| 1. |
- Mascher, Martin, et al.
(författare)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Tidskriftsartikel (refereegranskat)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 2. |
- Li, Cheng, et al.
(författare)
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Ridge planting with transparent plastic mulching improves maize productivity by regulating the distribution and utilization of soil water, heat, and canopy radiation in arid irrigation area
- 2023
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Ingår i: Agricultural Water Management. - : Elsevier BV. - 0378-3774. ; 280
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Tidskriftsartikel (refereegranskat)abstract
- Ridge-furrow mulching system is widely used for improving soil hydrothermal conditions and crop productivity in semiarid and arid rainfed areas. The response of crop productivity to resource capture and utilization is crucial for agricultural field management and sustainable development. However, few have simultaneously investigated the coupling effect of plastic film mulching (PM) types and planting patterns on root and shoot growth, photosynthesis, yield, resource capture and utilization as well as their potential links in the same experiment, especially in arid irrigation areas, limiting our understanding of PM and ridge planting application. This study conducted a two-year field experiment with four treatments: 1) flat planting with transparent plastic film mulch (FT); 2) flat planting with black plastic film mulch (FB); 3) ridge–furrow planting with transparent plastic film mulch (RT); 4) ridge–furrow planting with black plastic film mulch (RB). The results showed that RT significantly increased soil water storage and root growth at the silking and grain-filling stages in both years by enhancing soil thermal time with 151.9–176.2 °C d and the intercepted photosynthetic active radiation with 22.2–57.4 MJ m–2. In addition, RT had a significantly higher net photosynthetic rate than FT and FB at the 12-leaf and silking stages, enhancing the transportation of stem and leaf to grain. The logistic equation using growing degree days as the independent variable characterized the dynamic features of maize growth under different PM types (transparent or black) coupled with ridge–furrow planting. RT accelerated dry matter accumulation by enhancing the maximum growth rate and extending the rapid growth period, resulting in 12.9–15.2 % more dry matter accumulation and 10.0–16.7 % higher grain yields than FB. Furthermore, RT significantly increased resource use efficiencies by 10.1–17.3 % for water, 3.0–5.5 % for thermal, and 4.0–9.1 % for radiation compared with FB. Ridge planting had the highest contributor rates, with >40 % for yield and resource capture. This study suggests that RT maintains high maize productivity and resource use efficiencies in arid irrigation areas with limited water resources by regulating soil water, heat, and canopy radiation distribution and utilization.
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| 3. |
- Li, Yunyun, et al.
(författare)
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Understanding Enhanced Microbial MeHg Production in Mining-Contaminated Paddy Soils under Sulfate Amendment : Changes in Hg Mobility or Microbial Methylators?
- 2019
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 53:4, s. 1844-1852
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Tidskriftsartikel (refereegranskat)abstract
- Elevated methylmercury (MeHg) production in mining-contaminated paddy soils, despite the high fraction of refractory HgS(s), has been frequently reported, while the underlying mechanisms are not fully understood. Here, we hypothesized that sulfate input, via fertilization, rainfall, and irrigation, is critical in mobilizing refractory HgS(s) and thus enhancing Hg methylation in mining-contaminated paddy soils. To test this hypothesis, the effects of sulfate amendment on Hg methylation and MeHg bioaccumulation in mining-contaminated soil-rice systems were examined. The results indicated 28-61% higher net MeHg production in soils under sulfate amendment (50-1000 mg kg-1), which in turn increased grain MeHg levels by 22-55%. The enhancement of Hg methylation by Hg mobilization in sulfate-amended soils was supported by two observations: (1) the increased Hg(aq) release from HgS(s), the dominant Hg species in the paddy soils, in the presence of sulfide produced following sulfate reduction and (2) the decreases of refractory HgS(s) in soils under sulfate amendment. By contrast, changes in the abundances/activities of potential microbial Hg methylators in different Hg-contaminated soils were not significant following sulfate amendment. Our results highlight the importance to consider enhanced Hg mobility and thus methylation in soils under sulfate amendment.
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| 4. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 5. |
- Yang, Danni, et al.
