| 1. |
- Baison, J., et al.
(författare)
-
Genetic control of tracheid properties in Norway spruce wood
- 2020
-
Ingår i: Scientific Reports. - : Nature Research. - 2045-2322. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce. © 2020, The Author(s).
|
|
| 2. |
- Baison, John, et al.
(författare)
-
Genome-Wide Association Study (GWAS) identified novel candidate loci affecting wood formation in Norway spruce
- 2019
-
Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 100:1, s. 83-100
-
Tidskriftsartikel (refereegranskat)abstract
- Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional Genome-Wide Association Study (GWAS) of 17 wood traits in Norway spruce using 178101 single-nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings.We applied a LASSO based association mapping method using a functional multi-locus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multi-locus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
|
|
| 3. |
- Baison, John, et al.
(författare)
-
Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
- 2019
-
Ingår i: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 100:1, s. 83-100
-
Tidskriftsartikel (refereegranskat)abstract
- Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
|
|
| 4. |
- Chen, Zhi-Qiang, et al.
(författare)
-
Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce
- 2022
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover similar to 130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multilocus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide toots for future Norway spruce breeding and functional studies.
|
|
| 5. |
- Chen, Zhi-Qiang, et al.
(författare)
-
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
- 2021
-
Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.Results: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.Conclusion: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.
|
|
| 6. |
- Elfstrand, Malin, et al.
(författare)
-
Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance
- 2020
-
Ingår i: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 43, s. 1779-1791
-
Tidskriftsartikel (refereegranskat)abstract
- It is important to improve the understanding of the interactions between the trees and pathogens and integrate this knowledge about disease resistance into tree breeding programs. The conifer Norway spruce (Picea abies) is an important species for the forest industry in Europe. Its major pathogen is Heterobasidion parviporum, causing stem and root rot.In this study, we identified 11 Norway spruce QTLs (Quantitative trait loci) that correlate with variation in resistance to H. parviporum in a population of 466 trees by association genetics. Individual QTLs explained between 2.1 and 5.2% of the phenotypic variance. The expression of candidate genes associated with the QTLs was analysed in silico and in response to H. parviporum hypothesizing that (a) candidate genes linked to control of fungal sapwood growth are more commonly expressed in sapwood, and; (b) candidate genes associated with induced defences are respond to H. parviporum inoculation. The Norway spruce laccase PaLAC5 associated with control of lesion length development is likely to be involved in the induced defences. Expression analyses showed that PaLAC5 responds specifically and strongly in close proximity to the H. parviporum inoculation. Thus, PaLAC5 may be associated with the lignosuberized boundary zone formation in bark adjacent to the inoculation site.
|
|
| 7. |
- Elfstrand, Malin, et al.
(författare)
-
Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds
- 2020
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29, s. 199-213
-
Tidskriftsartikel (refereegranskat)abstract
- The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome-wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.
|
|
| 8. |
- Li, Lili, et al.
(författare)
-
Recent introductions, ancient recolonization events and local adaptation: a first fine-scale mapping of the population genetic structure of Norway spruce across Sweden
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Population genetic structure matters for a large range of issues: it is intrinsically related to speciation and local adaptation, it informs us on past demography, it conditions the response of populations to climate change or to the spread of diseases and it severely limits the power of genome wide association studies (GWAS). In the present study we genotyped all individuals from the base population of the Swedish P. abies breeding program using exome capture. In total 4769 individuals were genotyped. This very large and dense sampling along a latitudinal gradient ranging from 55°N to 67°N, together with a large number of polymorphisms (>300,000 SNPs) allowed us to analyze population genetic structure at an unprecedented scale and to test for associations between genetic polymorphisms and environmental variables We used clustering methods (PCA, Admixture) to obtain a first genetic clustering of the data. Moreover, in order to better capture the mixture of discrete and continuous processes that generated the distribution of the genetic variation of Norway spruce across Sweden two recently developed spatialized analyses (conStruct, EEMS) were also performed. The overall data comprises both trees of Swedish origin and a large number of trees recently introduced into Sweden from the rest of the range and is highly structured with a total of six clusters representing the main postglacial refugia and admixed populations originating from the refugia. Focusing on the trees of Swedish origin, the data shows that those can be divided into two main clusters with a contact zone in central Sweden and a third small cluster in northern Sweden. The contact zone is also observed in other species and likely reflects the meeting point of the two main waves of recolonization of Scandinavia after the Last Glacial Maximum. As to the northernmost cluster it was characterized by a high contribution from P. obovata. A large number of SNPs were found to be associated to environmental variables and exhibited a stronger pattern of isolation-by-distance than random SNP. Considering that P. abies has been in Sweden for less than 50 generations, this suggests a strong selection pressure during the expansion of the species through Scandinavia.
|
|
| 9. |
|
|
| 10. |
- Niu, Shihui, et al.
(författare)
-
p The Chinese pine genome and methylome unveil key features of conifer evolution
- 2022
-
Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 185:1, s. 204-
-
Tidskriftsartikel (refereegranskat)abstract
- Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.
|
|
