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Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.)

Abstract

Molecular genetic marker development in perennial ryegrass has largely been dependent on anonymous sequence variation. The availability of a large-scale EST resource permits the development of functionally-associated genetic markers based on SNP variation in candidate genes. Genic SNP loci and associated haplotypes are suitable for implementation in molecular breeding of outbreeding forage species. Strategies for in vitro SNP discovery through amplicon cloning and sequencing have been designed and implemented. Putative SNPs were identified within and between the parents of the F1(NA6 × AU6) genetic mapping family and were validated among progeny individuals. Proof-of-concept for the process was obtained using the drought tolerance-associated LpASRa2 gene. SNP haplotype structures were determined and correlated with predicted amino acid changes. Gene-length LD was evaluated across diverse germplasm collections. A survey of SNP variation across 100 candidate genes revealed a high frequency of SNP incidence (c. 1 per 54 bp), with similar proportions in exons and introns. A proportion (c. 50%) of the validated genic SNPs were assigned to the F1(NA6 × AU6) genetic map, showing high levels of coincidence with previously mapped RFLP loci. The perennial ryegrass SNP resource will enable genetic map integration, detailed LD studies and selection of superior allele content during varietal development.

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Acknowledgments

This work was supported by funding from the Victorian Department of Primary Industries, Dairy Australia Ltd., the Geoffrey Gardiner Dairy Foundation, Meat and Livestock Australia Ltd. and the Molecular Plant Breeding Cooperative Research Centre (MPB CRC). The authors thank Prof. Michael Hayward (Rhydgoch Genetics, Aberystwyth, UK) for careful critical reading of the manuscript.

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Correspondence to John W. Forster.

Additional information

Communicated by K. Shirasu

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Cogan, N.O.I., Ponting, R.C., Vecchies, A.C. et al. Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.). Mol Genet Genomics 276, 101–112 (2006). https://doi.org/10.1007/s00438-006-0126-8

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Keywords

  • Candidate gene
  • Amplicon cloning
  • Haplotype
  • Linkage disequilibrium
  • Asr gene