Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species

Abstract

BackgroundTropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families.ResultsPIP Aquaporin subfamily genes were isolated, and their DNA sequence polymorphisms characterised in natural populations. Sequence data were analysed with statistical tests of standard neutral equilibrium and demographic scenarios simulated to compare with the observed results. Chloroplast SSRs were also used to test demographic transitions. Most gene fragments are highly polymorphic and display signatures of balancing selection or bottlenecks; chloroplast SSR markers have significant statistics that do not conform to expectations for population bottlenecks. Although not incompatible with a purely demographic scenario, the combination of all tests tends to favour a selective interpretation of extant gene diversity.ConclusionsTropical tree PIP genes may generally undergo balancing selection, which may maintain high levels of genetic diversity at these loci. Genetic variation at PIP genes may represent a response to variable environmental conditions.

DNA sequence variation of drought-response candidate genes in Austrocedrus chilensis

“…The analyses carried out with neutral markers in the species do not support the presence of demographic process such as population structure, thus we can tentatively conclude that the departures from equilibrium at AcAQP2 loci are due to balancing selection. In San Ramón and Pedregoso populations, the observed departures from neutrality seem to be mostly situated in the exon-intron limit, suggesting selection in the intron splicing sites or perhaps, other regulatory functions by intronic sequences, such as those previously observed in the forest tree species Eperua falcata in Aquaporin genes (Audigeos et al 2010).…”

“…Since the DNA samples are diploid, the identification of the haplotypes may result ambiguous, especially in regions where heterozygous individuals are observed (Audigeos et al 2010). The haplotype reconstruction was performed with the PHASE algorithm (Stephens and Donnelly, 2003) to produce two haploid sequences per individual.…”

“…This approach has been used in forest species such as Cryptomeria japonica (Kado et al 2003;Fujimoto et al 2010), Pinus taeda (González-Martínez et al 2006;Eckert et al 2010), Populus nigra L. (Chu et al 2009), and forest Neotropical species such as Pachira quinata (Bombacaceae), Virola sebifera (Myristicaceae) and Carapa guianensis (Meliaceae) (Audigeos et al 2010).…”

Tracking Selection Signatures Based on Variation in <i>OsLEA</i>27 within Myanmar Landraces of Upland and Dryland Rice

“…The D * test statistic is based on the distribution of mutations in the genealogy and compares the number of old and new mutations [28]. These results showed an excess of intermediate allelic frequency in intron-splicing sites.…”

Isolation of primers for candidate genes for mechano-sensing in five Neotropical tree species

“…On the other hand, due to the experimental limits described above, only short gene fragments could be obtained, even for extremely well-characterised gene families (Audigeos et al 2010). This is a drawback in the analysis of evolutionary processes at the gene level, although in Neotropical tree species there appears to be sufficient polymorphism even in short fragments (Audigeos et al 2010). The extension of the isolated fragments by genomic methods (e.g.…”