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

Abstract

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

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

“…A total of 38 M. oryzae isolates used for the morphological and molecular characterization in our previous study (Amoghavarsha, Pramesh, Naik, et al, 2021) were used. All isolates were obtained from a field survey done during Kharif 2019–2020 in different rice ecosystems of Karnataka viz., rainfed hilly ecosystems and irrigated (Bhadra, Kaveri and Thunga‐Bhadra, command areas) (Figure 1; Table 1).…”

“…The PCR amplification for ITS was described in our previous study (Amoghavarsha, Pramesh, Naik, et al, 2021). PCR amplification for the four selected gene loci ( actin, ß ‐tubulin, calmodulin and TEF‐1‐α ) was carried out in the ABS‐Veriti™ 96‐well thermocycler (Applied Biosystems).…”

“…Control of rice blast is the most challenging task because the pathogen can survive and multiply in harsh environmental conditions and swiftly spread to new fields (Araujo et al, 2000). 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).…”

“…species recognition based on gene trees using multiple loci), and it has surpassed the traditional grouping of organisms based on morphological data (Dettman et al, 2003; Taylor et al, 2000). Later, many molecular tools were used to understand the population diversity of Magnaporthe species viz., M. grisea Repeats (MGR), RFLP, RAPD, rep‐PCR and AFLP (Amoghavarsha, Pramesh, Naik, et al, 2021; Sheoran et al, 2021).…”

Spatial distribution and identification of potential risk regions to rice blast disease in different rice ecosystems of Karnataka

“…The hilly ecosystem majorly consists of the districts of Western Ghats, whereas the coastal ecosystem consists of the districts alongside the Arabian Sea and called Karavali or Canara or Karnataka coast. Heavy rainfall pattern is the characteristic feature of hilly and coastal ecosystems 25 , 26 . Each ecosystem is unique concerning the availability of water, soil type, cultivars grown, etc.…”