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.
Highlights
A primary goal of association genetics in long-lived organisms such as trees is to develop capacity to predict, at early life stages, the trait values of mature trees
Association genetics of adaptive traits is of great interest to forestry and is being studied in many species such as Pinus contorta (Mahony et al 2019), Populus trichocarpa (Evans et al, 2014), Picea sitchensis (Holliday et al, 2010) and Pinus taeda (Lu et al, 2017) and the use of multiple species has the potential to improve the generality of models based upon them
Nearly a third of single nucleotide polymorphism (SNP) on the array were high quality in all three species and nearly half of all successfully converted SNPs were polymorphic in all three species – twice the number reported by Perry et al, (2020) sample sizes were much larger in this study
Summary
A primary goal of association genetics in long-lived organisms such as trees is to develop capacity to predict, at early life stages, the trait values of mature trees. A high number of genetic markers screened in a large number of samples, which have been accurately phenotyped, ideally in multiple environments, are required to develop robust predictive models for these traits. The power of genetic association studies is growing rapidly with improvements in the scale, accuracy and cost of high-throughput sequencing and genotyping. The accessibility of costeffective high-throughput genotyping has benefited the study of non-model organisms, especially those for which genome assembly is challenging due to genome size and/or complexity (Prunier et al, 2016, Zimin et al, 2017). Allied to parallel efforts in building phenotype datasets, these technical and analytical advances mean association genetics in a range of tree species is tractable
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