Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes
Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and...
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Published in | Genome Vol. 46; no. 2; pp. 277 - 290 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
Ottawa, Canada
NRC Research Press
01.04.2003
Canadian Science Publishing NRC Research Press |
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Abstract | Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity. |
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AbstractList | Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits. Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity. Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neotyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichlo isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichlo species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Original Abstract: Des endophytes fongiques du genre Neotyphodium sont communs chez les graminees poussant dans les prairies situees en zone temperee. Ces champignons conferent a leurs hotes des caracteres agronomiques tantot benefiques et tantot indesirables. le but de ce travail etait de developper des marqueurs moleculaires bases sur les microsatellites (locus SSR) pour des fins d'identification et de mesure de la diversite genetique au sein des endophytes Neotyphodium chez les graminees de paturage. Des etiquettes de sequences exprimees (EST) du Neotyphodium coenophialum et du Neotyphodium lolii ont ete examinees et des microsatellites a locus unique ont ete identifies chez 9,7 % des sequences du N. coenophialum et chez 6,3 % des sequences du N. lolii. Divers types de microsatellites etaient presents, mais les suites trinucleotidiques parfaites etaient les plus communes. Des amorces ont ete produites pour 50 locus du N. coenophialum et pour 57 locus du N. lolii et ces locus ont ete evalues chez 20 isolats des genres Neotyphodium et Epichloee. Une forte proportion des amorces ont permis d'obtenir des produits d'amplification chez la majorite des isolats et la plupart de ces amorces ont permis de detecter de la variation genetique. Les microsatellites des deux especes ont detecte beaucoup de polymorphisme entre les especes appartenant aux genres Neotypodium et Epichloee, mais peu de polymorphisme au sein des deux genres. Des combinaisons judicieuses de microsatellites permettent de distinguer les especes. Une comparaison de ces marqueurs avec des marqueurs AFLP (polymorphisme de longueur des fragments amplifies) a montre que les microsatellites etaient informatifs pour la mesure de la variation genetique tant au sein des especes d'endophytes qu'entre elles. Ces marqueurs pourront s'employer pour identifier les taxons d'endophytes et pour evaluer la diversite intraspecifique au sein des populations, une variation qui pourrait s'averer correlee avec la variation observee au niveau des consequences agronomiques de la presence d'endophytes. Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloe isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloe species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits. |
Abstract_FL | Des endophytes fongiques du genre Neotyphodium sont communs chez les graminées poussant dans les prairies situées en zone tempérée. Ces champignons confèrent à leurs hôtes des caractères agronomiques tantôt bénéfiques et tantôt indésirables. Le but de ce travail était de développer des marqueurs moléculaires basés sur les microsatellites (locus SSR) pour des fins d'identification et de mesure de la diversité génétique au sein des endophytes Neotyphodium chez les graminées de pâturage. Des étiquettes de séquences exprimées (EST) du Neotyphodium coenophialum et du Neotyphodium lolii ont été examinées et des microsatellites à locus unique ont été identifiés chez 9,7 % des séquences du N. coenophialum et chez 6,3 % des séquences du N. lolii. Divers types de microsatellites étaient présents, mais les suites trinucléotidiques parfaites étaient les plus communes. Des amorces ont été produites pour 50 locus du N. coenophialum et pour 57 locus du N. lolii et ces locus ont été évalués chez 20 isolats des genres Neotyphodium et Epichloë. Une forte proportion des amorces ont permis d'obtenir des produits d'amplification chez la majorité des isolats et la plupart de ces amorces ont permis de détecter de la variation génétique. Les microsatellites des deux espèces ont détecté beaucoup de polymorphisme entre les espèces appartenant aux genres Neotypodium et Epichloë, mais peu de polymorphisme au sein des deux genres. Des combinaisons judicieuses de microsatellites permettent de distinguer les espèces. Une comparaison de ces marqueurs avec des marqueurs AFLP (polymorphisme de longueur des fragments amplifiés) a montré que les microsatellites étaient informatifs pour la mesure de la variation génétique tant au sein des espèces d'endophytes qu'entre elles. Ces marqueurs pourront s'employer pour identifier les taxons d'endophytes et pour évaluer la diversité intraspécifique au sein des populations, une variation qui pourrait s'avérer corrélée avec la variation observée au niveau des conséquences agronomiques de la présence d'endophytes.Mots clés : Neotyphodium, microsatellites, étiquette de séquence exprimée, polymorphisme de longueur des fragments amplifiés, diversité génétique.[Traduit par la Rédaction] |
Author | Forster, J.W Spangenberg, G.C Guthridge, K.M Jong, E. van Z. de |
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BackLink | https://www.ncbi.nlm.nih.gov/pubmed/12723044$$D View this record in MEDLINE/PubMed |
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SubjectTerms | Acremonium lolii amplified fragment length polymorphism Ascomycota - genetics DNA primers DNA, Plant Endophytes Expressed Sequence Tags Flowers & plants Fungi Fungi - genetics Gene Library Genetic diversity Genetic Markers Genetic Variation Genetics Grasses loci Microsatellite Repeats Molecular Sequence Data Neotyphodium coenophialum Pasture Poaceae - microbiology polymerase chain reaction Polymorphism, Genetic Sequence Analysis, DNA Sequence Homology, Nucleic Acid Species Specificity Taxa |
Title | Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes |
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