| 1. |
- Mishra, A, et al.
(author)
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Diminishing benefits of urban living for children and adolescents' growth and development
- 2023
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 615:7954, s. 874-883
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Journal article (peer-reviewed)abstract
- Optimal growth and development in childhood and adolescence is crucial for lifelong health and well-being1–6. Here we used data from 2,325 population-based studies, with measurements of height and weight from 71 million participants, to report the height and body-mass index (BMI) of children and adolescents aged 5–19 years on the basis of rural and urban place of residence in 200 countries and territories from 1990 to 2020. In 1990, children and adolescents residing in cities were taller than their rural counterparts in all but a few high-income countries. By 2020, the urban height advantage became smaller in most countries, and in many high-income western countries it reversed into a small urban-based disadvantage. The exception was for boys in most countries in sub-Saharan Africa and in some countries in Oceania, south Asia and the region of central Asia, Middle East and north Africa. In these countries, successive cohorts of boys from rural places either did not gain height or possibly became shorter, and hence fell further behind their urban peers. The difference between the age-standardized mean BMI of children in urban and rural areas was <1.1 kg m–2 in the vast majority of countries. Within this small range, BMI increased slightly more in cities than in rural areas, except in south Asia, sub-Saharan Africa and some countries in central and eastern Europe. Our results show that in much of the world, the growth and developmental advantages of living in cities have diminished in the twenty-first century, whereas in much of sub-Saharan Africa they have amplified.
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| 2. |
- Baison, J., et al.
(author)
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Genetic control of tracheid properties in Norway spruce wood
- 2020
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In: Scientific Reports. - : Nature Research. - 2045-2322. ; 10:1
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Journal article (peer-reviewed)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).
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| 3. |
- Cruz, Raquel, et al.
(author)
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Novel genes and sex differences in COVID-19 severity
- 2022
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In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 31:22, s. 3789-3806
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Journal article (peer-reviewed)abstract
- Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10−8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10−22 and P = 8.1 × 10−12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10−8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10−8) and ARHGAP33 (P = 1.3 × 10−8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10−8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.
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| 4. |
- Zhou, Linghua, et al.
(author)
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Genetic analysis of wood quality traits in norway spruce open-pollinated progenies and their parent plus trees at clonal archives and the evaluation of phenotypic selection of plus trees
- 2019
-
In: Canadian Journal of Forest Research. - : Canadian Science Publishing. - 0045-5067 .- 1208-6037. ; 49:7, s. 810-818
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Journal article (peer-reviewed)abstract
- A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h2) estimates based on parent– offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h2 estimate, selection of the best clones from clonal archives would be an effective alternative.
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| 5. |
- Gil-Munoz, Francisco, et al.
(author)
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QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)
- 2023
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In: Tree Genetics & Genomes. - : Springer Nature. - 1614-2942 .- 1614-2950. ; 19:3
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Journal article (peer-reviewed)abstract
- Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned x normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.
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| 6. |
- Gil-Munoz, Francisco, et al.
(author)
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Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.)
- 2020
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In: Agronomy. - : MDPI. - 2073-4395. ; 10:11
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Journal article (peer-reviewed)abstract
- Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.
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| 7. |
- Abrahamsson, Sara, et al.
(author)
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Inheritance of height growth and autumn cold hardiness based on two generations of full-sib and half-sib families of Pinus sylvestris
- 2012
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In: Scandinavian Journal of Forest Research. - : Informa UK Limited. - 0282-7581 .- 1651-1891. ; 27, s. 405-413
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Journal article (peer-reviewed)abstract
- The genetic variability in height growth and autumn cold hardiness were evaluated in a full-sib family of Scots pine (Pinus sylvestris (L.)) in a field trial in northern Sweden and 358 open pollinated families generated from the progeny of the full-sib cross. Height and autumn cold hardiness were assessed in the progeny of the full-sib cross at 9-19 years of age and on 3995 open pollinated progenies at three years of age. The autumn cold hardiness [critical temperature (CT)] of trees and progenies was tested by artificial freeze testing of detached needles at various temperatures. Significant genetic variation was found among progenies in both height growth and cold hardiness with a narrow sense heritability of 0.16 and 0.37, respectively. There was also a significant positive genetic correlation (r(a) = 0.39) between height growth and CT with taller trees showing later autumn cold acclimation. It was concluded that there is significant additive genetic variance for height and CT which warrants a potential for mapping quantitative trait loci. Furthermore, the low heritability for height growth shows the importance of removing the environmental influence by using additive genetic predictions instead of phenotypic measurements thereby improving the accuracy of genetic associations.
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| 8. |
- Abrahamsson, Sara, et al.
