| 1. |
- Berlin Kolm, Sofia, et al.
(författare)
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QTL mapping of biomass and nitrogen economy traits in willows (Salix spp.) grown under contrasting water and nutrient conditions
- 2014
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Ingår i: Molecular Breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 34, s. 1987-2003
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Tidskriftsartikel (refereegranskat)abstract
- In order to efficiently grow Salix for biomass production in warmer climates, varieties with a desirable response to drought and nutrient-limiting conditions are needed. The main objective of this study was to investigate the genetic background of biomass production and nitrogen (N) economy in contrasting conditions of water and nutrient availability and to identify candidate genes with a putative function in the expression of the different traits. Quantitative trait loci (QTLs) analysis was conducted using data from 198 individuals of a back-cross population between S. viminalis and S. schwerinii grown in a greenhouse under three combinations of N and water supply. In total, 60 QTLs were identified for biomass and N economy traits in the different treatments. Most of the QTLs mapped to linkage groups II, III, VI, X, XIII and B. At linkage groups III, VI and X, QTLs for both N economy and biomass traits co-located. The phenotypic variation explained by each QTL varied from 7.7 to 41.9 % of the total variance. QTLs for N economy traits explained most of the variation. Gene ontology (GO) analyses, performed on QTL intervals for each trait and projected to the Populus trichocarpa genome, revealed that genomic intervals connected to 19 traits were enriched for at least one GO term. Candidate genes were selected among genes linked to the enriched GO terms. These results represent a first necessary step for additional mapping and functional studies and encourage the development of marker-assisted breeding of Salix varieties adapted to drier climates.
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| 2. |
- Chengjiang, Ruan
(författare)
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NMR metabolomics of berry quality in sea buckthorn (Hippophae L.)
- 2013
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Ingår i: Molecular Breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 31, s. 57-67
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Tidskriftsartikel (refereegranskat)abstract
- Sea buckthorn (Hippophae L.) is a woody perennial shrub or small tree whose berries are rich in bioactive compounds with powerful nutritional and medicinal properties. Untargeted H-1 nuclear magnetic resonance (NMR) spectroscopy and principal component analysis (PCA) were used to characterize the metabolic profile of berry quality. There was strong separation in the NMR signal intensity of bioactive compounds between pulp and seeds, such as amino acids [gamma-aminobutyric acid (GABA), aspartate, glutamate, theanine, and proline], organic acids (citrate, succinate, malate, acetate, quinate, and heriguard), and carbohydrates (sucrose, fructose, glucose, and melibiose). Sea buckthorn cultivars could be clearly separated into two groups using principal component analysis (PCA) based on NMR spectroscopy of bioactive compounds in the pulp and seeds. Several metabolic compounds such as sugar, organic acids, and amino acids could serve as biomarkers for prediction of berry quality and for classification of germplasm collections. This dataset provides potential information concerning the mechanisms of berry quality formation and contributes to increasing the breeding efficiency of sea buckthorn quality improvement.
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| 3. |
- Henz, A., et al.
(författare)
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Identification of major stable QTLs for flower color in roses
- 2015
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Ingår i: Molecular breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 35:10
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Tidskriftsartikel (refereegranskat)abstract
- Flower color is one of the most important traits of ornamental roses. Anthocyanins are the major secondary metabolites responsible for the red and pink colors found among rose cultivars. Color varies depending on the combination of particular anthocyanins, their co-factors and their concentrations. Several genetic investigations have indicated that variation in flower color is dependent on monogenic factors and quantitative trait loci (QTL). Here, we analyze quantitative variation of total anthocyanins in diploid rose progeny. We demonstrate that the environment produces relatively small effects; the main causes of variation in anthocyanin content are the genetic differences between individuals. Two major QTLs were detected in all six tested environments. Four additional QTLs were found only in a subset of the environments. Some of the QTLs either co-segregate or are located close to the map positions of known structural genes of the anthocyanin biosynthesis pathway or transcriptional regulators of anthocyanin biosynthesis. This information might be used to characterize tetraploid parental genotypes for their potential to pass on higher anthocyanin contents to their progeny.
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| 4. |
- Hu, Xian-Ge, et al.
(författare)
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Global transcriptome analysis of Sabina chinensis (Cupressaceae), a valuable reforestation conifer
- 2016
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Ingår i: Molecular breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 36:7
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Tidskriftsartikel (refereegranskat)abstract
- Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species' unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (similar to 9.0 bp) were obtained, and 116,814 unigenes (>= 200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.
