Genetic diversity and structure of Phakopsora pachyrhizi infecting soybean in Nigeria

Authors: TWIZEYIMANA, MATHIAS - University Of Illinois; OJIAMBO, PETER - North Carolina State University; HAUDENSHIELD, JAMES - University Of Illinois; CAETANO-ANOLLES, GUSTAVO - University Of Illinois; Pedley, Kerry; BANDYOPADHYAY, RANAJIT - University Of Illinois; Hartman, Glen

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/12/2010
Publication Date: 2/17/2011
Citation: Twizeyimana, M., Ojiambo, P.S., Haudenshield, J.S., Caetano-Anolles, G., Pedley, K.F., Bandyopadhyay, R., Hartman, G.L. 2011. Genetic diversity and structure of Phakopsora pachyrhizi infecting soybean in Nigeria. Phytopathology. 60:719-729.

Interpretive Summary: Soybean rust, caused by fungal pathogen, Phakopsora pachyrhizi, (P. pachyrhizi) has a significant impact on global soybean production because it causes rapid reduction in green leaf area and premature defoliation which reduces crop yield. Breeding for resistance has been hampered by the fact that the fungus has been able to overcome the known plant resistance sources of a single gene, Rpp1-4. Thus, approaches to promote durable resistance, and breeding programs are now focusing on selection criteria for quantitative resistance. Because the durability of host plant resistance is an evolutionary process, breeding and deployment of durable resistance would be more effective in the management of soybean rust if knowledge of the population structure of P. pachyrhizi was known. Little is known about the genetic variation in populations of P. pachyrhizi from soybean mainly because genetic markers to study the diversity of this pathogen were lacking. In this study, we characterize the genetic variation in P. pachyrhizi populations collected from different locations in Nigeria. We also assess the degree of genetic diversity in P. pachyrhizi populations in two single fields. We found that high gene flow existed between fungal populations from different geographic regions, indicating a significant potential risk for the regional spread of alternative genotypes that may enable breakdown of resistance genes. The results of this study provide valuable information for future work on the population biology of the soybean rust fungus and can serve as a baseline for monitoring population evolution in P. pachyrhizi.

Technical Abstract: The genetic structure of Nigerian field populations of the soybean rust pathogen Phakopsora pachyrhizi was determined using 18 simple sequence repeat markers. A total of 113 fungal isolates was collected by hierarchical sampling infected leaves from soybean fields in three agroecological zones in 2005. An additional 146 isolates were separately collected from infected plants in two fields (73 isolates in each field) located 292 km apart, during the same period. Genetic variation was high in Nigerian P. pachyrhizi populations. Among three agroecological zones, 84 distinct genotypes were identified, while 48 distinct genotypes were identified from 146 isolates analyzed from the two fields. Nei’s average genetic diversity across geographical regions and major soybean growing areas was 0.22. Hierarchical analysis of molecular variance was significant (P greater than 0.05) and low genetic differentiation among all populations of P. pachyrhizi and the majority (greater than 90 percent) of the genetic diversity was distributed within a soybean field, while approximately 6 percent of genetic diversity was distributed among fields within geographic regions. Low population differentiation was indicated by the low probability of identity by descent values among populations, suggesting a corresponding high degree of gene flow among these populations. Indirect estimation of gene flow rates (Nm) showed that high gene flow existed between populations from different geographic regions with Nm rates varying from 1.4 to 12.7. Cluster analysis showed that rust populations in Nigeria are composed of one main population of greater than 90 percent of the isolates. The possibility of high levels of gene flow on a regional level indicates a significant potential risk for the regional spread of alternative alleles that may enable breakdown of resistance genes.