(author)
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Maternal heterozygosity and progeny fitness association in an inbred Scots pine population
- 2013
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In: Genetica. - : Springer Netherlands. - 0016-6707 .- 1573-6857. ; 141:1-3, s. 41-50
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Journal article (peer-reviewed)abstract
- Associations between heterozygosity and fitness traits have typically been investigated in populations characterized by low levels of inbreeding. We investigated the associations between standardized multilocus heterozygosity (stMLH) in mother trees (obtained from12 nuclear microsatellite markers) and five fitness traits measured in progenies from an inbred Scots pine population. The traits studied were proportion of sound seed, mean seed weight, germination rate, mean family height of one-year old seedlings under greenhouse conditions (GH) and mean family height of three-year old seedlings under field conditions (FH). The relatively high average inbreeding coefficient (F) in the population under study corresponds to a mixture of trees with different levels of co-ancestry, potentially resulting from a recent bottleneck. We used both frequentist and Bayesian methods of polynomial regression to investigate the presence of linear and non-linear relations between stMLH and each of the fitness traits. No significant associations were found for any of the traits except for GH, which displayed negative linear effect with stMLH. Negative HFC for GH could potentially be explained by the effect of heterosis caused by mating of two inbred mother trees (Lippman and Zamir 2006), or outbreeding depression at the most heterozygote trees and its negative impact on the fitness of the progeny, while their simultaneous action is also possible (Lynch. 1991). However,since this effect wasn’t detected for FH, we cannot either rule out that the greenhouse conditions introduce artificial effects that disappear under more realistic field conditions.
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| 9. |
- Ahlinder, Jon, et al.
(author)
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Life stage-specific inbreeding depression in long-lived Pinaceae species depends on population connectivity
- 2021
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
-
Journal article (peer-reviewed)abstract
- Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.
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| 10. |
- Baison, John, et al.
(author)
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Genome-Wide Association Study (GWAS) identified novel candidate loci affecting wood formation in Norway spruce
- 2019
-
In: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 100:1, s. 83-100
-
Journal article (peer-reviewed)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.
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| 11. |
- Baison, John, et al.
(author)
-
Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
- 2019
-
In: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 100:1, s. 83-100
-
Journal article (peer-reviewed)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.
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| 12. |
- Bernhardsson, Carolina, et al.
(author)
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An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
- 2019
-
In: G3. - : Genetics Society of America. - 2160-1836. ; 9:5, s. 1623-1632
-
Journal article (peer-reviewed)abstract
- Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.
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| 13. |
- Bernhardsson, Carolina, et al.
(author)
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Present genetic structure is congruent with the common origin of distant Scots pine populations in its Romanian distribution
- 2016
-
In: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 361, s. 131-143
-
Journal article (peer-reviewed)abstract
- Owing to the fact that mitochondrial, chloroplast and nuclear genomes are differently affected by evolutionary forces, the comparative study of all three genomes in combination with paleobotanical evidences allows for a more accurate interpretation of present genetic make-up. In this study, we analyzed the nad1-nad7 mitotype, 14 cpSSR loci and 10 nSSR loci in 13 Romanian Scots pine (Pious sylvestris L.) populations from the Romanian Carpathians and two Hungarian populations. Previous analysis of the macro fossil records supports the presence of Scots pine and Swiss stone pine (Pinus cembra L.) during the glacial period in Hungary and Romania. For a better image into the population structure in the studied area we also included in the data analysis two outgroup populations (north and south of Sweden) of known post glacial origin, which resulted in a more defined genetic structure. Our study reveals that relatively high genetic diversity is preserved at all the Romanian and Hungarian populations, with no distinction among naturally regenerated, managed autochthonous and introduced populations. Furthermore, genetic differentiation analysis fails to distinguish the two introduced populations from the Romanian ones. AMOVA clustering is congruent with the paleobotanical-based evidences of contraction of Scots pine range since the Holocene to its present fragmented distribution. (C) 2015 Elsevier B.V. All rights reserved.
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| 14. |
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| 15. |
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| 16. |
- Calleja-Rodriguez, Ainhoa, et al.
(author)
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Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
- 2019
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 462, s. 283-292
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Journal article (peer-reviewed)abstract
- In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F-2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G x E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.
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| 17. |
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| 18. |
- Chen, Zhiqiang, et al.
