Molecular diversity of internal transcribed spacer among the monoconidial isolates of Magnaporthe oryzae isolated from rice in Southern Karnataka, India

Analysis of genetic diversity and population structure of Magnaporthe grisea, the causal agent of foxtail millet blast using microsatellites

Foxtail millet blast caused by Magnaporthe grisea is becoming a severe problem in foxtail millet growing regions of India. The genetic diversity and population structure of foxtail millet infecting M. grisea is crucial for developing effective management strategies, such as breeding blast-resistant cultivars. We analyzed thirty-two M. grisea isolates from ten foxtail millet-growing districts in Tamil Nadu, India for genetic diversity using twenty-nine microsatellite or simple sequence repeat (SSR) markers. A total of 103 alleles were identified with a mean of 3.55 alleles/locus. Gene diversity ranged from 0.170 to 0.717, while major allelic frequencies ranged from 0.344 to 0.906. The polymorphism information content (PIC) ranged from 0.155 to 0.680, with a mean value of 0.465. Population structure analysis of the genomic data sets revealed two major populations (SP1 and SP2) with different levels of ancestral admixture among the 32 blast isolates. Phylogenetic analysis classified the isolates into three major clusters. Analysis of molecular variance (AMOVA) showed high genetic variation among individuals and less among populations. Principal Coordinate Analysis (PCoA) revealed 27.16% genetic variation among populations. The present study provides the first report on the genetic diversity and population structure of the foxtail millet-infecting M. grisea population in Tamil Nadu, which could be useful for the development of blast-resistant foxtail millet cultivars.

Pyricularia's Capability of Infecting Different Grasses in Two Regions of Mexico

The genus Pyricularia includes species that are phytopathogenic fungi, which infect different species of Poaceae, such as rice and sorghum. However, few isolates have been genetically characterized in North America. The current study addresses this lack of information by characterizing an additional 57 strains of three grasses (Stenotaphrum secundatum, Cenchrus ciliaris and Digitaria ciliaris) from two distant regions of Mexico. A Pyricularia dataset with ITS sequences retrieved from GenBank and the studied sequences were used to build a haplotype network that allowed us to identify a few redundant haplotypes highly related to P. oryzae species. An analysis considering only the Mexican sequences allowed us to identify non-redundant haplotypes in the isolates of C. ciliaris and D. ciliaris, with a high identity with P. pennisetigena. The Pot2-TIR genomic fingerprinting technique resulted in high variability and allowed for the isolates to be grouped according to their host grass, whilst the ERIC-PCR technique was able to separate the isolates according to their host grass and their region of collection. Representative isolates from different host grasses were chosen to explore the pathogenic potential of these isolates. The selected isolates showed a differential pathogenic profile. Cross-infection with representative isolates from S. secundatum and C. ciliaris showed that these were unable to infect D. ciliaris grass and that the DY1 isolate from D. ciliaris was only able to infect its host grass. The results support the identification of pathogenic strains of Pyricularia isolates and their cross-infection potential in different grasses surrounding important crops in Mexico.

Morphological and Molecular Analysis of Fungal Species Associated with Blast and Brown Spot Diseases of Oryza sativa

