Assessment of the Virulence Spectrum and Its Association with Genetic Diversity in Magnaporthe oryzae Populations from Sub-Saharan Africa

A collection of 122 isolates of Magnaporthe oryzae, from nine sub-Saharan African countries, was assessed for virulence diversity and genetic relatedness. The virulence spectrum was assessed by pathotype analysis with a panel of 43 rice genotypes consisting of differential lines carrying 24 blast resistance genes (R-genes), contemporary African rice cultivars, and susceptible checks. The virulence spectrum among isolates ranged from 5 to 80%. Five isolates were avirulent to the entire rice panel, while two isolates were virulent to ∼75% of the panel. Overall, cultivar 75-1-127, the Pi9 R-gene donor, was resistant to all isolates (100%), followed by four African rice cultivars (AR105, NERICA 15, 96%; NERICA 4, 91%; and F6-36, 90%). Genetic relatedness of isolates was assessed by single nucleotide polymorphisms derived from genotyping-by-sequencing and by vegetative compatibility tests. Phylogenetic analysis of SNPs of a subset of isolates (n = 78) revealed seven distinct clades that differed in virulence. Principal component analysis showed isolates from East Africa were genetically distinct from those from West Africa. Vegetative compatibility tests of a subset of isolates (n = 65) showed no common groups among countries. This study shows that blast disease could be controlled by pyramiding of Pi9 together with other promising R-genes into rice cultivars that are adapted to East and West African regions.

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Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa

Phytopathology ◽

10.1094/phyto-12-16-0421-r ◽

2017 ◽

Vol 107 (9) ◽

pp. 1039-1046 ◽

Cited By ~ 4

Author(s):

Emmanuel M. Mgonja ◽

Chan Ho Park ◽

Houxiang Kang ◽

Elias G. Balimponya ◽

Stephen Opiyo ◽

...

Keyword(s):

Genetic Diversity ◽

Association Mapping ◽

Magnaporthe Oryzae ◽

Rice Blast ◽

Blast Resistance ◽

Genotyping By Sequencing ◽

Rice Breeding ◽

Rice Cultivars ◽

R Genes ◽

African Rice

Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.

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Evaluation of Rice Responses to the Blast Fungus Magnaporthe oryzae at Different Growth Stages

Plant Disease ◽

10.1094/pdis-12-17-1873-re ◽

2019 ◽

Vol 103 (1) ◽

pp. 132-136 ◽

Cited By ~ 3

Author(s):

Xinglong Chen ◽

Yulin Jia ◽

Bo Ming Wu

Keyword(s):

Disease Severity ◽

Magnaporthe Oryzae ◽

Rice Blast ◽

Growth Stage ◽

Disease Index ◽

Blast Disease ◽

Growth Stages ◽

Japonica Rice ◽

Rice Cultivars ◽

Different Growth Stages

Rice blast, caused by the fungus Magnaporthe oryzae, is the most damaging disease for rice worldwide. However, the reactions of rice to M. oryzae at different growth stages are largely unknown. In the present study, two temperate japonica rice cultivars, M-202 and Nipponbare, were inoculated synchronously at different vegetative growth stages, V1 to V10. Plants of M-202 at each stage from V1 to reproductive stage R8 were inoculated with M. oryzae race (isolate) IB-49 (ZN61) under controlled conditions. Disease reactions were recorded 7 days postinoculation by measuring the percentage of diseased area of all leaves, excluding the youngest leaf. The results showed that the plants were significantly susceptible at the V1 to V4 stages with a disease severity of 26.7 to 46.8% and disease index of 18.62 to 37.76 for M-202. At the V1 to V2 stages, the plants were significantly susceptible with a disease a severity of 28.6 to 39.3% and disease index of 23.65 to 29.82 for Nipponbare. Similar results were observed when plants of M-202 were inoculated at each growth stage with a disease severity of 29.7 to 60.6% and disease index of 21.93 to 59.25 from V1 to V4. Susceptibility decreased after the V5 stage (severity 4.6% and index 2.17) and became completely resistant at the V9 to V10 stages and after the reproductive stages, suggesting that plants have enhanced disease resistance at later growth stages. These findings are useful for managing rice blast disease in commercial rice production worldwide.

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A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

10.1101/418509 ◽

2018 ◽

Cited By ~ 1

Author(s):

Veena Devi Ganeshan ◽

Stephen O. Opiyo ◽

Samuel K. Mutiga ◽

Felix Rotich ◽

David M. Thuranira ◽

...

Keyword(s):

Association Study ◽

Magnaporthe Oryzae ◽

Genome Wide Association Study ◽

Significant Snps ◽

Sub Saharan Africa ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Sub Saharan ◽

Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

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Integrated strategies for durable rice blast resistance in sub-Saharan Africa

Plant Disease ◽

10.1094/pdis-03-21-0593-fe ◽

2021 ◽

Author(s):

Samuel K Mutiga ◽

Felix Rotich ◽

Vincent M Were ◽

John Kimani ◽

David Thuranira Mwongera ◽

...

