Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea Abies (L.) Karst]

PLoS One. 2014 May 8;9(5):e95306. doi: 10.1371/journal.pone.0095306. eCollection 2014.

Abstract

The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Circadian Clocks / genetics*
  • Circadian Rhythm / genetics*
  • Genes, Plant / genetics*
  • Genetics, Population
  • Nucleotides / genetics*
  • Photoperiod*
  • Picea / genetics*
  • Plant Proteins / genetics

Substances

  • Nucleotides
  • Plant Proteins

Grant support

Financial support were obtained from the Royal Swedish Academy of Agriculture and Forestry (ksla.se); the Swedish Research Council for Environmental, Agricultural Sciences and Spatial Planning; TREESNIPS, QLRT-2001-01973 (European commission); EVOLTREE (Framework 6 program EU); NOVELTREE, EUI2008-40 03713 (EU); Linktree and TipTree (Eranet Biodiversity); and Nilsson-Ehle foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.