scholarly journals Novel haplotypes and networks of AVR-Pik alleles in Magnaporthe oryzae

2018 ◽  
Author(s):  
Jin-bin Li ◽  
Qun Wang ◽  
Chengyun Li ◽  
Yunqing Bi ◽  
Xue Fu ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Yunnan Province ◽  
Sequence Variation ◽  
Specific Resistance ◽  
Blast Disease ◽  
Base Substitution ◽  
R Genes ◽  
Dna Sequence Variation ◽  
Pcr Products ◽  
Avr Genes

Rice blast disease is one of the most destructive fungal diseases of rice world-wide. The avirulence (AVR) genes of Magnaporthe oryzae are recognized by the cognate resistance (R) genes of rice, and trigger race specific resistance. Here, we studied the possible evolutionary pathways in the evolution of AVR-Pik alleles by analyzing the DNA sequence variation and assayed for their avirulence function to the cognate Pik alleles resistance genes under field conditions in China. Results of PCR products showed that 278 isolates of M. oryzae carry AVR-Pik alleles among genomic DNA of 366 isolates of M. oryzae collected from Yunnan Province, China. Among of them, 66.7-90.3% of M. oryzae carry AVR-Pik alleles from six regions of Yunnan. Moreover, 10 AVR-Pik haplotypes encoding five novel AVR-Pik variants were identified among 201 isolates. The AVR-Pik alleles stepwise evolved to virulence from avirulent forms via base substitution. These findings demonstrate that AVR-Pik alleles are under positive selection and mutations are responsible for defeating race-specific resistance Pik alleles in nature.

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

Plant Disease ◽  
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.

scholarly journals Effectiveness and Durability of the Rice Pi-ta Gene in Yunnan Province of China

2014 ◽  
Vol 104 (7) ◽  
pp. 762-768 ◽  
Author(s):  
Jinbin Li ◽  
Lin Lu ◽  
Yulin Jia ◽  
Chengyun Li
Keyword(s):  
Dna Sequence ◽  
Yunnan Province ◽  
Sequence Variation ◽  
Pcr Amplification ◽  
Base Substitution ◽  
Field Isolates ◽  
Specific Pcr ◽  
Dna Sequence Variation ◽  
Pcr Products ◽  
Polymerase Chain

Rice blast is one of the most damaging diseases of rice worldwide. In the present study, we analyzed DNA sequence variation of avirulence (AVR) genes of AVR-Pita1 in field isolates of Magnaporthe oryzae in order to understand the effectiveness of the resistance gene Pi-ta in China. Genomic DNA of 366 isolates of M. oryzae collected from Yunnan province of China were used for polymerase chain reaction (PCR) amplification to examine the existence of AVR-Pita1 using gene-specific PCR markers. Results of PCR products revealed that 218 isolates of M. oryzae carry AVR-Pita1. Among of them, 62.5, 56.3, 58.5, 46.7, 72.4, and 57.4% of M. oryzae carry AVR-Pita1 from northeastern, southeast, western, northwest, southwestern, and central Yunnan province, respectively. The detection rate of AVR-Pita1 was, in order: southwestern > northeastern > western > central > southeastern > northwestern Yunnan province. Moreover, in total, 18 AVR-Pita1 haplotypes encoding 13 novel AVR-Pita1 variants were identified among 60 isolates. Most DNA sequence variation was found to occur in the exon region, resulting in amino acid substitution. Six virulent haplotypes of AVR-Pita1 to Pita were identified among 60 field isolates. The AVR-Pita1 has evolved to virulence from avirulent origins via base substitution. These findings demonstrate that AVR-Pita1 is under positive selection and mutations of AVR-Pita1 are responsible for defeating race-specific resistance in nature.

scholarly journals Identification of a Pi9-Containing Rice Germplasm with a Newly Developed Robust Marker

2016 ◽  
Vol 106 (8) ◽  
pp. 871-876 ◽  
Author(s):  
Klaus Konrad Scheuermann ◽  
Yulin Jia
Keyword(s):  
Dna Markers ◽  
Sequence Variation ◽  
Blast Resistance ◽  
Blast Disease ◽  
Rice Germplasm ◽  
Oryza Minuta ◽  
Dna Sequence Variation ◽  
Aa Genome ◽  
Dna Primers ◽  
New Cultivars

The Pi9 gene in rice, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease. However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker-assisted selection (MAS). In addition, no known Pi9-containing rice germplasm is available to breeders. In the present study, DNA sequence variation of Pi9 alleles and their family members was analyzed in 40 diverse rice germplasm accessions from the AA genome to develop a robust Pi9 marker. In total, 29 DNA primers of 20 to 23 nucleotides were designed and each possible combination of primer pairs was used to detect Pi9. Only one combination of DNA primers, KS28/KS6, was identified to specifically detect Pi9 in the monogenic line IRBL9-W. The presence of Pi9 was verified with the predicted Pi9-specific blast reaction. Subsequently, 201 genetically diverse mini-core rice accessions from 114 countries were screened with KS28/KS6. One germplasm, IR 9660-48-1-1-2, was identified to carry Pi9 and the function of Pi9 was verified with pathogenicity assays. This robust Pi9 marker and a rice germplasm, IR9660-48-1-1-2 (GSOR310687), carrying Pi9 can be used to improve blast resistance with a MAS approach.

