Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment

Ngernmuen, Athipat; Suktrakul, Worawit; Damchuay, Katanyutita; Longya, Apinya; Kate-Ngam, Sureeporn; Jantasuriyarat, Chatchawan

doi:10.2478/s11756-019-00264-5

Cited by 7 publications

(3 citation statements)

References 33 publications

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“…Molecular phylogenetic grouping obtained by ISSR and SRAP analyses did not correlate with morphological characteristics, but morphology may affect conidia germination or pathogenicity. Ngernmuen et al [17] developed SSR markers from whole genome sequences of rice blast fungus strains and evaluated the genetic diversity of rice blast strains from Thailand. The results showed a high level of genetic diversity, and blast strains could be clustered based on geographic distribution and collection time.…”

Section: Genetic Diversity Of Pyricularia Oryzae Using Srap and Issr mentioning

confidence: 99%

Morphological Characterization and Genetic Diversity of Rice Blast Fungus, Pyricularia oryzae, from Thailand Using ISSR and SRAP Markers

Longya

Talumphai

Jantasuriyarat

2020

JoF

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Rice blast disease is caused by the ascomycete fungus Pyricularia oryzae and is one of the most destructive rice diseases in the world. The objectives of this study were investigating various fungal morphological characteristics and performing a phylogenetic analysis. Inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to examine the genetic variation of 59 rice blast fungus strains, including 57 strains collected from different fields in Thailand and two reference strains, 70-15 and Guy11. All isolates used in this study were determined to be P. oryzae by internal transcribed spacer (ITS) sequence confirmation. A total of 14 ISSR primers and 17 pairs of SRAP primers, which produced clear and polymorphic bands, were selected for assessing genetic diversity. A total of 123 polymorphic bands were generated. The similarity index value for the strains ranged from 0.25 to 0.95. The results showed that the blast fungus population in Thailand has both morphological and genetic variations. A high level of genetic variation, or genome adaptation, is one of the fungal mechanisms that could overcome host resistance to avoid host recognition. Results from this research study could bring substantial benefits and ultimately help to understand the blast fungal pathogen genome and the population structure in Thai blast fungus.regions with primers targeting open reading frames (ORFs) [5]. The molecular markers differ in cost, speed, complication, labor, degree of polymorphism, and repeatability. ISSR and SRAP marker techniques are fast and low cost, they do not require sequence information, have high repeatability, and use only one-step PCR. They provide highly discriminating information with good reproducibility and are relatively abundant, while AFLP and RAPD are more labor intensive and time consuming [4,6]. We characterized blast fungal morphology, performed DNA sequence analyses of the internal transcribed spacer (ITS), and used 20 ISSR and 30 SRAP markers to assess the genetic diversity of 59 rice blast strains, including 57 strains collected from Thai rice-growing areas and two reference strains, 70-15 and Guy11. The information obtained from this study will help to understand the population structure and evolution of rice blast fungus in Thailand. Materials and Methods Rice Blast MaterialsA total of 59 rice blast strains were used, including 57 strains collected from Thai rice-growing areas representing central, northern, and north-eastern parts of Thailand. Two rice blast strains, 70-15 and Guy11, were used as reference strains (Table 1). The stock of each blast strain as in filter paper was cultured and DNA was extracted using the cetyl-trimethyl-ammonium-bromide (CTAB) method described by Longya et al. [7].

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Section: Genetic Diversity Of Pyricularia Oryzae Using Srap and Issr mentioning

confidence: 99%

Morphological Characterization and Genetic Diversity of Rice Blast Fungus, Pyricularia oryzae, from Thailand Using ISSR and SRAP Markers

Longya

Talumphai

Jantasuriyarat

2020

JoF

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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: 59%

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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“…Compared with traditional methods, modern sequencing technology could provide a precise and rich source for developing specific markers [ 52 ]. For example, specific markers on the Dasypyrum villosum chromosome were designed via genotyping-by-sequencing (GBS) [ 53 ]. A DNA marker depicted for variety discrimination specific to ‘Manten-Kirari’ based on an NGS-RNA sequence in Fagopyrum tataricum [ 54 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Cytological Analysis and Specific Marker Development in Wheat-Psathyrostachys huashanica Keng 3Ns Additional Line with Elongated Glume

Pang

Huang

Wang

et al. 2023

IJMS

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Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) is an excellent gene resource for wheat breeding, which is characterized by early maturity, low plant height, and disease resistance. The wheat-P. huashanica derivatives were created by the elite genes of P. huashanica and permeate into common wheat through hybridization. Among them, a long-glume material 20JH1155 was identified, with larger grains and longer spike than its parents. In the present study, the methods of cytological observation, GISH, and sequential FISH analysis showed that 20JH1155 contained 21 pairs of wheat chromosomes and a pair of P. huashanica. There were some differences in 5A and 7B chromosomes between 20JH1155 and parental wheat 7182. Molecular marker, FISH, and sequence cloning indicated 20JH1155 alien chromosomes were 3Ns of P. huashanica. In addition, differentially expressed genes during immature spikelet development of 20JH1155 and 7182 and predicted transcription factors were obtained by transcriptome sequencing. Moreover, a total of 7 makers derived from Ph#3Ns were developed from transcriptome data. Taken together, the wheat-P. huashanica derived line 20JH1155 provides a new horizon on distant hybridization of wheat and accelerates the utilization of genes of P. huashanica.

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Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment

Cited by 7 publications

References 33 publications

Morphological Characterization and Genetic Diversity of Rice Blast Fungus, Pyricularia oryzae, from Thailand Using ISSR and SRAP Markers

Morphological Characterization and Genetic Diversity of Rice Blast Fungus, Pyricularia oryzae, from Thailand Using ISSR and SRAP Markers

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

Molecular Cytological Analysis and Specific Marker Development in Wheat-Psathyrostachys huashanica Keng 3Ns Additional Line with Elongated Glume

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