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SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.)

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Abstract

Development of accurate high-throughput molecular marker systems such as SNPs permits evaluation and selection of favourable gene variants to accelerate elite varietal production. SNP discovery in perennial ryegrass has been based on PCR amplification and sequencing of multiple amplicons designed to scan all components of the transcriptional unit. Full-length genes (with complete intron–exon structure and promoter information) corresponding to well-defined biochemical functions such as lignin biosynthesis and oligosaccharide metabolism are ideal for complete SNP haplotype determination. Multiple SNPs at regular intervals across the transcriptional unit were detected within and between the heterozygous parents and validated in the progeny of the F 1(NA6 × AU6) genetic mapping family. Haplotype structures in the parental genotypes were defined and haplotypic abundance, structure and variation were assessed in diverse germplasm sources. Decay of LD to r 2 values of c. 0.2 typically occurs over 500–3,000 bp, comparable with gene length and with little apparent variation between diverse, ecotypic and varietal population sub-groups. Similar patterns were revealed as limited blocks of intragenic LD. The results are compatible with the reproductive biology of perennial ryegrass and the effects of large ancestral population size. This analysis provides crucial information to validate strategies for correlation of haplotypic diversity and phenotypic variation through association mapping.

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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. The authors thank Prof. Michael Hayward and Dr. Ben Hayes for careful critical assessment of the manuscript.

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Authors and Affiliations

  1. Primary Industries Research Victoria, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, VIC, 3083, Australia

    Rebecca C. Ponting, Michelle C. Drayton, Noel O. I. Cogan, Germán C. Spangenberg & John W. Forster

  2. Primary Industries Research Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia

    Mark P. Dobrowolski & Kevin F. Smith

  3. Molecular Plant Breeding Cooperative Research Centre, Bundoora, Australia

    Rebecca C. Ponting, Michelle C. Drayton, Noel O. I. Cogan, Mark P. Dobrowolski, Germán C. Spangenberg, Kevin F. Smith & John W. Forster

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  1. Rebecca C. Ponting
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  2. Michelle C. Drayton
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  3. Noel O. I. Cogan
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  4. Mark P. Dobrowolski
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Correspondence to John W. Forster.

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Communicated by R. Waugh.

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Ponting, R.C., Drayton, M.C., Cogan, N.O.I. et al. SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Mol Genet Genomics 278, 585–597 (2007). https://doi.org/10.1007/s00438-007-0275-4

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  • DOI: https://doi.org/10.1007/s00438-007-0275-4

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