Nucleotide Polymorphism and Phenotypic Associations Within and Around the phytochrome B2 Locus in European Aspen (Populus tremula, Salicaceae)

Abstract

We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the ''hinge region,'' close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits

“…The degree of overestimation is thereby a function of the power of the study such that QTL effects will be more upwardly biased with low power, that is, small effect sizes (Xu 2003;Zöllner and Pritchard 2007). Ingvarsson et al (2008) performed a candidate gene association mapping approach in European aspen and identified two singlenucleotide polymorphisms significantly associated with bud set. They used an ad hoc method described by Allison et al (2002) to obtain less biased estimates of QTL effects.…”

Local Selection Across a Latitudinal Gradient Shapes Nucleotide Diversity in Balsam Poplar, Populus balsamifera L

“…In balsam poplar, our analyses implicate FRI in the response to local selection at different latitudes, probably reflecting a role of FRI in the temperaturesensitive timing of seasonal development. Because floweringtime homologs in Populus can affect a range of developmental traits, including flowering and bud dormancy (Böhlenius et al 2006;Ingvarsson et al 2008;Lagercrantz 2009;Ma et al 2010), the link between allelic variation in FRI and variation in specific phenotypes in poplar awaits further study.…”

“…Comparative research across diverse taxa suggests that this gene network is responsible for variation in multiple phenological traits responsive to photoperiod, including flowering, tuberization, and seasonal dormancy (Lagercrantz 2009). Based upon transgenic and QTL mapping experiments in Populus, genes in this network are also associated with flowering and vegetative bud development in trees (Frewen et al 2000;Chen et al 2002;Böhlenius et al 2006;Ingvarsson et al 2008;Jackson 2009;Ma et al 2010;Rohde et al 2010).…”

“…Surveys of natural allelic variation among A. thaliana accessions sampled from diverse latitudes have identified two flowering-time genes, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), that show evidence of local adaptation with latitude (Caicedo et al 2004;Stinchcombe et al 2004;Le Corre 2005). In other species, local selection has targeted members of the phytochrome gene family (PHYE) in Cardamine japonica (Ikeda et al 2009) and PHYB2 in Populus tremula (Ingvarsson et al 2006;Ingvarsson et al 2008) and components of the circadian clock (Böhlenius et al 2006;Slotte et al 2007;Brachi et al 2010;Ma et al 2010). These studies suggest that homologs of the A. thaliana flowering-time gene network underlie ecologically important adaptive variation in phenological responses in other species, making them promising candidates for studying the molecular basis of local adaptation, as well as testing the repeatability of evolution across taxa in genes that influence quantitative traits.…”

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

“…In forest trees, the candidate gene association study (AS) approach has identified SNPs and genes linked to wood and growth traits in many tree species such as Eucalyptus nitens (Thumma et al ., 2009), Populus spp, (Ingvarsson et al ., 2008; Wegrzyn et al ., 2010; Guerra et al ., 2013), pines (Dillon et al ., 2010; Cumbie et al ., 2011; Jaramillo‐Correa et al ., 2015) and spruces (Beaulieu et al ., 2011; Prunier et al ., 2013). However, the variation in quantitative traits explained by individual SNP markers is generally low and rarely exceeds 5% (Dillon et al ., 2010; Guerra et al ., 2013), consistent with multigenic control (Evans et al ., 2014) and the relatively shallow genomic sampling in most studies to date (< 1% and 10% of estimated gene coding loci per genome) (Nystedt et al ., 2013; Neale et al ., 2014).…”