(författare)
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Drip irrigation improves spring wheat water productivity by reducing leaf area while increasing yield
- 2023
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Ingår i: European Journal of Agronomy. - : Elsevier BV. - 1161-0301. ; 143
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Tidskriftsartikel (refereegranskat)abstract
- To mitigate the climate change-induced water shortage and realize the sustainable development of agriculture, drip irrigation, a more efficient water-saving irrigation method, has been intensively implemented in most arid agricultural regions in the world. However, compared to traditional border irrigation, how drip irrigation affects the biophysical conditions in the cropland and how crops physiologically respond to changes in biophysical conditions in terms of water, heat and carbon exchange remain largely unknown. In view of the above situation, to reveal the mechanism of drip irrigation in improving spring wheat water productivity, paired field experiments based on drip irrigation and border irrigation were conducted to extensively monitor water and heat fluxes at a typical spring wheat field (Triticum aestivum L.) in Northwest China during 2017–2020. The results showed that drip irrigation improved yield by 10.3 % and crop water productivity (i.e., yield-to-evapotranspiration-ratio) by 15.6 %, but reduced LAI by 16.9 % in contrast with border irrigation. Under drip irrigation, the lateral development of spring wheat roots was promoted by higher soil temperature combined with frequent dry-wet alternation in the shallow soil layer (0–20 cm), which was the basis for efficient absorption of water and fertilizer, as well as efficient formation of photosynthate. Meanwhile, drip irrigation increased net radiation and decreased latent heat flux by inhibiting leaf growth, thereby increased sensible heat, causing a higher soil temperature (+1.10 ℃) and canopy temperature (+1.11 ℃). Further analysis proved that soil temperature was the key factor affecting yield formation. Based on the above conditions, the decrease in leaf distribution coefficient (−0.030) led to the decrease in evapotranspiration (−5.7 %) and the increase in ear distribution coefficient (+0.029). Therefore, drip irrigation emphasized the role of soil moisture in the soil-plant-atmosphere continuum, enhanced crop activity by increasing field temperature, especially soil temperature, and finally improved yield and water productivity via carbon reallocation. The study revealed the mechanism of drip irrigation for improving spring wheat yield, and would contribute to improving Earth system models in representing agricultural cropland ecosystems with drip irrigation and predicting the subsequent biophysical and biogeochemical feedbacks to climate change.
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| 6. |
- Li, Faji, et al.
(författare)
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Genetic architecture of grain yield in bread wheat based on genome-wide association studies
- 2019
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Ingår i: BMC Plant Biology. - : BioMed Central. - 1471-2229. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIdentification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits.ResultsA total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90K and 660K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4-725.8Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS.ConclusionsThe loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY.
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| 7. |
- Qin, Ning, 1990, et al.
(författare)
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Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast
- 2023
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 186:4, s. 748-763.e15
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Tidskriftsartikel (refereegranskat)abstract
- Although many prokaryotes have glycolysis alternatives, it's considered as the only energy-generating glucose catabolic pathway in eukaryotes. Here, we managed to create a hybrid-glycolysis yeast. Subsequently, we identified an inositol pyrophosphatase encoded by OCA5 that could regulate glycolysis and respiration by adjusting 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7) levels. 5-InsP7 levels could regulate the expression of genes involved in glycolysis and respiration, representing a global mechanism that could sense ATP levels and regulate central carbon metabolism. The hybrid-glycolysis yeast did not produce ethanol during growth under excess glucose and could produce 2.68 g/L free fatty acids, which is the highest reported production in shake flask of Saccharomyces cerevisiae. This study demonstrated the significance of hybrid-glycolysis yeast and determined Oca5 as an inositol pyrophosphatase controlling the balance between glycolysis and respiration, which may shed light on the role of inositol pyrophosphates in regulating eukaryotic metabolism.
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| 8. |
- Zhang, Shengrui, et al.
(författare)
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Characteristic pollen source area and vertical pollen dispersal and deposition in a mixed coniferous and deciduous broad-leaved woodland in the Changbai mountains, northeast China.