(author)
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Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce
- 2018
-
In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 19
-
Journal article (peer-reviewed)abstract
- BackgroundGenomic selection (GS) can increase genetic gain by reducing the length of breeding cycle in forest trees. Here we genotyped 1370 control-pollinated progeny trees from 128 full-sib families in Norway spruce (Picea abies (L.) Karst.), using exome capture as genotyping platform. We used 116,765 high-quality SNPs to develop genomic prediction models for tree height and wood quality traits. We assessed the impact of different genomic prediction methods, genotype-by-environment interaction (GxE), genetic composition, size of the training and validation set, relatedness, and number of SNPs on accuracy and predictive ability (PA) of GS.ResultsUsing G matrix slightly altered heritability estimates relative to pedigree-based method. GS accuracies were about 11-14% lower than those based on pedigree-based selection. The efficiency of GS per year varied from 1.71 to 1.78, compared to that of the pedigree-based model if breeding cycle length was halved using GS. Height GS accuracy decreased to more than 30% while using one site as training for GS prediction and using this model to predict the second site, indicating that GxE for tree height should be accommodated in model fitting. Using a half-sib family structure instead of full-sib structure led to a significant reduction in GS accuracy and PA. The full-sib family structure needed only 750 markers to reach similar accuracy and PA, as compared to 100,000 markers required for the half-sib family, indicating that maintaining the high relatedness in the model improves accuracy and PA. Using 4000-8000 markers in full-sib family structure was sufficient to obtain GS model accuracy and PA for tree height and wood quality traits, almost equivalent to that obtained with all markers.ConclusionsThe study indicates that GS would be efficient in reducing generation time of breeding cycle in conifer tree breeding program that requires long-term progeny testing. The sufficient number of trees within-family (16 for growth and 12 for wood quality traits) and number of SNPs (8000) are required for GS with full-sib family relationship. GS methods had little impact on GS efficiency for growth and wood quality traits. GS model should incorporate GxE effect when a strong GxE is detected.
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| 19. |
- Chen, Zhiqiang, et al.
(author)
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Increased Prediction Ability in Norway Spruce Trials Using a Marker X Environment Interaction and Non-Additive Genomic Selection Model
- 2019
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 110, s. 830-843
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Journal article (peer-reviewed)abstract
- A genomic selection study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in 2 Northern Swedish trials at 2 locations using exome capture as a genotyping platform. Nonadditive effects including dominance and first-order epistatic interactions (including additive-by-additive, dominance-by-dominance, and additive-by-dominance) and marker-by-environment interaction (MxE) effects were dissected in genomic and phenotypic selection models. Genomic selection models partitioned additive and nonadditive genetic variances more precisely than pedigree-based models. In addition, predictive ability in GS was substantially increased by including dominance and slightly increased by including MxE effects when these effects are significant. For velocity, response to genomic selection per year increased up to 78.9/80.8%, 86.9/82.9%, and 91.3/88.2% compared with response to phenotypic selection per year when genomic selection was based on 1) main marker effects (M), 2) M + MxE effects (A), and 3) A + dominance effects (AD) for sites 1 and 2, respectively. This indicates that including MxE and dominance effects not only improves genetic parameter estimates but also when they are significant may improve the genetic gain. For tree height, Pilodyn, and modulus of elasticity (MOE), response to genomic selection per year improved up to 68.9%, 91.3%, and 92.6% compared with response to phenotypic selection per year, respectively.
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| 20. |
- Chen, Zhiqiang, et al.
(author)
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Inheritance of growth and solid wood quality traits in a large Norway spruce population tested at two locations in southern Sweden
- 2014
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In: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 10:5, s. 1291-1303
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Journal article (peer-reviewed)abstract
- Unfavorable genetic correlations between growth and wood quality traits are one of the biggest challenges in advanced conifer breeding programs. To examine and deal with such correlation, increment cores were sampled at breast height from 5,618 trees in 524 open-pollinated families in two 21-year-old Norway spruce progeny trials in southern Sweden, and age trends of genetic variation, genetic correlation, and efficiency of selection were investigated. Wood quality traits were measured on 12-mm increment cores using SilviScan. Heritability was moderate (~0.4-0.5) for wood density and modulus of elasticity (MOE) but low (~0.2) for microfibril angle (MFA). Different age trends were observed for wood density, MFA, and MOE, and the lower heritability of MFA relative to wood density and MOE in Norway spruce contrasted with general trends of the three wood quality traits in pine. Genetic correlations among growth, wood density, MFA, and MOE increased to a considerably high value from pith to bark with unfavorable genetic correlations (−0.6 between growth and wood density, −0.74 between growth and MOE). Age-age genetic correlations reached 0.9 after ring 4 for diameter at breast height (DBH), wood density, MFA, and MOE traits. Early selections at ring 10 for diameter and at ring 6 or 7 for wood quality traits had similar effectiveness as selection conducted at reference ring 15. Selection based on diameter alone produced 19.0 % genetic gain in diameter but resulted in 4.8 % decrease in wood density, 9.4 % decrease in MOE, and 8.0 % increase in MFA. Index selection with a restriction of no change in wood density, MOE, and MFA, respectively, produced relatively lower genetic gains in diameter (16.4, 12.2, and 14.1 %, respectively), indicating such index selection could be implemented to maintain current wood density. Index selection using economic weights is, however, recommended for maximum economic efficiency
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| 21. |
- Chen, Zhiqiang, et al.
(author)
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Method for accurate fiber length determination from increment cores for large-scale population analyses in Norway spruce
- 2016
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In: Holzforschung. - : Walter de Gruyter GmbH. - 0018-3830 .- 1437-434X. ; 70:9, s. 829-838
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Journal article (peer-reviewed)abstract
- Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce (Picea abies (L.) Karst) trees on fibers from rings 8-11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7% and low scatter. Length-weighing and length2-weighing gave biases of-7.3% and +9.3%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.
