excess of nonsynonymous polymorphism and extensive haplotype structure at the PtABI1B locus in European aspen (Populus tremula): a case of balancing selection in an obligately outcrossing plant?

• Published in: Heredity Vol. 99; no. 4; pp. 381 - 388
• Main Authors: Garcia, M.V, Ingvarsson, P.K
• Format: Journal Article
• Language: English
• Published: England Springer Nature B.V 01-10-2007
• Subjects: Alleles; Base Sequence; Crosses, Genetic; exons; Gene loci; genes; Genes, Plant; genetic polymorphism; Genetic Variation; Genome, Plant; Genotype & phenotype; Haplotypes; Linkage Disequilibrium; loci; Models, Genetic; Models, Statistical; Molecular Sequence Data; Mutation; nonsynonymous polymorphism; nucleotide sequences; outcrossing; Plant ecology; Polymorphism; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Populus - genetics; Populus tremula; PtABI1B locus; Recombination, Genetic; Sequence Analysis, DNA; Statistical analysis; Trees; Variation (Genetics); France; Austria; Sweden; Crosses; Plant; Recombination; Genes; DNA; Genetic; Statistical; Models; Sequence Analysis; Genome; Single Nucleotide; Polymorphism
• ISSN: 0018-067X; 1365-2540
• DOI: 10.1038/sj.hdy.6801012

Here, we describe an unusually pronounced haplotype structure at the PtABI1B locus in the obligately outcrossing tree Populus tremula. Both nucleotide diversity and divergence at PtABI1B was low compared to other P. tremula genes suggesting that the gene is located in a region with a low mutation rate. Despite this, PtABI1B shows a very marked excess of nonsynonymous polymorphisms across the entire coding region and linkage disequilibrium (LD) extending across the entire PtABI1B region of approximately 2.6 kb. Such extensive LD is normally not seen in P. tremula. The extensive LD at PtABI1B is caused by the presence of two distinct haplotypes. The haplotype structure is not caused by a lack of recombination in the region, because evidence of recombination can be detected. In addition, several statistical tests strongly reject neutrality for the PtABI1B region, suggesting that the unusual haplotype structure could be actively maintained by balancing selection.