Keyword(s):

Rice Blast ◽

Crop Production ◽

Blast Resistance ◽

Research Effort ◽

Rice Production ◽

Rice Blast Disease ◽

Sub Saharan Africa ◽

Blast Disease ◽

Small Scale ◽

Sub Saharan

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional and multinational efforts to develop germplasm and policy initiatives to boost production for a more food secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under sub-optimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally-based blast resistance breeding programs. To develop blast resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

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A Rapid Survey of Avirulence Genes in Field Isolates of Magnaporthe oryzae

Plant Disease ◽

10.1094/pdis-08-19-1688-re ◽

2020 ◽

Vol 104 (3) ◽

pp. 717-723

Author(s):

Zhen Zhang ◽

Yulin Jia ◽

Yanli Wang ◽

Guochang Sun

Keyword(s):

United States ◽

Magnaporthe Oryzae ◽

Blast Resistance ◽

Blast Disease ◽

Southern United States ◽

R Genes ◽

Field Isolates ◽

Pcr Products ◽

Avr Gene ◽

Avr Genes

Magnaporthe oryzae is the causal agent for the devastating disease rice blast. The avirulence (AVR) genes in M. oryzae are required to initiate robust disease resistance mediated by the corresponding resistance (R) genes in rice. Therefore, monitoring pathogen AVR genes is important to predict the stability of R gene-mediated blast resistance. In the present study, we analyzed the DNA sequence dynamics of five AVR genes, namely, AVR-Pita1, AVR-Pik, AVR-Pizt, AVR-Pia, and AVR-Pii, in field isolates of M. oryzae in order to understand the effectiveness of the R genes, Pi-ta, Pi-k, Pi-zt, Pia, and Pii in the Southern U.S. rice growing region. Genomic DNA of 258 blast isolates collected from commercial fields of the Southern UNITED STATES during 1975–2009 were subjected to PCR amplification with AVR gene-specific PCR markers. PCR products were obtained from 232 isolates. The absence of PCR products in the remaining 26 isolates suggests that these isolates do not contain the tested AVR genes. Amplified PCR products were subsequently gel purified and sequenced. Based on the presence or absence of the five AVR genes, 232 field isolates were classified into 10 haplotype groups. The results revealed that 174 isolates of M. oryzae carried AVR-Pita1, 225 isolates carried AVR-Pizt, 44 isolates carried AVR-Pik, 3 isolates carried AVR-Pia, and one isolate carried AVR-Pii. AVR-Pita1 was highly variable, and 40 AVR-Pita1 haplotypes were identified in avirulent isolates. AVR-Pik had four nucleotide sequence site changes resulting in amino acid substitutions, whereas three other AVR genes, AVR-Pizt, AVR-Pia, and AVR-Pii, were relatively stable. Two AVR genes, AVR-Pik and AVR-Pizt, were found to exist in relatively larger proportions of the tested field isolates, which suggested that their corresponding R genes Pi-k and Pi-zt can be deployed in preventing blast disease in the Southern UNITED STATES in addition to Pi-ta. This study demonstrates that continued AVR gene monitoring in the pathogen population is critical for ensuring the effectiveness of deployed blast R genes in commercial rice fields.

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Carolina Foxtail (Alopecurus carolinianus): Susceptibility and Suitability as an Alternative Host to Rice Blast Disease (Magnaporthe oryzae [formerly M. grisea])

Plant Disease ◽

10.1094/pdis-92-4-0504 ◽

2008 ◽

Vol 92 (4) ◽

pp. 504-507 ◽

Cited By ~ 1

Author(s):

Y. Jia ◽

D. Gealy ◽

M. J. Lin ◽

L. Wu ◽

H. Black

Keyword(s):

Magnaporthe Oryzae ◽

Rice Blast ◽

Rice Blast Disease ◽

Blast Disease ◽

Artificial Inoculation ◽

Rice Cultivars ◽

Alternative Host ◽

Lesion Development ◽

Disease Symptoms ◽

Rice Leaves

Carolina foxtail (Alopecurus carolinianus) has not been reported to host Magnaporthe oryzae. A collection of Carolina foxtail obtained from several Arkansas locations over a 4-year period was inoculated with four races of the fungus under greenhouse conditions and, in all cases, inoculation resulted in the formation of irregular, yellow and brown lesions without obvious gray centers that are characteristic for blast on rice. Differences in these lesions were not observed among our collection. These lesions appeared to differ from typical blast lesions on inoculated rice leaves but were evident following artificial inoculation of Carolina foxtail in the greenhouse. M. oryzae races that differed in pathogenicity toward rice cultivars also displayed differences in lesion development on Carolina foxtail. The most virulent race on rice cultivars also produced lesions most rapidly on Carolina foxtail. These lesions developed more quickly on Carolina foxtail than on the most susceptible rice cultivars tested, including a susceptible California cultivar, M202. M. oryzae isolates cultured from these lesions in the infected Carolina foxtail caused typical disease symptoms of blast on inoculated rice cultivars. We suggest that Carolina foxtail is a new and previously unrecognized host for the blast pathogen.

