Assessment of genetic diversity and population structure of Magnaporthe oryzae causing rice blast disease using SSR markers

Yadav, Manoj Kumar; Aravindan, S; Raghu, S.; Prabhukarthikeyan, S.R.; Keerthana, U.; Ngangkham, Umakanta; Pramesh, D.; Banerjee, Amrita; Adak, Totan; Kar, Meera Kumari; Parameswaran, C.; Deshmukh, Rupesh; Tiwari, Jitendra Kumar; Mohanty, Mahendra Kumar; Rath, Prakash Chandra

doi:10.1016/j.pmpp.2019.02.004

Cited by 18 publications

(9 citation statements)

References 47 publications

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“…The population analysis of isolates may help to know the potential of a pathogen development into new races. Previously, different markers such as amplified fragment length polymorphism (Vos et al, 1995), random amplification of polymorphic DNA (Prashanthi et al, 2010) and simple sequence repeats (Yadav, Aravindan, Raghu, et al, 2019) were used for deducing genetic diversity. The internal transcribed spacer (ITS) is still a valuable marker for taxonomic identification and deducing diversity in fungi (Schoch et al, 2012; Seifert, 2009).…”

Section: Introductionmentioning

confidence: 99%

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

Chittaragi

Pramesh

Naik

et al. 2021

J of Applied Microbiology

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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. 7 MF716846.1 M. oryzae isolate AMA UOC-01 8 KT693184.1 M. oryzae strain UPM-PO Malaysia 9 KM249937.1 M. oryzae strain PO-FA01 10 MW042178.1 P. oryzae strain Pos-3 China 11 MW042177.1 P. oryzae strain Pos-2 12 MT588875.1 P. grisea isolate DW-2016-2 13 MW042176.1 P. oryzae strain Pos-1 14 MG642970.1 M. e grisea 15 MF946553.1 Pyricularia sp. strain F2 United Kingdom 16 MN203028.1 P. oryzae isolate T49 17 FN555121.1 M. oryzae 18 JX469384.1 M. oryzae culture-collection NFCCI:2605 India (NE) 19 MF678836.1 M. oryzae isolate Gudalur India (TN) 20 MF669475.1 M. oryzae isolate Nagaranai 21 MF668695.1 M. oryzae isolate Aduthurai 22 MF668692.1 M. oryzae isolate Maduranthakam 23 KM816799.1 M. oryzae strain w11-65 18S Korea 24 KM816801.1 M. oryzae strain w11-110 25 KM816797.1 M. oryzae strain w11-58 26 KM816796.1 M. oryzae strain w11-23 27 AB269937.1 M. grisea genes Japan 28 MT103091.1 P. oryzae isolate Mf3 Iran 29 MT103090.1 P. oryzae isolate Mb3 30 LC552959.1

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Section: Introductionmentioning

confidence: 99%

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

Chittaragi

Pramesh

Naik

et al. 2021

J of Applied Microbiology

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“…Recent studies include the use of SSR markers (Jagadeesh et al, 2020;Yadav et al, 2019;Ngernmuen et al, 2019). Similar to this study is Anjum et al (2016) who evaluated finger millet using SSR markers to show genetic variability in P. grisea.…”

Section: Genetic Diversity Of P Grisea In Major Finger Millet Growing Areas In Kenyamentioning

confidence: 61%

Characterization of diversity and pathogenecity of Pyricularia grisea affecting finger millet in Kenya

Tracyline¹,

Kimurto²,

Mafurah³

2021

Afr. J. Microbiol. Res.

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Pyricularia grisea characterization is a prerequisite for species differentiation and understanding of the pathosystem, evolution and diversity of species. The aim of this study is to determine the morphological variation, pathogen virulence and molecular diversity of P. grisea isolates. Five isolates from infected heads of finger millet were collected from Bomet, Nakuru, Baringo, Busia and Machakos counties in 2019. The samples were cultured in the lab for both characterization and spore suspension preparation. Data on morphological characterization included colony diameter, color and shape of conidia. Pathogenicity test was done in the greenhouse in a randomized complete block design using KNE 741, a susceptible genotype and disease data scored. Molecular characterization involved the use of seven SSR markers. Data analyses included use of softwares such as AUDPC, Power Maker, GeneAlex and Darwin. Results showed that P. grisea isolates had different growth pattern with respect to color, colony diameter and conidia shape. Pathogenicity test revealed that all sites had significant different (P<0.01) virulence on the test genotype. Neck blast, scored at physiological maturity was prominent in Koibatek and Bomet strains while leaf blast was severe in Bomet and Alupe strains. Molecular analysis showed that ENA ranged from 1.30 (MGM 437) -1.99 (Pyrm 61-62) with an average of 1.71. PIC varied between 0.20-0.37 for primers MGM 437 and Pyrm 61-62, respectively. Factorial and phylogenetic analysis revealed that P. grisea isolates were diverse with no geographical grouping. AMOVA indicated diversity occurred within populations (87%) as opposed to among populations (13%). The high P. grisea variability found in the study is a clear indication of the high sexual recombination among strains collected in major growing areas of Kenya.

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“…However, the losses can be minimized by managing the disease using different strategies viz., modification of cultural practices, nutrition management, botanicals, biological agents, chemicals and resistant varieties (Amoghavarsha, Pramesh, Chidanandappa, et al, 2021; Amoghavarsha, Pramesh, Naik, et al, 2021; Hubert et al, 2015; Pramesh et al, 2020; Pramesh, Muniraju, et al, 2016; Pramesh, Nataraj, et al, 2016; Yang et al, 2008). Among the different strategies used, managing blast by host plant resistance is considered the most economical and best method (Sharma et al, 2021; Yadav, Aravindan, Raghu, et al, 2019). Even though effective resistance ( R ) genes are deployed, the genetic diversity of the pathogen has weakened this approach by modification of corresponding avirulence ( Avr ) genes in the pathogen (Zhong et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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

Chittaragi

Pramesh

Naik

et al. 2022

Journal of Applied Microbiology

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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 analysed for their diversity at actin, β-tubulin, calmodulin, translation elongation factor 1α (TEF-1α), 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 analysed 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 genespecific 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% 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 behaviour of M. oryzae is important in developing region-specific blastresistant rice cultivars. This is the first report of MAT1 idiomorphs distribution in the M. oryzae population in any Southern state of India.

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Assessment of genetic diversity and population structure of Magnaporthe oryzae causing rice blast disease using SSR markers

Cited by 18 publications

References 47 publications

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

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

Characterization of diversity and pathogenecity of Pyricularia grisea affecting finger millet in Kenya

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

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