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Molecular markers to assess genetic diversity

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Abstract

Molecular markers play an essential role today in all aspects of plant breeding, ranging from the identification of genes responsible for desired traits to the management of backcrossing programs. The emergence of marker systems has, for the last 30 years, closely tracked developments in biochemistry and molecular biology. Following the demonstration that retrotransposons are ubiquitous, active, and abundant in plant genomes, markers were developed that are based on the insertional polymorphism they create upon replication. They virtually all exploit the joint that is formed, during retrotransposon integration, between genomic DNA and the long terminal repeats at either end of retrotransposon. The various retrotransposon marker systems differ in the nature of the second primer used in the amplification reactions. All except one of these marker methods is dominant (RBIP is co-dominant). Hence, the availability of effective means to generate doubled haploid populations through gametophytic embryogenesis is valuable for the efficient use of these markers. Over the last eight years, retrotransposon-based markers have been developed for crop species and trees across the plant kingdom, as well as for fungi and insects. Many retrotransposons features make them appealing as the basis of molecular marker systems. They are usually dispersed throughout the genome and produce large genetic changes at the point of insertion that can be detected with family-specific amplification primers. The ancestral state of a retrotransposon insertion is known, and subsequent changes at the locus are not subject to homoplasy. Retrotransposon markers are useful in accelerating backcrossing programs, tagging genes of interest, tracking germplasm, verifying and producing pedigrees, and examining crop evolution.

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Abbreviations

AFLP® :

amplified fragment length polymorphism

DH:

double haploid

IRAP:

inter-retrotransposon amplified polymorphism

LTR:

long terminal repeat

PIC:

polymorphism information content

RAPD:

randomly amplified polymorphic DNA

RBIP:

retrotransposon-based amplified polymorphism

REMAP:

retrotransposon-microsatellite amplified polymorphism

RFLP:

restriction-fragment length polymorphism

SNP:

single nucleotide polymorphism

SSAP:

sequence-specific amplified polymorphism

SSR:

simple sequence repeat

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Acknowledgements

This work is a contribution under COST Action 851: Gametic Cells and Molecular Breeding for Crop Improvement. Much of the work cited was carried out under EU contracts QLK5-2000-01502 (TEGERM) and QLRT-1999-01499 (MMEDV) as well as through the ESGEMO project supported by the Academy of Finland and the Ministry of Agriculture and Forestry of Finland. Anne-Mari Narvanto and Ursula Lönnqvist are thanked for their always excellent technical assistance.

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  1. Biotechnology and Food Research, MTT Agrifood Research Finland and MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki and MTT Agrifood Research Finland, Helsinki, 00014, Finland

    Alan H. Schulman

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Correspondence to Alan H. Schulman.

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Schulman, A.H. Molecular markers to assess genetic diversity. Euphytica 158, 313–321 (2007). https://doi.org/10.1007/s10681-006-9282-5

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