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Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris

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Abstract

Allozyme variation has been and continues to be a major source of information on the level of genetic variation among plant species. Deciphering the molecular basis of electrophoretic variation is essential for understanding the forces affecting the protein level variation. In this study, the relationship between allozyme heterozygosity and nucleotide diversity in plants is investigated among and within species. Allozyme and nucleotide diversity in 27 plant species was reviewed. At the multilocus level, the two methods are congruent: a clear correlation between the two measures of genetic diversity among plant species was observed, strengthening the view that effective population size is the major determinant of genome-wide diversity. Nucleotide diversity at six allozyme coding genes (6pgdB, aco, gdh, gotC, mdhA, and mdhB) in conifer Pinus sylvestris was investigated jointly with electrophoretic data. Single non-synonymous charge-changing mutations were found together with electrophoretic alleles that consequently were mutationally unique. Synonymous site nucleotide diversity (point estimate of θ W—0.009 per bp) and silent site divergence from Pinus pinaster at allozyme coding loci were at comparable levels with other loci in the species. Linkage disequilibrium was extensive compared to earlier estimates from P. sylvestris and other trees, spanning several kilobases. Allozyme coding genes had an excess of closely related haplotypes whose frequency has recently increased possibly as a result of partial selective sweeps or balancing selection, but complex demographic effects cannot be excluded.

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Acknowledgments

We thank Soile Finne, Matti Salmela, and Pekka Lankinen for valuable technical assistance; Timo Knürr for consulting on statistical issues; Pär K. Ingvarsson, Thomas Bataillon, and Helmi Kuittinen for commenting on the manuscript; and Torgny Persson from The Forestry Research Institute of Sweden and Katri Kärkkäinen from the Finnish Forest Research Institute for seed material. This work was supported by the European Union (EVOLTREE 016322), Finnish Graduate School in Population Genetics and Centre for Population Genetic Analyses funded by the Academy of Finland, and Biocenter Oulu.

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  1. Department of Biology, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland

    Tanja Pyhäjärvi, Sonja T. Kujala & Outi Savolainen

  2. Biocenter Oulu, University of Oulu, 90014, Oulu, Finland

    Sonja T. Kujala & Outi Savolainen

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  1. Tanja Pyhäjärvi
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  2. Sonja T. Kujala
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Correspondence to Tanja Pyhäjärvi.

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Communicated by R. Sederoff

Tanja Pyhäjärvi and Sonja T. Kujala contributed equally to the manuscript.

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Pyhäjärvi, T., Kujala, S.T. & Savolainen, O. Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris . Tree Genetics & Genomes 7, 385–397 (2011). https://doi.org/10.1007/s11295-010-0340-8

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