AFLP analysis of Trichoderma spp. from India compared with sequence and morphological-based diagnostics

H. K. Buhariwalla; P. Srilakshmi; S. Kannan; R. S. Kanchi; S. Chandra; K. Satyaprasad; F. Waliyar; R. P. Thakur; J. H. Crouch

doi:10.1111/j.1439-0434.2005.00989.x

AFLP analysis of Trichoderma spp. from India compared with sequence and morphological-based diagnostics

H. K. Buhariwalla, P. Srilakshmi, S. Kannan, R. S. Kanchi, S. Chandra, K. Satyaprasad, F. Waliyar, R. P. Thakur, J. H. Crouch

Bioinformatics & Computational Biology

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

Trichoderma species offer considerable potential for controlling aflatoxin contamination in groundnut and other crops. Initial classification of 48 Trichoderma isolates, derived from four different groundnut cultivation sites in India was based on alignment of 28S rDNA sequences to GenBank sequences of ex-type strains. This was found to be substantially more reliable than our routine morphological characterization, but did not provide a comprehensive diagnostic solution, as unique single nucleotide polymorphism (SNP) haplotypes could not be identified for all species. However, all the Trichoderma isolates could be readily distinguished by amplified fragment length polymorphism (AFLP) analysis, based on six primer pair combinations, which generated 234 polymorphic bands. In addition, individual AFLP bands were identified which differentiate closely related species. Similarly, AFLP bands were identified that correlated with different types of antagonism to Aspergillus flavus. The implications of these results for the development of simple polymerase chain reaction (PCR)-based diagnostic assays for antagonistic isolates of Trichoderma is discussed.

Original language	English (US)
Pages (from-to)	389-400
Number of pages	12
Journal	Journal of Phytopathology
Volume	153
Issue number	7-8
DOIs	https://doi.org/10.1111/j.1439-0434.2005.00989.x
State	Published - 2005

Keywords

Aflatoxin
Amplified fragment length polymorphism
Groundnut
Internal transcribed spacer
Trichoderma

ASJC Scopus subject areas

Physiology
Agronomy and Crop Science
Genetics
Plant Science

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10.1111/j.1439-0434.2005.00989.x

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title = "AFLP analysis of Trichoderma spp. from India compared with sequence and morphological-based diagnostics",

abstract = "Trichoderma species offer considerable potential for controlling aflatoxin contamination in groundnut and other crops. Initial classification of 48 Trichoderma isolates, derived from four different groundnut cultivation sites in India was based on alignment of 28S rDNA sequences to GenBank sequences of ex-type strains. This was found to be substantially more reliable than our routine morphological characterization, but did not provide a comprehensive diagnostic solution, as unique single nucleotide polymorphism (SNP) haplotypes could not be identified for all species. However, all the Trichoderma isolates could be readily distinguished by amplified fragment length polymorphism (AFLP) analysis, based on six primer pair combinations, which generated 234 polymorphic bands. In addition, individual AFLP bands were identified which differentiate closely related species. Similarly, AFLP bands were identified that correlated with different types of antagonism to Aspergillus flavus. The implications of these results for the development of simple polymerase chain reaction (PCR)-based diagnostic assays for antagonistic isolates of Trichoderma is discussed.",

keywords = "Aflatoxin, Amplified fragment length polymorphism, Groundnut, Internal transcribed spacer, Trichoderma",

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year = "2005",

doi = "10.1111/j.1439-0434.2005.00989.x",

language = "English (US)",

volume = "153",

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AU - Buhariwalla, H. K.

AU - Srilakshmi, P.

AU - Kannan, S.

AU - Kanchi, R. S.

AU - Chandra, S.

AU - Satyaprasad, K.

AU - Waliyar, F.

AU - Thakur, R. P.

AU - Crouch, J. H.

PY - 2005

Y1 - 2005

N2 - Trichoderma species offer considerable potential for controlling aflatoxin contamination in groundnut and other crops. Initial classification of 48 Trichoderma isolates, derived from four different groundnut cultivation sites in India was based on alignment of 28S rDNA sequences to GenBank sequences of ex-type strains. This was found to be substantially more reliable than our routine morphological characterization, but did not provide a comprehensive diagnostic solution, as unique single nucleotide polymorphism (SNP) haplotypes could not be identified for all species. However, all the Trichoderma isolates could be readily distinguished by amplified fragment length polymorphism (AFLP) analysis, based on six primer pair combinations, which generated 234 polymorphic bands. In addition, individual AFLP bands were identified which differentiate closely related species. Similarly, AFLP bands were identified that correlated with different types of antagonism to Aspergillus flavus. The implications of these results for the development of simple polymerase chain reaction (PCR)-based diagnostic assays for antagonistic isolates of Trichoderma is discussed.

AB - Trichoderma species offer considerable potential for controlling aflatoxin contamination in groundnut and other crops. Initial classification of 48 Trichoderma isolates, derived from four different groundnut cultivation sites in India was based on alignment of 28S rDNA sequences to GenBank sequences of ex-type strains. This was found to be substantially more reliable than our routine morphological characterization, but did not provide a comprehensive diagnostic solution, as unique single nucleotide polymorphism (SNP) haplotypes could not be identified for all species. However, all the Trichoderma isolates could be readily distinguished by amplified fragment length polymorphism (AFLP) analysis, based on six primer pair combinations, which generated 234 polymorphic bands. In addition, individual AFLP bands were identified which differentiate closely related species. Similarly, AFLP bands were identified that correlated with different types of antagonism to Aspergillus flavus. The implications of these results for the development of simple polymerase chain reaction (PCR)-based diagnostic assays for antagonistic isolates of Trichoderma is discussed.

KW - Aflatoxin

KW - Amplified fragment length polymorphism

KW - Groundnut

KW - Internal transcribed spacer

KW - Trichoderma

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AFLP analysis of Trichoderma spp. from India compared with sequence and morphological-based diagnostics

Abstract

Keywords

ASJC Scopus subject areas

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