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| 22. |
- Chen, Zhi‑Qiang, et al.
(author)
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Early selection for resistance to Heterobasidion parviporum in Norway spruce is not likely to adversely affect growth and wood quality traits in late-age performance
- 2018
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In: European Journal of Forest Research. - : Springer Science and Business Media LLC. - 1612-4669 .- 1612-4677. ; 137:4, s. 517-525
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Journal article (peer-reviewed)abstract
- Infections with Heterobasidion parviporum devalue the Norway spruce timber as the decayed wood does not meet the necessary quality requirements for sawing. To evaluate the incorporation of disease resistance in the Norway spruce breeding strategy, an inoculation experiment with H. parviporum on 2-year-old progenies of 466 open-pollinated families was conducted under greenhouse (nursery) conditions. Lesion length in the phloem (LL), fungal growth in sapwood (FG) and growth (D) were measured on an average of 10 seedlings for each family. The genetic variation and genetic correlations between both LL, FG and growth in the nursery trial and wood quality traits measured previously from 21-year old trees in two progeny trials, including solid-wood quality traits (wood density, and modulus of elasticity) and fiber properties traits (radial fiber width, tangential fiber width, fiber wall thickness, fiber coarseness, microfibril angle and fiber length). For both LL and FG, large coefficients of phenotypic variation (> 26%) and genetic variation (> 46%) were detected. Heritabilities of LL and FG were 0.33 and 0.42, respectively. We found no significant correlations between wood quality traits and growth in the field progeny trials with neither LL nor FG in the nursery trial. Our data suggest that the genetic gains may reach 41 and 52% from mass selection by LL and FG, respectively. Early selection for resistance to H. parviporum based on assessments of fungal spread in the sapwood in nursery material, FG, will not adversely affect growth and wood quality traits in late-age performance.
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| 23. |
- Chen, Zhi-Qiang, et al.
(author)
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Estimating solid wood properties using Pilodyn and acoustic velocity on standing trees of Norway spruce
- 2015
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In: Annals of Forest Science. - : Springer Science and Business Media LLC. - 1286-4560 .- 1297-966X. ; 72:4, s. 499-508
-
Journal article (peer-reviewed)abstract
- Key message: Strong genetic correlations were observed between Pilodyn measurement and wood density, and between acoustic velocity and MFA. Combination of Pilodyn penetration and acoustic velocity measurements from standing trees can provide reliable prediction of stiffness of Norway spruce for breeding selection.Context: Traditional methods for the estimation of solid wood quality traits of standing tree such as wood density, microfibril angle (MFA), and modulus of elasticity (MOE) are time-consuming and expensive, which render them unsuitable for rapidly screening a large number of trees in tree breeding programs.Aim: This study aims to evaluate the suitability of using Pilodyn penetration and acoustic velocity (nondestructive evaluation) to assess wood density, MFA, and MOE for Norway spruce.Methods: Pilodyn penetration and Hitman acoustic velocity, as well as wood density, MFA, and MOE using benchmark SilviScan were measured on 5618 standing trees of 524 open-pollinated families in two 21-year-old Norway spruce (Picea abies) progeny trials in southern Sweden.Results: Strong genetic correlations were observed between Pilodyn measurement and wood density (rg = −0.96), and between acoustic velocity and MFA (rg = −0.94). Combination of Pilodyn penetration and Hitman acoustic velocity measurements (Formula presented.) obtained from standing trees showed a genetic correlation with benchmark MOE of 0.99. This combined MOE(Formula presented.) had higher selection efficiency for benchmark MOE (92 %) compared to 58–60 % using acoustic velocity alone and 78 % using Pilodyn penetration alone.Conclusion: Combination of Pilodyn penetration with Hitman acoustic velocity provided very high selection efficiency for the three most important quality traits for wood mechanical properties in Norway spruce.
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| 24. |
- Chen, Zhi-Qiang, et al.
