Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato

Dan Milbourne; Rhonda Meyer; John E. Bradshaw; Eileen Baird; Nicky Bonar; Jim Provan; Wayne Powell; Robbie Waugh

doi:10.1023/A:1009633005390

Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato

Dan Milbourne, Rhonda Meyer, John E. Bradshaw, Eileen Baird, Nicky Bonar, Jim Provan, Wayne Powell, Robbie Waugh

Department of Life Sciences

Scottish Crop Research Institute

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

372 Citations (Scopus)

Abstract

The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.

Original language	English
Pages (from-to)	127-136
Number of pages	10
Journal	Molecular Breeding
Volume	3
Issue number	2
DOIs	https://doi.org/10.1023/A:1009633005390
Publication status	Published - Apr 1997

Keywords

AFLP
genetic relationships
potato
RAPD
SSR
FRAGMENT LENGTH POLYMORPHISMS
RAPD MARKERS
SOLANUM-TUBEROSUM
DNA
RFLP
MICROSATELLITES
SEQUENCE
LINKAGE
FINGERPRINTS
ABUNDANCE
Genetic relationships
Potato

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title = "Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato",

abstract = "The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.",

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author = "Dan Milbourne and Rhonda Meyer and Bradshaw, {John E.} and Eileen Baird and Nicky Bonar and Jim Provan and Wayne Powell and Robbie Waugh",

note = "Funding Information: The authors would like to thank Dr J. McNicol for useful discussion of the statistical aspects of this paper, and Dr J. Russell for sharing unpublished data. D. Milbourne is a PMB-funded Ph.D. student. R. Meyer is funded by UNDP/CIP. All other authors are funded by the Scottish Office Agriculture, Environment and Fisheries Department.",

year = "1997",

month = apr,

doi = "10.1023/A:1009633005390",

language = "English",

volume = "3",

pages = "127--136",

journal = "Molecular Breeding",

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AU - Milbourne, Dan

AU - Meyer, Rhonda

AU - Bradshaw, John E.

AU - Baird, Eileen

AU - Bonar, Nicky

AU - Provan, Jim

AU - Powell, Wayne

AU - Waugh, Robbie

N1 - Funding Information: The authors would like to thank Dr J. McNicol for useful discussion of the statistical aspects of this paper, and Dr J. Russell for sharing unpublished data. D. Milbourne is a PMB-funded Ph.D. student. R. Meyer is funded by UNDP/CIP. All other authors are funded by the Scottish Office Agriculture, Environment and Fisheries Department.

PY - 1997/4

Y1 - 1997/4

N2 - The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.

AB - The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.

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KW - SSR

KW - FRAGMENT LENGTH POLYMORPHISMS

KW - RAPD MARKERS

KW - SOLANUM-TUBEROSUM

KW - DNA

KW - RFLP

KW - MICROSATELLITES

KW - SEQUENCE

KW - LINKAGE

KW - FINGERPRINTS

KW - ABUNDANCE

KW - Genetic relationships

KW - Potato

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DO - 10.1023/A:1009633005390

M3 - Review Article

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SP - 127

EP - 136

JO - Molecular Breeding

JF - Molecular Breeding

IS - 2

ER -

Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato

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Keywords

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