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Evolution of Compatibility Range in the Rice−Magnaporthe oryzae System: An Uneven Distribution of R Genes Between Rice Subspecies

Phytopathology ◽

10.1094/phyto-07-15-0169-r ◽

2016 ◽

Vol 106 (4) ◽

pp. 348-354 ◽

Cited By ~ 10

Author(s):

Romain Gallet ◽

Colin Fontaine ◽

François Bonnot ◽

Joëlle Milazzo ◽

Christophe Tertois ◽

...

Keyword(s):

Magnaporthe Oryzae ◽

Ecological Factors ◽

Blast Disease ◽

R Genes ◽

Host Genotype ◽

Rice Varieties ◽

Genetic Groups ◽

Plant Variety ◽

Plant Pathogen Interaction ◽

The Impact

Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant−pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

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Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)

10.1101/708735 ◽

2019 ◽

Cited By ~ 2

Author(s):

Leonid M. Irenge ◽

Jerôme Ambroise ◽

Prudence N. Mitangala ◽

Bertrand Bearzatto ◽

Raphaël K.S. Kabangwa ◽

...

Keyword(s):

Vibrio Cholerae ◽

East Africa ◽

Democratic Republic ◽

Genetic Relatedness ◽

Sub Saharan Africa ◽

The Third ◽

The Past ◽

Republic Of The Congo ◽

Sub Saharan ◽

El Tor

AbstractBackgroundOver the past recent years, Vibrio cholerae has been associated with outbreaks in Sub Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries.Methods/Principal findingsPhenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of V. cholerae associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to V. cholerae isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other V. cholerae isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates.Conclusions/SignificanceCurrent data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.Author’s summaryCholera is a severe diarrheal disease caused by the Gram-negative bacterium Vibrio cholerae. After originating in Asia, the disease spread across sub-Saharan Africa, notably Democratic Republic of the Congo. The aim of our study was to assess the transmission pattern of V. cholerae strains prevailing in eastern DRC, and determine their genetic relatedness to strains from other African countries and other parts of the world. Between 2014 and 2017, we isolated V. cholerae from fecal samples of patients with acute diarrhea in eastern DRC, and subsequently examined the DNA of the bacteria. The results show that they all clustered in two genetic groups (ST69 and ST515) falling within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and T10 introduction event in East Africa. The genetic signature of ST515 may be involved in its adaptation to environmental conditions found in eastern DRC, and contribute to its extended geographic distribution. Indeed, unlike the locally endemic ST69, ST515 is spreading extensively through DRC cross-border countries such as South Sudan, Tanzania, Uganda and Zambia. This plainly justifies a regional strategy to strengthen the fight against cholera in eastern Africa.

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Determination of Resistance Spectra of the Pi-ta and Pi-k Genes to U.S. Races of Magnaporthe oryzae Causing Rice Blast in a Recombinant Inbred Line Population

Plant Disease ◽

10.1094/pdis-93-6-0639 ◽

2009 ◽

Vol 93 (6) ◽

pp. 639-644 ◽

Cited By ~ 19

Author(s):

Yulin Jia ◽

Fleet N. Lee ◽

Anna McClung

Keyword(s):

Inbred Line ◽

Recombinant Inbred Line ◽

Magnaporthe Oryzae ◽

Recombinant Inbred ◽

Blast Disease ◽

R Gene ◽

R Genes ◽

Marker Assisted Breeding ◽

Simple Sequence

Molecular tagged resistance (R) genes are useful for developing improved cultivar resistance using marker-assisted breeding. In the present study, R genes to common races of Magnaporthe oryzae, the causal agent of blast disease of rice (Oryza sativa), were mapped using an F10 recombinant inbred line (RIL) population derived from a cross of tropical japonica cv. Katy with breeding line RU9101001. Katy was resistant to 10 common U.S. races: IA-45, IB-1, IB-45, IB-49, IB-54, IC-17, ID-1, IE-1, IG-1, and IH-1 of M. oryzae. RU9101001 was resistant to races IA-45, IB-45, IB-54, IG-1, and IH-1. Katy and RU9101001 were susceptible to race IE-1k. Twenty-three polymorphic simple sequence repeat (SSR) markers were used to map R genes. Segregation ratios of 1:1 (resistant/susceptible) to races IB-1, IB-49, IC-17, ID-1, and IE-1 indicated the presence of a single dominant R gene in Katy. Ratios of 3:1 (resistant/susceptible) to races IA-45, IB-45, IG-1, and IH-1 indicated that a single R gene was present in Katy and a different R gene was present in RU9101001. Resistance to the abovementioned races was correlated with the presences of the Pi-ta gene and 11 Katy SSR alleles, suggesting that Pi-ta confers resistance to IA-45, IB-1, IB-45, IB-49, IC-17, IG-1, ID-1, IE-1, and IH-1. Katy, RU9101001, and all RILs were resistant to race IB-54, which was consistent with the presence of Pi-ks in Katy and Pi-kh in RU9101001. Resistance to IA-45, IB-45, IG-1, and IH-1 correlated with the presence of Pi-kh, suggesting that Pi-kh confers resistance to IA-45, IB-45, IG-1, and IH-1. These data suggest that Pi-ta and Pi-kh are effective R genes with overlapped resistance to the 10 common races of M. oryzae.

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