(author)
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Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in Norway spruce
- 2016
-
In: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 12:6
-
Journal article (peer-reviewed)abstract
- Adverse genetic correlations between growth traits and solid-wood, as well as fiber traits are a concern in conifer breeding programs. To evaluate the impact of selection for growth and solid-wood properties on fiber dimensions, we investigated the inheritance and efficiency of early selection for different wood-fiber traits and their correlations with stem diameter, wood density, modulus of elasticity (MOE), and microfibril angle (MFA) in Norway spruce (Picea abies L). The study was based on two large open-pollinated progeny trials established in southern Sweden in 1990 with material from 524 families comprising 5618 trees. Two increment cores were sampled from each tree. Radial variations from pith to bark were determined for rings 3–15 with SilviScan for fiber widths in the radial (RFW) and tangential (TFW) direction, fiber wall thickness (FWT), and fiber coarseness (FC). Fiber length (FL) was determined for rings 8–11. Heritabilities based on rings 8–11 using joint-site data were moderate to high (0.24–0.51) for all fiber-dimension traits. Heritabilities based on stem cross-sectional averages varied from 0.34 to 0.48 and reached a plateau at rings 6–9. The “age-age†genetic correlations for RFW, TFW, FWT, and FC cross-sectional averages at a particular age with cross-sectional averages at ring 15 reached 0.9 at rings 4–7. Our results indicated a moderate to high positive genetic correlation for density and MOE with FC and FWT, moderate and negative with RFW, and low with TFW and FL. Comparison of several selection scenarios indicated that the highest profitability is reached when diameter and MOE are considered jointly, in which case, the effect on any fiber dimension is negligible. Early selection was highly efficient from ring 5 for RFW and from rings 8–10 for TFW, FWT, and FC.
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| 25. |
- Chen, Zhi-Qiang, et al.
(author)
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Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce
- 2022
-
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
-
Journal article (peer-reviewed)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.
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| 26. |
- Chen, Zhi-Qiang, et al.
(author)
-
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
- 2021
-
In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
-
Journal article (peer-reviewed)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.
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| 27. |
- Elfstrand, Malin, et al.
(author)
-
Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds
- 2020
-
In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29, s. 199-213
-
Journal article (peer-reviewed)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.
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| 28. |
- Floran, Valentina, et al.
(author)
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Organelle Genetic Diversity and Phylogeography of Scots Pine (Pinus sylvestris L.)
- 2011
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In: Notulae Botanicae Horti Agrobotanici Cluj-Napoca. - 0255-965X .- 1842-4309. ; 39, s. 317-322
-
Journal article (peer-reviewed)abstract
- The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to he analyzed in conjunction with evidence from pollen and fossil analysis.
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| 29. |
- Ganea, Laura Stefana, et al.
(author)
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Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)
- 2015
-
In: Journal of Forestry Research. - : Springer Science and Business Media LLC. - 1007-662X .- 1993-0607. ; 26, s. 361-368
-
Journal article (peer-reviewed)abstract
- Single sequence repeat (SSR) multiplexing is a semi high-throughput PCR methodology for the analysis of multiple SSRs. We developed two SSR multiplexes selected from SSR loci previously reported in the pine literature and tested the transferability of both SSR multiplexes in nine other pine species. We tested 234 nuclear SSR loci (nSSRs) previously described in the pine literature and selected ten nSSRs following the simple criteria of interpretability and reproducibility. Selected nuclear loci were divided into two nSSRs multiplex sets and their amplification was optimized for three different multiplex PCR methods based on: (a) a custom PCR protocol, (b) a custom protocol with hotstart taq polymerase, and (c) a commercially available kit for SSR multiplexing. To validate their performance, the level of genetic diversity was assessed in three Scots pine natural populations (Hungary, northern Sweden and southern Sweden). In addition, we also tested the transferability of these multiplexes in nine other pine species. We have developed two nSSRs multiplexes of five loci each that will contribute to reduce the costs of nSSR scoring, while increasing the capacity of nSSR loci analysis. Amplification was successful in all three populations (94 % success) and the level of polymorphism (7.1 alleles/marker) was similar to that previously reported for other Scots pine natural populations. Transferability of both multiplexes was successful for those pine species closely related to Scots pine.
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| 30. |
- García-Esquinas, Esther, et al.
(author)
-
Blood Selenium Concentrations Are Inversely Associated with the Risk of Undernutrition in Older Adults
- 2023
-
In: Nutrients. - 2072-6643. ; 15:22
-
Journal article (peer-reviewed)abstract
- Background: Selenium is an essential trace element with an antioxidant and anti-inflammatory capacity that has been associated in experimental studies with beneficial effects on appetite control, the regulation of the gut microbiota, and control of the anabolic–catabolic balance. The main aim of the present study was to evaluate the association between circulating selenium concentrations and the risk of developing undernutrition in older adults. Methods: This was a cohort study with 1398 well-nourished community-dwelling individuals aged ≥ 65 years residing in Spain in 2017, who were followed for a mean of 2.3 years. Whole blood selenium was measured at baseline using inductively coupled plasma-mass spectrometry. Undernutrition was assessed at baseline and at follow-up, and defined as having at least one of the three GLIM phenotypic criteria (involuntary weight loss, a low body mass index, and a reduced muscle mass) and at least one of the two etiologic criteria (reduced food consumption or nutrient assimilation and inflammation/disease burden). Results: During the follow-up, 142 participants (11%) developed moderate undernutrition and 113 (8.8%) severe undernutrition. The standardized relative risks of moderate and severe undernutrition at the 75th percentile of Se levels versus the 25th were 0.90 and 0.70, respectively. In dose–response analyses, the risk of severe undernutrition decreased linearly with increasing selenium concentrations. This association was independent of protein intake or diet quality and was stronger among participants with a diagnosis of a musculoskeletal disorder. Conclusions: The results suggest that an adequate dietary selenium status is needed to prevent undernutrition in older adults. Also, this may open the door for clinical trials with selenium supplementation, at doses considered as safe, to prevent undernutrition.