Fungal diseases blast and brown spot in rice cause severe yield losses worldwide. Blast is caused by Magnaporthe oryzae, and Bipolaris oryzae is reported as the main causal organism of brown spot. Both diseases cause leaf lesions that are difficult differentiate until the later stages. Early detection and differentiation of the lesions would help the adoption of disease management strategies specific to the pathogens and prevent reductions in the quality and quantity of rice yields. This study was conducted in the Northern Province of Sri Lanka over five consecutive rice cultivating seasons to characterize the causal fungi of rice blast and brown spot diseases by morphological and molecular means and to develop a visual guide to differentiate the two diseases. Disease incidence was recorded in 114 fields from 2017 to 2019, and fungal isolates associated with the lesions of both diseases were cultured and subjected to morphological and molecular characterization. Competitive growth interactions between M. oryzae and the more common individual fungal isolates of the brown spot lesions were evaluated. Fungal metagenomic analysis was conducted for the fungal species isolated from brown spot lesions. A suppression of blast accompanied by an increased incidence of brown spot disease was observed during the study period. M. oryzae was confirmed to be the causal organism of the blast, and >20 species of fungi were identified to be associated with brown spot lesions through morphological and molecular studies and metagenomic analyses. Fungal internal transcribed spacer region sequencing revealed genetic variation in the highly conserved region of DNA sequences of blast and brown spot fungal isolates. B. oryzae, Curvularia, and Microdochium species were commonly isolated from brown spot lesions. In vitro competitive growth interactions between the fungal isolates revealed growth suppression of M. oryzae by the fungal isolates associated with brown spot lesions. Similarly, it can be speculated that the abundance and severity of blast in the field may have an influence on brown spot-associated fungi. A simple visual guide was developed to differentiate blast and brown spot lesions. The findings would be highly useful in the timely management of these major fungal diseases affecting rice.

Multilocus sequence analysis and identification of mating-type idiomorphs distribution in Magnaporthe oryzae population of Karnataka state of India

AIMS

To investigate the genetic diversity, population structure, and mating-type distribution among the eco-distinct isolates of Magnaporthe oryzae from Karnataka, India.

METHODS AND RESULTS

A set of 38 isolates of M. oryzae associated with leaf blast disease of rice were collected from different rice ecosystems of Karnataka, India, and analyzed for their diversity at actin, β-tubulin, calmodulin, translation elongation factor 1-α (TEF-1-α), and internal transcribed spacer (ITS) genes/region. The isolates were grouped into two clusters based on the multilocus sequence diversity, the majority being in cluster-IA (n=37), and only one isolate formed cluster-IB. Population structure was analyzed using 123 SNP data to understand the genetic relationship. Based on K=2 and ancestry threshold of >70%, blast strains were classified into two subgroups (SG1 and SG2) whereas, based on K=4 and ancestry threshold of >70%, blast strains were classified into four subgroups (SG1, SG2, SG3, and SG4). We have identified 13 haplotype groups where haplotype-group-2 was predominant (n=20) in the population. The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Further, the mating-type analysis was also performed using MAT1 gene-specific primers to find the potentiality of sexual reproduction in different ecosystems. The majority of the isolates (54.5%) had MAT1-2 idiomorph, whereas 45.5 per cent of the isolates possessed MAT1-1 idiomorph.

CONCLUSIONS

The present study found the genetically homogenous population of M. oryzae by multilocus sequence analysis. Both mating types, MAT1-1 and MAT1-2, were found within the M. oryzae population of Karnataka.

SIGNIFICANCE AND IMPACT OF STUDY

The study on the population structure and sexual mating behavior of M. oryzae is important in developing region-specific blast-resistant rice cultivars. This is the first report of MAT1 idiomorphs distribution in the M. oryzae population in any Southern state of India.

Morpho-molecular diversity and avirulence genes distribution among the diverse isolates of Magnaporthe oryzae from Southern India

AIMS

To investigate the diversity of eco-distinct isolates of Magnaporthe oryzae for their morphological, virulence and molecular diversity and relative distribution of five Avr genes.

METHODS AND RESULTS

Fifty-two M. oryzae isolates were collected from different rice ecosystems of southern India. A majority of them (n = 28) formed a circular colony on culture media. Based on the disease reaction on susceptible cultivar (cv. HR-12), all 52 isolates were classified in to highly virulent (n = 28), moderately virulent (n = 11) and less-virulent (13) types. Among the 52 isolates, 38 were selected for deducing internal transcribed spacer (ITS) sequence diversity. For deducing phylogeny, another set of 36 isolates from other parts of the world was included, which yielded two distinct phylogenetic clusters. We identified eight haplotype groups and 91 variable sites within the ITS sequences, and haplotype-group-2 (Hap_2) was predominant (n = 24). The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Furthermore, PCR analysis for detecting the presence of five Avr genes in the different M. oryzae isolates using Avr gene-specific primers in PCR revealed that Avr-Piz-t, Avr-Pik, Avr-Pia and Avr-Pita were present in 73.68%, 73.68%, 63.16% and 47.37% of the isolates studied, respectively; whereas, Avr-Pii was identified only in 13.16% of the isolates.

