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UBC Theses and Dissertations

Genetic evaluation of natural and domesticated lodgepole pine populations using molecular markers Liewlaksaneeyanawin, Cherdsak


Lodgepole pine (P. contorta ssp. latifolia) has been recently subject to breeding and artificial propagation, and has also undergone migration and range expansion since the Pleistocene glaciation. This thesis studied the genetic effects of these processes, in terms of patterns of genetic diversity, sibship structure, and mating system. For these inferences, cross-species transfer of Pinus teada microsatellite (SSR) markers provided a battery of 23 polymorphic microsatellite primer pairs for lodgepole pine, and amplified fragment length polymorphism (AFLP) markers were also developed. Genetic variability in natural and domesticated populations from interior British Columbia (Prince George breeding zone) was investigated with both SSRs and AFLPs. Changes from the natural population, to the breeding population, to the seed orchard, and finally to seed and seedling populations, were estimated. AFLPs and SSRs did not always reveal the same trends, except in portraying the genetic relationship among natural and domesticated populations. Overall, some reduction of genetic diversity was observed along the domestication process (2-10%), but only for some stages and dependent on marker type. Two peripheral lodgepole pine populations, representing outcomes of the historical migration-expansion of this species, were sampled and genotyped for progeny arrays. Estimation of mating system parameters revealed high outcrossing rate and low correlated paternity in both populations, as well as the difficulties in using dominant AFLP markers for these inferences. Sibship analyses of SSRs supported low correlated paternity. Biparental inbreeding was significant in both, and more pronounced in the most northern population (compared to the eastern population), reflecting lower stand density and founder effects. A new characterization of genomic diversity, the "correlation of diversity between linked loci", was estimated in both populations, as well as in the central (Prince George) population. Significant correlations were observed in both peripheral populations, but not in the central population, suggesting range-expansion effects. As expected, higher correlations were observed for more closely linked loci. The correlation of diversity extended out to ca. 10 map units in both peripheral populations, much further than linkage disequilibrium can extend. While such correlations may be due to genetic drifts, it is possible that the signature of selection may be obscured by demographic factors associated with mating system.

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