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| 31. |
- Garcia Gil, Rosario
(author)
-
Establishment of Regenerative Callus, Cell Suspension System, and Molecular Characterization of Taxus wallichiana Zucc. for the in vitro production of Taxol
- 2021
-
In: Journal of applied pharmaceutical science. - 2231-3354. ; 11, s. 22-34
-
Journal article (peer-reviewed)abstract
- Taxus wallichiana, an endangered Taxus species native to Nepal, is a source of Taxol (paclitaxel), an anticancer drug, which if produced via plant cell culture in vitro not only reduces the pressure on natural habitat but also allows continuous production throughout the seasons. Gamborg’s B5 medium was the culture medium to develop callus and suspension culture. Quantification of Taxol was carried out via high performance liquid chromatography (HPLC) using C18 column, water-acetonitrile mobile phase, and 1 ml/minute flowrate at 227 nm wavelength. Genetic variation among population was determined using the POPGEN32, version 1.31. Best callus response was in medium with 1 mg/l 2,4-D for both stem and needle explants. For cell suspension culture, callus from needle explants showed better response compared to stem. Fructose and sucrose proved to be the best carbon sources. Cell count increased as carbon concentration increased. 2,4-D at low concentration (< 2 mg/l) and naphthaleneacetic acid at high concentration (>5 mg/l) showed higher cell growth rate. Inoculum volume was directly proportional to cell count. Extra addition of macronutrients had inhibitory effect on cell count, but the effect was reversed for MgSO4. Using HPLC, for bark, the highest Taxol yield was 0.057 mg/g distilled water (DW), while for needle was 0.056 mg/g DW. For suspension cultured HPLC samples, Taxol yield ranged at 0.004%. Size range of amplified Deoxyribonucleic acids was between 200 and 2,000 bp. Thus, this investigation generated a concrete data for Taxus population of Nepal providing efficient protocols for establishment of callus and cell suspension culture with the aim of producing Taxol in in vitro conditions.
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| 32. |
- Garcia Gil, Rosario
(author)
-
Evaluation of antimicrobial, antioxidant and cytotoxic properties of bioactive compounds produced from endophytic fungi of Himalayan yew (Taxus wallichiana) in Nepal
- 2020
-
In: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 9
-
Journal article (peer-reviewed)abstract
- Background: Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study, Taxus wallichiana, which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties.Methods: The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts.Results: Out of 16 different Taxus trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera: Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella and Daldinia. The ethyl acetate extracts isolated from three endophytic fungi: Alternaria alternata, Cladosporium cladosporioides and Alternaria brassicae showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC50 concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of C. cladosporioides and A. brassicae also showed promising antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC50 of 104.2 and 125.9µg/ml, respectively.Conclusions: The crude fungal extracts obtained from endophytes: A. alternata, C. cladosporioides and A. brassicae upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.
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| 33. |
- Garcia Gil, Rosario, et al.
(author)
-
Genetic diversity and inbreeding in natural and managed populations of Scots pine
- 2015
-
In: Tree Genetics and Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 11
-
Journal article (peer-reviewed)abstract
- We carried out a study on Scots pine (Pinus sylvestris L.) in Sweden, where our objective was to quantify the genetic diversity and inbreeding associated with two widely used managed-regeneration practices, planting with improved material from seed orchards and seed-tree regeneration, and compare these with that found in unmanaged natural forests. A total of 196 evenly spaced trees were sampled from a naturally regenerated and two managed-regeneration stands (plantation and seed-tree), in each of three different regions in Sweden (Arjeplog, Vihelmina, and Hammerdal). Population parameters were estimated for microsatellite loci from the nuclear and chloroplast genomes (5 and 11 loci, respectively) and a single mitochondrial locus (nad7). Analysis of variance (ANOVA) shows no significant effects of stand management on the level of nuclear and mitochondrial genetic diversity or inbreeding (p<0.05). Duncan post-hoc analysis suggested significantly lower values for the chloroplast number of effective alleles (N-ea_CP) and total gene diversity (H-t_CP) for natural and plantation practices, as compared with seed-tree regeneration. The ANOVA supported a rather weak effect of the management factor (M) on N-ea_CP and H-t_CP, with p values of 0.08 and 0.07, respectively. Inbreeding coefficient (F-5) indicated a deviation from random mating in all stands caused by an excess of homozygotes. All the stands are composed of a mixture of half-and full-sibs, but no pattern of spatial relatedness was detected in any of them. Our data suggest that genetic diversity is similar in both natural stands and those with managed regeneration, probably because regeneration practices did not decrease the population size to a point where random drift effects might be important. The estimates for the nuclear and mitochondrial (mt) genomes should be regarded with caution, as only five nuclear microsatellite (nSSR) loci less affected by null alleles (<25 %) were analyzed. Our investigation indicates that the reduction to five nSSR loci does not change the main finding of an absence of differences in genetic diversity among stands, except for the number of rare alleles (RA), which is lower when estimated from data for eight nSSR loci.
