Identifying and testing marker–trait associations for growth and phenology in three pine species: Implications for genomic prediction

Abstract

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker–trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 single nucleotide polymorphisms (SNPs) from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034–0.037) and negatively associated with budburst timing at the other (YA: r = −0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.

Evolutionary targets of gene expression divergence in a complex of closely related pine species

“…This close genetic similarity between the species is usually explained by relatively recent speciation in presence of gene flow (Christensen, 1987;Monteleone et al, 2006;Jasińska et al, 2010) and segregation of ancestral variation (Wachowiak et al, 2011(Wachowiak et al, , 2013. Comparative transcriptome analysis of these pines (Wachowiak et al, 2015) revealed thousands of polymorphic markers that were used for the development of SNP genotyping array (Perry et al, 2020), which has since been used to identify loci significantly associated with key adaptive traits, including growth and phenology (Perry et al, 2022). Genomic studies support the phylogenetically close relationship between two mountain pine taxa as compared to Scots pine and reveal some candidate regions under selection during the species evolution (Zaborowska et al, 2021).…”