Monitoring and managing genetic diversity in Sitka spruce (Picea sitchensis (Bong.) Carr.)
The British breeding programme (Programme) for Sitka spruce (Picea sitchensis (Bong.) Carr.) began in 1963 by selecting individual plus trees with superior characteristics for construction-grade timber. With the establishment of seed orchards and vegetative propagation programmes, the production of improved forest reproductive material from the Programme intensified. Currently, the vast majority (>90%) of Sitka plants sold in Great Britain come from the Programme. Since the beginnings of genetic improvement of Sitka spruce in GB predates the readily available molecular genotyping methods, little is known about the genetic diversity inside the Programme. The thesis explores genetic diversity inside the different stages of the Programme. Using microsatellite (SSR) markers, chapter Chapter 1 assesses the stepwise reduction of diversity from natural populations to vegetative propagation programmes, differentiation between different seed years/provenances, and considers the origin of plus trees. Chapter 2 focuses on simple, nonmolecular methods for assessing unequal parentage contributions in a seed orchard that lead to the loss of genetic diversity. Chapter 3 utilises SSR markers to assign parents to the seed crop, quantifies and spatially analyses gene flow inside a seed orchard, and provides G-statistics of the seed crop from the orchard. Chapter 4 explores the appropriateness of SNP markers for internal control and tracking of forest reproductive material from clonal archives through seed nurseries and forest plantations. Results presented in Chapter 1 suggest that the breeding population of Sitka spruce in Britain exhibits high levels of genetic diversity. The levels are comparable and sometimes exceed those of unimproved natural populations. The highest average and effective number of alleles (12.58 and 6.27, respectively) were found in the 60 elite plus trees subsample. Similar levels are also found in the natural regeneration cores sampled under unimproved Sitka stands, which is promising for any continuous cover forest management. Genetic transfer from parents inside the studied seed orchard in Chapter 2 was incomplete and varied substantially between years. Effective population sizes based on seed viability of collected crops ranged from 7.6 in 2020 to 29.5 in 2019 (total population size is 35). The general health status of each ramet, male and female cone abundance and frost effect were all significant factors for yearly variations in genetic diversity. A molecular approach for studying the extent of genetic transfer inside the tree orchard in Chapter 3 confirms incomplete transfer and yearly variations. Low contamination rates from beyond the orchard were also detected (5.12%). A strong correlation between male flowering abundance and father contributions in successful pollinations (R2=0.41) suggests that forestry practitioners can use simple non-molecular methods for basic genetic monitoring of orchards. Finally, Chapter 4 reveals worrying levels of genetic diversity in highly improved vegetatively propagated full-sib families (VP FRM). Most samples (98%) inside the VP FRM plantations were assigned to the wrong pedigree due to mislabelled maps, clerical errors, replanting after high mortality and contaminations at the tree nurseries. Discrepancies between clonal identities inside the clonal archives were also found (27% error), suggesting that systematic testing of the breeding population would benefit further improvement efforts. Molecular markers proved to be a helpful tool for internal quality control. Comparison between SSR and SNP markers suggests that SSR markers outperform the SNP Sequenom array in the current state, and further efforts would be needed to optimize the SNP method for internal control of the breeding programme. In each of the chapters, practical advice for forestry practitioners is given. In conclusion, genetic diversity inside the Sitka spruce British breeding programme stores plenty of genetic diversity ready to be deployed. More efforts should be put into optimizing the yearly variation of seed quality from seed orchards by mixing different seed years and maintaining the general health of ramets. Additionally, levels of genetic diversity at the most improved stages of the improvement programme need to be lowered by controlling contaminations and human errors as they undermine breeding efforts to achieve desired high genetic gains.