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| 34. |
- Garcia Gil, Rosario, et al.
(author)
-
Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine
- 2009
-
In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 103, s. 90-96
-
Journal article (peer-reviewed)abstract
- We have investigated the fine-scale spatial genetic structure in a managed Scots pine forest. For this purpose, we perform a Bayesian genetic-cluster analysis of 96 geographically mapped individual seed trees of Swedish Scots pine based on 14 microsatellite loci. The analysis was carried out with the recently developed program GENECLUST (Francois et al., 2006), which provides the facility to jointly incorporate both spatial information from a geographical neighborhood structure through a Potts-Dirichlet model and account for variable degrees of inbreeding within the clusters. To evaluate whether inbreeding and spatial interaction should be included in the best-fitting statistical model for our data, we used the deviance information criterion (DIC), a weighted measure of model fit that accounts for an effective number of free parameters in a model. Analysis shows that a model with a single estimated cluster, with high levels of inbreeding (0.25) and with a moderate amount of spatial dependency within the unique cluster (Psi = 0.2-0.4), best explains the data. We also carried out Bayesian parentage analysis, which enabled us to exclude the possibility that the sample constitutes one single full-sib family. Heredity (2009) 103, 90-96; doi: 10.1038/hdy.2009.33; published online 22 April 2009
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| 35. |
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| 36. |
- Hallingbäck, Henrik, et al.
(author)
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Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits
- 2014
-
In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 4, s. 2365-2379
-
Journal article (peer-reviewed)abstract
- Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.
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| 37. |
- Hayatgheibi, Haleh, et al.
(author)
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Genetic control of transition from juvenile to mature wood with respect to microfibril angle in Norway spruce (Picea abies) and lodgepole pine (Pinus contorta)
- 2018
-
In: Canadian Journal of Forest Research. - : Canadian Science Publishing. - 0045-5067 .- 1208-6037. ; 48:11, s. 1358-1365
-
Journal article (peer-reviewed)abstract
- Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h2) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (∆G) obtained in direct selection of this trait were very high in both species.
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| 38. |
- Hayatgheibi, Haleh, et al.
(author)
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Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in Norway spruce
- 2024
-
In: BMC Genomic Data. - : BioMed Central Ltd. - 2730-6844. ; 25:1
-
Journal article (peer-reviewed)abstract
- Background: Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B). Results: Our results indicate that models incorporating population structure significantly reduce estimates of additive genetic variance, resulting in substantial reduction of narrow-sense heritability. However, these models considerably improve prediction accuracies. This was particularly significant for growth and solid-wood properties, which showed to have the highest population genetic differentiation (QST) among the studied traits. Additionally, although the pattern of correlations remained similar across the models, their magnitude was slightly lower for models that included population structure as a fixed effect. This suggests that selection, consistently performed within populations, might be less affected by unfavourable genetic correlations compared to mass selection conducted without pedigree restrictions. Conclusion: We conclude that the results of models properly accounting for population structure are more accurate and less biased compared to those neglecting this effect. This might have practical implications for breeders and forest managers where, decisions based on imprecise selections can pose a high risk to economic efficiency.
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| 39. |
- Lecoy, Jonathan, et al.
(author)
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Analysis of the ASR and LP3 homologous gene families reveal positive selection acting on LP3-3 gene
- 2023
-
In: Gene. - : Elsevier BV. - 0378-1119 .- 1879-0038. ; 850
-
Journal article (peer-reviewed)abstract
- Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.
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| 40. |
- Li, Lili, et al.
(author)
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Recent introductions, ancient recolonization events and local adaptation: a first fine-scale mapping of the population genetic structure of Norway spruce across Sweden
-
Other publication (other academic/artistic)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.
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| 41. |
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| 42. |
- Lundqvist, Sven- Olof, et al.