- 2016
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Ingår i: Vegetation History and Archaeobotany. - : Springer Science and Business Media LLC. - 0939-6314 .- 1617-6278. ; 25:1, s. 29-43
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Tidskriftsartikel (refereegranskat)abstract
- Pollen influx (number of pollen grains cm−2 year−1) can objectively reflect the dispersal and deposition features of pollen within a certain time and space, and is often used as a basis for the quantitative reconstruction of palaeovegetation; however, little is known about the features and mechanisms of vertical dispersal of pollen. Here we present the results from a 5 year (2006–2010) monitoring program using pollen traps placed at different heights from ground level up to 60 m and surface soil samples in a mixed coniferous and deciduous broad-leaved woodland in the Changbai mountains, northeastern China. The pollen percentages and pollen influx from the traps have very similar characteristics to the highest values for Betula,Fraxinus, Quercus and Pinus, among the tree taxa and Artemisia, Chenopodiaceae and Asteraceae among the herb taxa. Pollen influx values vary significantly with height and show major differences between three distinct layers, above-canopy (≥32 m), within the trunk layer (8 ≤ 32 m) and on the ground (0 m). These differences in pollen influx are explained by differences in (i) the air flows in each of these layers and (ii) the fall speed of pollen of the various taxa. We found that the pollen recorded on the ground surface is a good representation of the major part of the pollen transported in the trunk space of the woodland. Comparison of the pollen influx values with the theoretical, calculated “characteristic pollen source area” (CPSA) of 12 selected taxa indicates that the pollen deposited on the ground surface of the woodland is a fair representation with 85–90 % of the total pollen deposited at a wind speed of 2.4 m s−1 coming from within ca. 1–5 km for Pinus and Quercus, ca. 5–10 km for Ulmus, Tilia, Oleaceae and Betula, ca. 20–40 km for Fraxinus, Poaceae, Chenopodiaceae, Populus andSalix, and ca. 30–60 km for Artemisia; it is also a good representation with 90–98 % of the total pollen deposited coming from within 60 km at a wind speed of 2.4 m s−1, or 100 km at a wind speed: 6 m s−1, for the 12 selected taxa used in the CPSA calculation. Furthermore, comparison with the vegetation map of the area around the sampling site shows that the pollen deposited on the ground represents all plant communities which grow in the study area within 70 km radius of the sampling site. In this study, the pollen percentages obtained from the soil surface samples are significantly biased towards pollen taxa with good preservation due to thick and robust pollen walls. Therefore, if mosses are available instead, soil samples should be avoided for pollen studies, in particular for the study of pollen-vegetation relationships, the estimation of pollen productivities and quantitative reconstruction of past vegetation. The results also indicate that the existing model of pollen dispersal and deposition, Prentice’s model, provides a fair description of the actual pollen dispersal and deposition in this kind of woodland, which suggests that the application of the landscape reconstruction algorithm would be relevant for reconstruction of this type of woodland in the past.
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| 9. |
- Ishfaq, Muhammad, et al.
(författare)
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Improvement of nutritional quality of food crops with fertilizer : a global meta-analysis
- 2023
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Ingår i: Agronomy for Sustainable Development. - : Springer Nature. - 1774-0746 .- 1773-0155. ; 43:6
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Tidskriftsartikel (refereegranskat)abstract
- Providing the world’s population with sufficient and nutritious food through sustainable food systems is a major challenge of the twenty-first century. Fertilizer use is a major driver of crop yield, but a comprehensive synthesis of the effect of fertilizer on the nutritional quality of food crops is lacking. Here we performed a comprehensive global meta-analysis using 7859 data pairs from 551 field experiment-based articles published between 1972 and 2022, assessing the contribution of fertilization with a wide set of plant nutrients to the nutritional quality of food crops (i.e., fruits, vegetables, cereals, pulses/oil crops, and sugar crops). On average, fertilizer application improved crop yield by 30.9% (CI: 28.2–33.7%) and nutritional quality (referring to all nutritionally relevant components assessed; carbohydrates, proteins, oil, vitamin C, representative mineral nutrients, and total soluble solids) by 11.9% (CI: 10.7–12.1%). The improvements were largely nutrient- and crop species dependent, with vegetables being the most responsive. Potassium, magnesium, and micronutrients played important roles in promoting crop nutritional quality, whereas the combined application of inorganic and organic source(s) had the greatest impact on quality. Desirable climatic conditions and soil properties (i.e., silt loam, soil organic matter 2.5–5.0%, and pH 4.5–8.5) supported further enhancements. Considering cross-continent responsiveness, the increase in the nutritional quality of food crops with fertilizer application was greatest in Africa. In a nutshell, our findings pave the way towards a quantitative understanding of nutrient management programs and responsible plant nutrition solutions that foster the sustainable production of nutritious and healthy food crops for human consumption.
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| 10. |
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