Academic journal article Genetics

Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?

Academic journal article Genetics

Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?

Article excerpt

IDENTIFYING the loci underlying the variation in quanti- tative traits and detecting the selection acting on them remains, to this day, one of the main challenges in biology (Rockman 2012; Marjoram et al. 2013). In his Nobel lecture Sidney Brenner (Brenner 2003) predicted that genome-wide association studies (GWAS) would become the main ap- proach to identifying the genetic factors controlling complex traits. The past decade has amply vindicated Brenner's pre- diction: GWAS have blossomed and identified a large num- ber of single nucleotide polymorphism (SNP) associated to various quantitative traits (Visscher et al. 2012). Limitations of GWAS have, however, started to become evident and different strategies have been offered to alleviate those (Rockman 2012; Marjoram et al. 2013; Vilhjalmsson and Nordborg 2013). In particular, GWAS have limited power unless very large data sets are used. They therefore remain prohibitively expensive, and often not so informative, for nonmodel organisms with limited or nascent genome re- sources such as conifers. In such organisms a more targeted strategy, combining population genetics, physiology, and ex- pression studies of candidate genes remains a very fruitful approach, at least in the short term. We recently adopted such a strategy in an attempt to unravel the genetic basis of growth cessation, a trait of adaptive value with a strong and well-documented clinal variation, in Norway spruce (Picea abies) (Chen et al. 2012a and references therein). Two of the most promising candidate genes that emerged from these studies are PaFTL2, from the photoperiodic pathway, and the circadian clock gene Gigantea (PaGI). PaFTL2 expres- sion level is associated with growth cessation (Gyllenstrand et al. 2007), transgenic studies in Norway spruce confirm that high expression induces growth cessation (Karlgren et al. 2013), and SNPs within its promoter show a strong clinal variation in Scandinavia (Chen et al. 2012a). Gigantea harbors nonsynonymous variants showing clinal variation correlating with growth cessation. Gigantea is further of focal interest as there is mounting evidence of its involve- ment with phenology in a broad range of tree species (pop- lars, Rohde et al. 2011, Keller et al. 2012; oaks, Alberto et al. 2013; and spruces, Holliday et al. 2010, Chen et al. 2012a).

In this study we analyzed the relationship between latitude and variation at PaFTL2,PaGI, and other candidate genes for growth cessation in Siberian spruce. One major difficulty when studying clines from Scandinavia is the com- plex genetic structure of species found in this region. In great parts this complex population structure reflects the extent of the glaciations in this area and the existence of at least three major postglaciation recolonization routes (e.g., Giesecke and Bennett 2004, Chen et al. 2012a for spruce). In contrast, central Siberia, from where the Siberian spruce populations studied here originate, was much less affected by glaciations than northwestern Europe (Binney et al. 2009; Väliranta et al. 2011). Most of central and west- ern Siberia was likely a cold desert as westerly moisture, which is today the source of both rain and snow in this region, was blocked by the Scandinavian ice sheet during the glacial periods (Velichko et al. 2011). The extent and the depth of permafrost during the last glacial maxima were also much greater than they are today. However, macrofossils collected on lower river terraces, high floodplains, and mountain areas suggest that, while most of the region con- sisted of aeolian dunes, mountain areas and river valleys were a separate habitat where spruce trees were likely able to survive. Some of these populations were even found at high latitudes (Binney et al. 2009; Väliranta et al. 2011) and there is genetic evidence in Siberian larch that southern montane refugia did not contribute to the recolonization of western Siberia (Semerikov et al. 2013). We therefore expect the population history and genetic structure of the Siberian spruce to differ markedly from that of Norway spruce and, based on what has been observed in Siberian larch (Semerikov et al. …

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