Genotyping for the study of population genetics and trait evaluation in Picea sitchensis

Abstract

Genotyping provides information on the genetic makeup of an individual or a population of individuals. Molecular markers are commonly used as an affordable method of genotyping individuals, and the most popular modern marker is the Single Nucleotide Polymorphism (SNP). SNPs have a wide range of applications, including their use in understanding the evolutionary history and genetics of populations. In breeding they can be used for discovery, prediction and selection of traits. Furthermore, they can be used in the comparison of populations and understanding of parentage. In this thesis there were two large populations genotyped using SNPs and study, compare and investigate the populations. Sitka spruce, Picea sitchensis, is native to North America, occupying coastal regions along the pacific North West and has become the predominant forestry species in Ireland since its introduction but little is known about the genetic makeup of these forests or the collections used to breed and select new spruce in Ireland (chapter 1). In chapter two the IUFRO (International Union of Forest Research Organisation) population was genotyped, a representative breeding population of the native range of Sitka spruce. The population consists of 80 provenances with 9-15 genotypes per provenance. The two genotyping platforms explored were Genotyping by Sequencing (GBS) and SNPseq. It was found that due to number of SNPs sequenced and price points that GBS was more efficient and less at risk of bias because it uses short read Whole genome sequencing (WGS). 1177 samples representing all 80 provenances were genotyped. 36567 SNPs were discovered after SNP filtration. Genetic diversity studies show the population is very diverse and has similar diversity levels to other spruces in this region that have been studied. Using PCA and DAPC it was discovered that the population was structured into one main cluster and isolation of North Alaskan provenances, including two islands, Montague and Kodiak Island. There was an isolation effect based off these two islands. Admixture analysis reveals a genetic distribution pattern that correlates with the retreat of the cordilleran ice sheet. This suggests a recolonization pattern akin to some of the previous hypothesis. Sitka spruce occupies various different ecological and environmental gradients. This wide range of climates allows for local adaptations at the provenance level. In chapter 3 local adaptation was investigated using various analyses. A Genome Wide Association Study (GWAS) and a Genotype Environment Analysis (GEA) was used to study the IUFRO population. From these analyses, loci involved with traits and various climatic measures were discovered. A Canonical Correlation (CANCOR) analysis was used which combines genotypes, environments and phenotypes together to study the interaction between the three. From the CANCOR analysis there were 121 loci positively correlated with an environmental trait and ten loci positively correlated to a phenotypic trait. There were two significant clusters of loci, one was correlated with adaptations to cold wintering conditions and the other was correlated with adaptations to conditions ideal for growing. The distribution of these loci involved with height are positively correlated below the 50th latitude and negatively correlated above the 50th latitude. Overall local adaption across the range that appears to be characterised by subtle to moderate shifts in Minor Allele Frequency (MAF) in the traits tested. This is similar to what is seen in other species such as Loblolly Pine, Pinus taeda. A second population was genotyped as part of this thesis. The Irish Sitka Spruce Tree Improvement Programme (ISSTIP) collection is a breeding population that originates from the native range of Sitka spruce, from Haida Gwaii to Oregon. In chapter 4, GBS was used to genotype 215 samples of Sitka spruce from the ISSTIP population to compare to the IUFRO population. There is a subtle loss in genetic diversity after restricting the provenances used in the breeding program. The range selected for breeding was less diverse than the entire breeding range leading to loss of potentially interesting traits. The DAPC demonstrated that the ISSTIP population has become genetically differentiated from the IUFRO population. Admixture analyses reveal the ISSTIP population primarily shares no admixture with other populations apart from Haida Gwaii. This genotyping has captured and been used compared the population genetics of a breeding population. Seed orchard dynamics were studied as part of this thesis. A custom KASP assay to inexpensively and efficiently genotype Irish Sitka spruce seed orchards was designed using a minimal set of markers. The markers were designed to distinguish between all genotyped material from the ISSTIP population. The assay was deployed to test the offspring of an Irish seed orchard and test for contamination and inbreeding. 54.41% of the offspring were from outcrossing parent pairs, 21.53% were as a result of inbreeding and 24.65% were as a result of contamination from fraternal sources. The presence of over contributing parental genotypes in the population, with some parents being responsible for 31.60% of offspring. Overall this thesis aimed to establish a baseline for genetic diversity in Sitka spruce and compare it to a breeding population. The IUFRO population has also be used to understand the evolution of Sitka spruce and potential loci correlated with traits of interest. Two diverse populations have been genotyped in this study, which can act as resources for spruce research including analysis of traits and evolution. These resources will also be useful for breeders for progeny selection, genomic selection and deployment of trees in seed orchards.