(author)
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Age and weather effects on between and within ring variations of number, width and coarseness of tracheids and radial growth of young Norway spruce
- 2018
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In: European Journal of Forest Research. - : Springer Science and Business Media LLC. - 1612-4669 .- 1612-4677. ; 137:5, s. 719-743
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Journal article (peer-reviewed)abstract
- Annual growth, fibre and wood properties of Norway spruce are all under strong influence from genetics, age and weather. They change dynamically, particularly at young ages. Most genetic research and tree improvement programs are based on data from this most dynamic phase of the life of trees, affected by differences in weather among sites and years. In the work presented, influences of age and weather were investigated and modelled at the detail of annual rings and at the sub-tree ring level of earlywood, transitionwood and latewood. The data used were analysed from increment cores sampled at age 21Â years from almost 6000 Norway spruce trees of known genetic origin, grown on two sites in southern Sweden. The traits under investigation were radial growth, cell widths, cell numbers, cell wall thickness and coarseness as a measure of biomass allocation at cell level. General additive mixed models (GAMMs) were fitted to model the influences of age, local temperature and precipitation. The best models were obtained for number of tracheids formed per year, ring width, average radial tracheid width in earlywood, and ring averages for tangential tracheid width and coarseness. Considering the many sources behind the huge variation, the explained part of the variability was high. For all traits, models were developed using both total tree age and cambial age (ring number) to express age. Comparisons indicate that the number of cell divisions and ring width are under stronger control of tree age, but the other traits under stronger control of cambial age. The models provide a basis to refine data prior to genetic evaluations by compensating for estimated differences between sites and years related to age and weather rather than genetics. Other expected applications are to predict performance of genotypes in relation to site or climate and simulation of climate change scenarios.
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| 43. |
- Nystedt, Björn, et al.
(author)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Journal article (peer-reviewed)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 44. |
- Ortiz Rios, Rodomiro Octavio, et al.
(author)
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Genomic Prediction for Inbred and Hybrid Polysomic Tetraploid Potato Offspring
- 2024
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In: Agriculture. - 2077-0472. ; 14
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Journal article (peer-reviewed)abstract
- Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti ). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1 ) and hybrid (F1 ) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63◦4903000 N 20◦1505000 E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56◦0104600 N 14◦0902400 E), respectively, along with their parents (S0 ) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0 . The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1 ) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.
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| 45. |
- Ortiz Rios, Rodomiro Octavio, et al.
(author)
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Inbreeding Effects on the Performance and Genomic Prediction for Polysomic Tetraploid Potato Offspring Grown at High Nordic Latitudes
- 2023
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In: Genes. - 2073-4425. ; 14
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Journal article (peer-reviewed)abstract
- Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S-1) and two hybrid (F-1) offspring and their parents (S-0) were used in the experiment, with a field layout of an augmented design with the four S-0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umea (63 & DEG;49 & PRIME;30 & DPRIME; N 20 & DEG;15 & PRIME;50 & DPRIME; E), Sweden. S-0 was significantly (p < 0.01) better than both S-1 and F-1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F-1 was significantly (p < 0.01) better than S-1 for all tuber weight and uniformity traits. Some F-1 hybrid offspring (15-19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from -0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F-1 full sib's GEBV accuracy was higher, on average, than that of S-1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.
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| 46. |
- Ranade, Sonali, et al.
(author)
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Adaptive strategies of Scots pine under shade: Increase in lignin synthesis and ecotypic variation in defense-related gene expression
- 2022
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In: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 174
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Journal article (peer-reviewed)abstract
- Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growing season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defense-related genes (growth-defense trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defense-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.
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| 47. |
- Ranade, Sonali, et al.
(author)
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Application of monochromatic blue light during germination and hypocotyl development improves outplanted Scots pine (Pinus sylvestris L.) trees performance
- 2016
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In: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 361, s. 368-374
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Journal article (peer-reviewed)abstract
- Light quality has been recognized as an important factor to enhance plant production and quality, and it is extensively used in horticulture. Conifer seedlings are also known to respond to light quality, which can serve as a mean to improve seedling quality during its nursery production. We conducted a novel study regarding the effect of three monochromatic (blue, red and far-red) and white light treatments during germination and hypocotyl development in Scots pine seedlings which had an impact on the quantitative morphological attributes of shoot, root, fibre dimensions, survival and lignin content, after long-term transplantation in natural conditions. Our approach is a proxy to the effect of nursery light treatments on seedling performance following its post-planting establishment in the forest. Our study conducted during three growing seasons, reveals that monochromatic blue light applied at nursery significantly improved the outplanted Scots pine trees quality. (C) 2015 Published by Elsevier B.V.
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| 48. |
- Ranade, Sonali, et al.
(author)
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Clinal variation in PHY (PAS domain) and CRY (CCT domain)-Signs of local adaptation to light quality in Norway spruce
- 2023
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In: Plant Cell & Environment. - 0140-7791 .- 1365-3040. ; 46, s. 2391-2400
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Journal article (peer-reviewed)abstract
- Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.
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| 49. |
- Ranade, Sonali, et al.
(author)
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Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera
- 2014
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14
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Journal article (peer-reviewed)abstract
- Background: Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). Results: Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. Conclusions: Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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| 50. |
- Ranade, Sonali, et al.
(author)
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Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)
- 2015
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In: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 16
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Journal article (peer-reviewed)abstract
- Background: Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (>= 20) and class II (>= 12 and < 20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species.Results: Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10(-9) and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005).Conclusions: Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species.
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