizi is a biotrophic fungus that causes rust on soybean, leading to devastating yield losses. Development of resistant cultivars for deployment in different geographic regions requires a comprehensive understanding of the prevalent P. pachyrhizi pathotypes. To determine the pathotypes existing in four East African countries, 65 isolates were tested on 11 soybean host differentials. In addition, the virulence spectrum of isolates collected from the same region over multiple years was compared. The majority of the isolates (54%) belonged to pathotype 1000, which was found in all countries. The pathotypes with the most complex virulence spectrum, which comprised isolates from Kenya and Malawi, were virulent on four differentials. All pathotypes were virulent on soybean genotypes carrying the Rpp1 resistance gene to P. pachyrhizi, but they were avirulent on cultivars carrying the Rpp1b, Rpp2, or Rpp3 gene, as well as on cultivar No6-12-1 that carries Rpp2, Rpp4, and Rpp5. Two of the pathotypes were virulent on cultivar UG 5 that carries Rpp1 and Rpp3 and on Hyuuga that carries Rpp3 and Rpp5. The isolates collected from different countries differed in their virulence spectrum across the years. Shannon's index (H) and Simpson's index (S) of diversity indicated that the isolates from Malawi were more diverse (H = 1.55, S = 0.90) while those from Uganda had lower diversity (H = 0.78, S = 0.46). The Rpp genes that were found to provide resistance to all pathotypes of P. pachyrhizi can be employed for soybean breeding aimed at durable rust resistance.

Original languageEnglish
Pages (from-to)655-666
JournalPlant Pathology
Issue number3
Early online date29 Nov 2020
Publication statusPublished - Apr 2021


  • pathotype
  • Phakopsora pachyrhizi
  • Rpp gene
  • soybean rust
  • virulence diversity


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