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Fine-scale comparative genetic and physical mapping supports map-based cloning strategies for the self-incompatibility loci of perennial ryegrass (Lolium perenne L.)

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Abstract

Perennial ryegrass is an obligate outbreeding pasture grass of the Poaceae family, with a two-locus (S and Z) gametophytic self-incompatibility (SI) mechanism. This system has provided a major obstacle to targeted varietal development, and enhanced knowledge is expected to support more efficient breeding strategies. Comparative genetics and physical mapping approaches have been developed to permit molecular cloning of the SI genes. SI gene-linked genetic markers based on heterologous cDNA restriction fragment length polymorphisms (RFLPs) and homologous genomic DNA-derived simple sequence repeats (SSRs) were converted to single nucleotide polymorphism (SNP) format for efficient genotyping. Genetic mapping identified the location of SI loci and demonstrated macrosynteny between related grass species. S- and Z-linked bacterial artificial chromosome (BAC) clones were sequenced using massively parallel pyrosequencing technology to provide the first physical mapping data for Poaceae SI loci. The sequence assembly process suggested a lower prevalence of middle repetitive sequences in the Z locus region and hence precedence for positional cloning strategy. In silico mapping using data from rice, Brachypodium distachyon and Sorghum revealed high sequence conservation in the vicinity of the Z locus region between SI and self-compatible (SC) grass species. Physical mapping identified a total of nine genes encoded in the Z locus region. Expression profiling and nucleotide diversity assessment identified two Z-linked genes, LpTC116908 and LpDUF247, as plausible candidates for the male and female determinants of the S-Z SI system.

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Acknowledgments

This work was supported by funding from the Victorian Department of Primary Industries and the Molecular Plant Breeding Cooperative Research Centre (MPB CRC). The authors thank Dr. Ute Baumann (Australian Centre for Plant Functional Genomics, Adelaide, Australia) for provision of information prior to publication and helpful discussions.

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Authors and Affiliations

  1. Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe Research and Development Park, Bundoora, VIC, 3083, Australia

    Hiroshi Shinozuka, Noel O. I. Cogan, German C. Spangenberg & John W. Forster

  2. Molecular Plant Breeding Cooperative Research Centre, Australia www.molecularplantbreeding.com

    Hiroshi Shinozuka, Noel O. I. Cogan, Kevin F. Smith, German C. Spangenberg & John W. Forster

  3. Department of Primary Industries, Biosciences Research Division, Hamilton Centre, Mount Napier Road, Hamilton, VIC, 3330, Australia

    Kevin F. Smith

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  1. Hiroshi Shinozuka
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  2. Noel O. I. Cogan
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  4. German C. Spangenberg
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  5. John W. Forster
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Correspondence to John W. Forster.

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Shinozuka, H., Cogan, N.O.I., Smith, K.F. et al. Fine-scale comparative genetic and physical mapping supports map-based cloning strategies for the self-incompatibility loci of perennial ryegrass (Lolium perenne L.). Plant Mol Biol 72, 343–355 (2010). https://doi.org/10.1007/s11103-009-9574-y

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