Population genetic analysis of magnaporthe oryzae in sub-Saharan Africa using SNP calling from whole genome sequencing and de novo assembly of magnaporthe oryzae from Pacbio and Illumina Sequencing

Name: Worrawit Suktrakul

LCSH: Kasetsart University -- Theses. M.S. (Genetics) 2021

Classification :.LCCS: QK495.G74

LCSH: Kasetsart University. -- Department of Genetics -- Theses

LCSH: Rice -- Disease and pest resistance -- Genetic aspects

LCSH: Rice -- Genetics

LCSH: Pyricularia oryzae

LCSH: Rice blast disease

Abstract: Rice blast caused by Magnaporthe oryzae is one of the most economically damaging diseases on rice crop worldwide. This disease originated in Asia but was detected for the first time in Sub-Saharan Africa (SSA) around 100 years ago. Despite its importance, the evolutionary processes involved in shaping the population structure of M. oryzae in SSA remain unclear. In this study, we investigate the population history of M. oryzae using a combined dataset of 164 genomes. A total of 66,744 single nucleotide polymorphism (SNP) among the global population were identified. Furthermore, the phylogenetic tree was constructed and the population was divided into four genetic groups. Our results showed that SSA populations are more diverse than earlier perceived. While M. oryzae populations in SSA and Asia belong to the same genetic pool, both are experiencing different evolutionary trajectories resulting from unknown selection pressure or demographic processes. The distribution of rare alleles, measured as Tajima’s D values, show significant differences at the substructure level. Genomewide analysis indicates potential events of population contraction strongly affecting M. oryzae in SSA. These findings provide additional clues about the evolutionary history of M. oryzae outside the center of origin and help build customized disease management strategies. Moreover, avirulence genes of rice blast fungus were studied. In Thailand, four Avr-Pik variants were found in the Thai blast population: Avr-PikA, Avr-PikD, and Avr-PikE, and novel variant Avr-PikF. Furthermore, some blast isolates of the Thai population contained two copies of the Avr-Pik alleles, which is always in the combination of Avr-PikD and Avr-PikF. However, the location of the two copies of Avr-Pik in the chromosome is still unclear. Therefore, the de novo assembly was used to provide the location of two allele copies on the Thailand rice blast genome. The Pacbio sequencing was used to perform the sequencing of M. oryzae isolate 10100 containing the Avr-PikF and Avr-PikD and TH196031 containing Avr-PikF. The assembly results showed that the Avr-PikF allele was located on chromosome 2 between position 8229571 to 8229912, which a total length of this gene is 342 bp. However, the location of Avr-PikD allele on the chromosome is still unclear.

Kasetsart University. Office of the University Library

Address: Bangkok

Email: tdckulib@ku.ac.th

Name: Chatuporn Kuleung

Role: Thesis Advisor

Name: Tanee Sreewongchai

Role: Thesis CO-Advisor

Name: Chatchawan Jantasuriyarat

Role: Thesis CO-Advisor

Created: 2021

Modified: 2025-07-17

Issued: 2025-07-17

วิทยานิพนธ์/Thesis

application/pdf

URL: https://www.lib.ku.ac.th/KUthesis/2564/worrawit-suk-all.pdf

CallNumber: QK495.G74 .W67

eng

DegreeName: Master of Science

Level: Master's Degree

Descipline: Genetics

Grantor: Kasetsart University

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