In plants, balancing selection may cause the retention of polymorphism important for adaptation in populations over long time spans and is best known to affect genes for disease and abiotic stress responses. The inadvertent removal of polymorphism from domesticated populations otherwise maintained by balancing selection, has sometimes met with catastrophic consequences in the past. e.g. Irish potato famine. Similarly, the unintentional threats from the loss of adaptive diversity and inbreeding to the fitness of natural populations that undergo reductions in size or fragmentation, are also widely documented. A better understanding of the prevalence of balancing selection, its modes of action (heterozygote advantage, frequency-dependent selection and selection varying in time and space), and the genes it affects, might reveal new ways to manage and mitigate against the loss of adaptive variation during domestication or range depletion.
The present study used comparative genome analysis to identify genes under balancing selection. Thirty four candidate genes for wood formation were screened for SNP common to the Symphyomyrtus and Eucalyptus subgenera of the Eucalyptus genus. These trans-subgeneric SNP derive from ancestral polymorphisms that are maintained in each lineage post-speciation by balancing selection. Genes containing clusters of trans-specific SNP are good models for monitoring the loss of adaptive variation because the drivers of selection in these genes may be universal in eucalypts. The study showed balancing selection was more common among candidate genes for wood formation than might be expected on average in a genome, nonetheless, this high frequency was congruent with potential pleiotropic roles for these genes in disease and abiotic stress responses. Strong evidence for balancing selection was found in ten genes where there was a prevalence of trans-subgeneric SNP clustered in functional gene regions. Association testing was used to find candidate genes subject to balancing selection that also influenced physical and chemical wood phenotypes of interest for tree improvement. Pectin methylesterases catalyse the de-methyl-esterification of homogalacturonan, the major constituent of pectin, and have pleiotropic functions in wood formation, seed dormancy, fruit ripening and stress responses. Associated with wood quality and a gene where adaptive variation was maintained through a heterozygote advantage, one member of the pectin methylesterase gene-class may be a useful subject for exploring the consequences of diversity reduction at genes subject to balancing selection