scholarly journals Geographic Distribution of Avirulence Genes of the Rice Blast Fungus Magnaporthe oryzae in the Philippines

2019 ◽  
Vol 7 (1) ◽  
pp. 23 ◽  
Author(s):  
Ana Lopez ◽  
Tapani Yli-Matilla ◽  
Christian Cumagun
Keyword(s):  
Geographic Distribution ◽  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Rice Blast Fungus ◽  
The Philippines ◽  
R Genes ◽  
Avirulence Genes ◽  
Geographic Locations ◽  
Avr Genes ◽  
Pcr Test

A total of 131 contemporary and 33 reference isolates representing a number of multi-locus genotypes of Magnaporthe oryzae were subjected to a PCR test to detect the presence/absence of avirulence (Avr) genes. Results revealed that the more frequently occurring genes were Avr-Pik (81.50%), Avr-Pita (64.16%) and Avr-Pii (47.98%), whereas the less frequently occurring genes were Avr-Pizt (19.08%) and Avr-Pia (5.20%). It was also laid out that the presence of Avr genes in M. oryzae is strongly associated with agroecosystems where the complementary resistant (R) genes exist. No significant association, however, was noted on the functional Avr genes and the major geographic locations. Furthermore, it was identified that the upland varieties locally known as “Milagrosa” and “Waray” contained all the R genes complementary to the Avr genes tested.

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

2016 ◽  
Vol 106 (4) ◽  
pp. 348-354 ◽  
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.

scholarly journals 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 ◽  
2009 ◽  
Vol 93 (6) ◽  
pp. 639-644 ◽  
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.

scholarly journals Avirulence (AVR) Gene-Based Diagnosis Complements Existing Pathogen Surveillance Tools for Effective Deployment of Resistance (R) Genes Against Rice Blast Disease

2017 ◽  
Vol 107 (6) ◽  
pp. 711-720 ◽  
Author(s):  
S. M. Selisana ◽  
M. J. Yanoria ◽  
B. Quime ◽  
C. Chaipanya ◽  
G. Lu ◽  
...  
Keyword(s):  
Rice Blast ◽  
Polymerase Chain Reaction Amplification ◽  
Rice Blast Disease ◽  
Blast Disease ◽  
R Gene ◽  
R Genes ◽  
Pathogen Population ◽  
Avr Gene ◽  
Avr Genes ◽  
Virulence Spectrum

Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of a rice blast pathogen population and for predicting the effectiveness of target R genes in rice varieties.

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

2017 ◽  
Vol 107 (7) ◽  
pp. 852-863 ◽  
Author(s):  
S. K. Mutiga ◽  
F. Rotich ◽  
V. Devi Ganeshan ◽  
D. T. Mwongera ◽  
E. M. Mgonja ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Genetic Relatedness ◽  
Vegetative Compatibility ◽  
Sub Saharan Africa ◽  
Blast Disease ◽  
Rice Cultivars ◽  
R Genes ◽  
African Rice ◽  
Sub Saharan ◽  
Virulence Spectrum

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.

scholarly journals Evidence for Selection at the fused1 Locus of Drosophila americana

Genetics ◽  
2001 ◽  
Vol 158 (1) ◽  
pp. 279-290 ◽  
Author(s):  
Jorge Vieira ◽  
Bryant F McAllister ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Sequence Variation ◽  
Amino Acid Replacement ◽  
Population Subdivision ◽  
Amino Acid Substitutions ◽  
Clinal Variation ◽  
Haplotype Structure ◽  
Common Amino Acid ◽  
Chromosome Arrangement ◽  
Dna Sequence Variation

Abstract We analyze genetic variation at fused1, a locus that is close to the centromere of the X chromosome-autosome (X/4) fusion in Drosophila americana. In contrast to other X-linked and autosomal genes, for which a lack of population subdivision in D. americana has been observed at the DNA level, we find strong haplotype structure associated with the alternative chromosomal arrangements. There are several derived fixed differences at fused1 (including one amino acid replacement) between two haplotype classes of this locus. From these results, we obtain an estimate of an age of ∼0.61 million years for the origin of the two haplotypes of the fused1 gene. Haplotypes associated with the X/4 fusion have less DNA sequence variation at fused1 than haplotypes associated with the ancestral chromosome arrangement. The X/4 haplotypes also exhibit clinal variation for the allele frequencies of the three most common amino acid replacement polymorphisms, but not for adjacent silent polymorphisms. These patterns of variation are best explained as a result of selection acting on amino acid substitutions, with geographic variation in selection pressures.

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