CONCLUSIONS

Morpho-molecular and virulence studies revealed the significant diversity among eco-distinct isolates. PCR detection of Avr genes among the M. oryzae population revealed the presence of five Avr genes. Among them, Avr-Piz-t, Avr-Pik and Avr-Pia were more predominant.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study documented the morphological and genetic variability of eco-distinct M. oryzae isolates. This is the first study demonstrating the distribution of the Avr genes among the eco-distinct population of M. oryzae from southern India. The information generated will help plant breeders to select appropriate resistant gene/s combinations to develop blast disease-resistant rice cultivars.

Elucidation of genetic relatedness of Magnaporthe grisea, an incitent of pearl millet blast disease by molecular markers associated with virulence of host differential cultivars

In recent years, blast disease caused by Magnaporthe grisea, an ascomycete fungus is becoming a serious threat to pearl millet crop in India and worldwide. Due to the increase in virulent races of pathogen, blast disease management strategies seemed to be very limited. Hence, unraveling the occurrence of blast isolates across India and understanding their virulence and genetic relatedness using molecular markers are the key objectives of this study. From Farmer's field survey we have evidenced variability in blast pathogen across India by recording 10.6 to 7.9 disease severities. A fair to good variation in cultural and conidial characters were also noticed for 17 field isolates. The identity of 17 isolates was confirmed as Magnaporthe grisea by internal transcribed spacer (ITS) region. Based on 12 host differential virulence reactions, five isolates BgKMg1, BdmMg2, MtgMg11, JprMg16 and JmnMg17 recorded highly susceptible (>5 grade) to nine differentials used in the study. While, host differentials ICMB95444, ICMR06222, ICMR11003, IP21187 and ICMV155 found effective for screening virulence of blast disease. Furthermore, genetic relatedness assessed by ITS, inter simple sequence repeats (ISSR) and simple sequence repeats (SSR) markers produced high degree of polymorphism and was able to distinguish the virulence pattern of 17 isolates that correlated with phenotypic screening. Among markers, clustering of isolates within groups was significantly different with remarkable genetic similarity coefficient and bootstrap values. Overall, these results confirm a significant morphological and genetic variation among 17 isolates, thereby helping to elucidate the virulence of pearl millet blast populations in India that could avoid breakdown of resistance and assist breeding improved pearl millet cultivars.

Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions

Ganoderma boninense causes basal stem rot (BSR) and is responsible for substantial economic losses to Southeast Asia’s palm oil industry. Sarawak, a major producer in Malaysia, is also affected by this disease. Emergence of BSR in oil palm planted on peat throughout Sarawak is alarming as the soil type was previously regarded as non-conducive. Phylogenetic analysis indicated a single species, G. boninense as the cause of BSR in Sarawak. Information on evolutionary and demographic history for G. boninense in Sarawak inferred through informative genes is lacking. Hence, a haplotype study on single nucleotide polymorphisms in internal transcribed spacers (SNPs-ITS) of G. boninense was carried out. Sequence variations were analysed for population structure, phylogenetic and phylogeographic relationships. The internal transcribed spacers (ITS) region of 117 isolates from four populations in eight locations across Sarawak coastal areas revealed seven haplotypes. A major haplotype, designated GbHap1 (81.2%), was found throughout all sampling locations. Single nucleotide polymorphisms were observed mainly in the ITS1 region. The genetic structure was not detected, and genetic distance did not correlate with geographical distance. Haplotype network analysis suggested evidence of recent demographic expansion. Low genetic differences among populations also suggested that these isolates belong to a single G. boninense founder population adapting to oil palm as the host.