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| 5. |
- Jahoor, Ahmed
(författare)
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Genome-wide association study of production and stability traits in barley cultivated under future climate scenarios
- 2015
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Ingår i: Molecular Breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 35
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Tidskriftsartikel (refereegranskat)abstract
- Future barley cultivars will have to produce under the constraints of higher temperature in combination with increased concentrations of atmospheric carbon dioxide and ozone as a consequence of climate change. A diverse set of 167 spring barley genotypes was cultivated under elevated levels of temperature (+5 degrees C) and [CO2] (700 ppm) as single factors and in combination as well as under elevated [O-3] (100-150 ppb) as single factor. The setting in general resembled changes projected by IPCC (AR5) to take place at the end of this century. A genome-wide association study (GWAS) was performed to identify markers for increased primary production under climate change conditions and reveal possible genes of interest. Phenotyped traits included grain yield, number of grains, number of ears per plant, above-ground vegetative biomass, harvest index and stability of the production parameters over the five applied treatments. The GWAS encompassed 7864 SNP markers (Illumina iselect), a compressed mixed linear model with the GAPIT package, and conservative validation of markers. A total of 60 marker-trait associations [-log(10)(P value) 2.97-5.58] were identified, e.g. grain yield under elevated temperature on barley chromosome 2H, static stability of grain yield on 7H, sites for exploitation of elevated [CO2] on 4H and 7H and associations under the two-factor treatment. Marker-trait associations identified from single-factor treatments were not retrieved, when elevated [CO2] and temperature were combined emphasizing the need for multifactor experiments. This GWA study identified markers and chromosome regions to be targeted in breeding for development of climate resilient cultivars.
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| 6. |
- Lerceteau, Estelle, et al.
(författare)
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AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris : a preliminary study
- 2000
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Ingår i: Molecular breeding. - : KLUWER ACADEMIC PUBL. - 1380-3743 .- 1572-9788. ; 6:5, s. 451-458
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Tidskriftsartikel (refereegranskat)abstract
- We have applied a two-way pseudo-testcross strategy in an analysis of Pinus sylvestris for genetic mapping and detection of quantitative trait loci (QTLs) associated with economically important traits targeted in the Swedish tree-breeding programme. Based on 94 full-sib progeny of a cross between two plus-trees from northern Sweden we generated two parental maps using AFLP markers. The female map was comprised of 94 markers assigned to 15 linkage groups giving a size of 796 cM. On the male map 155 markers were assigned to 15 linkage groups, giving a total size of 1335 cM. The recombination frequency was found to be sex-dependent, being 29.3% higher in male than in female gametes. On the female map, 12 QTLs were detected (but none for branch diameter or wood density). Three QTLs for tree height accounted for 25.8% of the total phenotypic variation of this trait. When the QTLs detected for all the traits were taken independently, the percentages of phenotypic variance ranged from 9.3% to 22.7%. The highest value was observed for frost hardiness, an important trait in northern Sweden for which a major gene seemed to be involved. A cluster of QTLs for tree height, trunk diameter and volume was located on one linkage group. On the male map, four QTLs for trunk diameter and volume were detected. Due to the reduced number of individuals under study, the results are preliminary and have to be validated on more trees.
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| 7. |
- Shamloo-Dashtpagerdia, Roohollah, et al.
(författare)
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LOS2 gene plays a potential role in barley (Hordeum vulgare L.) salinity tolerance as a hub gene
- 2019
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Ingår i: Molecular breeding. - : Springer. - 1380-3743 .- 1572-9788. ; 39:8
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how plants respond to salinity stress is essential for developing tolerant genotypes, to keep human food secure since it is threaten by climate changes and increasing population worldwide. Barley (Hordeum vulgare) is a crop that possesses various salinity tolerance mechanisms that remain to be explored. In this study, data from an RNA-Seq experiment in barley was analyzed to identify changes in genome activities as well as differentially expressed genes (DEGs) in response to salinity stress. A gene network was predicted among identified DEGs and was subjected to network topology analysis, which resulted in the prediction of a hub gene, namely low expression of osmotically responsive gene 2 (LOS2). LOS2 and its two hierarchical downstream genes, salt-tolerant zinc finger (ZAT10) and ascorbate peroxidase 1 (APX1), were used in a genome-wide association (GWA) survey to confirm their importance. A field experiment was conducted to recognize susceptible and tolerant genotypes among 10 different barley genotypes based on the principle component analysis (PCA) of stress-related indices. In a separate salinity experiment, two of the genotypes were assessed to assign their physiological and biochemical responses as well as to identify expression profiles of LOS2, ZAT10, and APX1. From the results, the activity of the barley genome was significantly altered toward response to stress. In total, 5692 DEGs were identified and the gene network derived from these genes contained 131 nodes and 257 edges. The identified genotypes clearly showed the difference in water status, osmolyte accumulation, cell membrane damages, and ion homeostasis as well as in expression profiles for studied genes during salinity stress. Our results suggest that LOS2 along with the ZAT10 and APX1 genes may serve as an important part of barley salinity stress tolerance pathways. To our knowledge, this is the first report on the role(s) of LOS2 in barley salinity stress tolerance in a gene network system.
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