| 1. |
- Apuli, Rami-Petteri, et al.
(författare)
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
- 2020
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Ingår i: G3. - : GENETICS SOCIETY AMERICA. - 2160-1836. ; 10:1, s. 299-309
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Tidskriftsartikel (refereegranskat)abstract
- The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.
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| 2. |
- Apuli, Rami-Petteri
(författare)
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Opportunities in small population breeding in black cottonwood : or The little population that could
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Small and structured populations are problematic for breeding due to low levels of genetic variability and increased levels of linkage disequilibrium (LD). The increased LD causes problems with utilization of common genomic tools and may lead into increased accruement of deleterious alleles through the intense selection and bottlenecks characteristic of breeding. In forest trees, maintaining a large breeding population to alleviate these issues is difficult due to large physical size of most trees. The aim of this thesis was to study and resolve some of the LD dependent issues of small populations and establish small populations as an option in breeding. We established the accuracy of LD-based estimation methods of recombination using data from European aspen, allowing confident use of these methods later in the project. The small black cottonwood breeding population contained enough genetic diversity to facilitate future adaptive selection to novel Swedish climate and light conditions, suggesting that small populations consisting of offspring with diverse parentage are feasible options for breeding in species with high outcrossing and recombination rates. We identified candidate genes that can be targeted for selection on phenology and growth using a genome wide association study (GWAS). We also show that GWAS is useful for identifying large effect alleles even in small populations and that efficient growth under novel conditions likely require different allele combinations than in native habitats. Finally, we quantified deleterious load and identified effects of the deleterious load on growth. Accounting for deleterious load allowed for more effective genomic selection and increased breeding cycle gain in breeding programs based on small populations.
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| 3. |
- Apuli, Rami-Petteri, et al.
(författare)
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The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)
- 2021
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Ingår i: BMC Plant Biology. - : BioMed Central (BMC). - 1471-2229. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- Background: Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment.Results: We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions.Conclusions: In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.
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| 4. |
- Richards, Thomas, et al.
(författare)
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Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. And Gray)
- 2020
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 125, s. 449-458
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Tidskriftsartikel (refereegranskat)abstract
- In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology inPopulus trichocarpato determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017-2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h(2) = 0.5-0.8) and in lifetime growth (h(2) = 0.8). The combination of additive variation and favourable genetic correlations in phenology traits suggests that populations of cultivated varieties of P. Trichocarpa may have the capability to adapt their phenology to climatic changes without negative impacts on growth.
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