| 1. |
- 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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| 2. |
- 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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| 3. |
- Zhou, Fang, et al.
(författare)
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A New Red-Emitting Fluorescence Probe for Rapid and Effective Visualization of Bisulfite in Food Samples and Live Animals
- 2019
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Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 67:15, s. 4375-4383
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Tidskriftsartikel (refereegranskat)abstract
- The development of new methods for rapid and effective detection of bisulfite (HSO3-) in food samples and imaging of HSO3- intake in animals is of significant importance due to the key roles of HSO3- in food quality assurance and community health. In this work, a new responsive fluorescence probe, EQC, is reported for the quantitative detection of HSO3- in food samples and visualization of HSO3- intake in animals. Upon addition of HSO3-, the UV-vis absorption and red emission of EQC were significantly decreased within 120 s. The changes in absorption and emission spectra of EQC were rationalized by theoretical computations. The proposed reaction mechanism of EQC with HSO3- was confirmed by high-resolution mass spectrometry (HRMS) and spectroscopic titration measurements. EQC has the advantages of high sensitivity, selectivity (a detection limit of 18.1 nM), and fast response toward HSO3-, which enable rapid and effective HSO3- detection in buffer solution. The practical applications of EQC were demonstrated by the detection of HSO3- in food samples and the imaging of HSO3- intake in live animals.
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| 4. |
- Du, Qian, et al.
(författare)
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Porcine circovirus type 2 infection promotes the SUMOylation of nucleophosmin-1 to facilitate the viral circular single-stranded DNA replication
- 2024
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 20:2
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism of genome DNA replication in circular single-stranded DNA viruses is currently a mystery, except for the fact that it undergoes rolling-circle replication. Herein, we identified SUMOylated porcine nucleophosmin-1 (pNPM1), which is previously reported to be an interacting protein of the viral capsid protein, as a key regulator that promotes the genome DNA replication of porcine single-stranded DNA circovirus. Upon porcine circovirus type 2 (PCV2) infection, SUMO2/3 were recruited and conjugated with the K263 site of pNPM1's C-terminal domain to SUMOylate pNPM1, subsequently, the SUMOylated pNPM1 were translocated in nucleoli to promote the replication of PCV2 genome DNA. The mutation of the K263 site reduced the SUMOylation levels of pNPM1 and the nucleolar localization of pNPM1, resulting in a decrease in the level of PCV2 DNA replication. Meanwhile, the mutation of the K263 site prevented the interaction of pNPM1 with PCV2 DNA, but not the interaction of pNPM1 with PCV2 Cap. Mechanistically, PCV2 infection increased the expression levels of Ubc9, the only E2 enzyme involved in SUMOylation, through the Cap-mediated activation of ERK signaling. The upregulation of Ubc9 promoted the interaction between pNPM1 and TRIM24, a potential E3 ligase for SUMOylation, thereby facilitating the SUMOylation of pNPM1. The inhibition of ERK activation could significantly reduce the SUMOylation levels and the nucleolar localization of pNPM1, as well as the PCV2 DNA replication levels. These results provide new insights into the mechanism of circular single-stranded DNA virus replication and highlight NPM1 as a potential target for inhibiting PCV2 replication. Different types of DNA viruses employ different mechanisms to replicate their genome DNA. Porcine circovirus type 2 (PCV2) is the most representative circular single-stranded DNA virus that harms the pig industry all over the world. In this study, we found that the PCV2 Cap interacting protein pNPM1 also interacts with PCV2 DNA in a SUMOylated form to promote PCV2 DNA replication. The SUMOylation of pNPM1 at the conserved K263 site is critical for the interaction of pNPM1 with PCV2 DNA and the replication of PCV2 DNA. Furthermore, we found that PCV2 infection promotes the SUMO2/3 mediated SUMOylation of pNPM1, while does not significantly alter the expression level of pNPM1. PCV2 Cap is the major component that promotes pNPM1 SUMOylation by activating ERK/Ubc9/TRIM24 signalings. These results contribute to a better understanding of the replication mechanism of circular single-stranded DNA viruses, particularly PCV2.
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| 5. |
- Hussain, Muhammad Mahroz, et al.
(författare)
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Arsenic biogeochemical cycling in paddy soil-rice system : Interaction with various factors, amendments and mineral nutrients
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 773
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Tidskriftsartikel (refereegranskat)abstract
- Arsenic (As) contamination is a well-recognized environmental and health issue, threatening over 200 million people worldwide with the prime cases in South and Southeast Asian and Latin American countries. Rice is mostly cultivated under flooded paddy soil conditions, where As speciation and accumulation by rice plants is controlled by various geo-environmental (biotic and abiotic) factors. In contrast to other food crops, As uptake in rice has been found to be substantially higher due to the prevalence of highly mobile and toxic As species, arsenile (As(Ill)), under paddy soil conditions. In this review, we discussed the biogeochemical cycling of As in paddy soil-rice system, described the influence of critical factors such as pH, iron oxides, organic matter, microbial species, and pathways affecting As transformation and accumulation by rice. Moreover, we elucidated As interaction with organic and inorganic amendments and mineral nutrients. The review also elaborates on As (im) mobilization processes and As uptake by rice under the influence of different mineral nutrients and amendments in paddy soil conditions, as well as their role in mitigating As transfer to rice grain. This review article provides critical information on As contamination in paddy soil-rice system, which is important to develop suitable strategies and mitigation programs for limiting As exposure via rice crop, and meet the UN's key Sustainable Development Goals (SDGs: 2 (zero hunger), 3 (good health and well-being), 12 (responsible consumption and production), and 13 (climate action)).
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| 6. |
- Xie, Wenjing, et al.
(författare)
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Unexpected Dioxin Formation During Digestion of Soil with Oxidizing Acids
- 2023
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Ingår i: Environmental Science and Technology. - : AMER CHEMICAL SOC. - 0013-936X .- 1520-5851. ; 57:39, s. 14717-14725
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Tidskriftsartikel (refereegranskat)abstract
- Dioxins, such as polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs), are among the most toxic unintentionally produced persistent organic pollutants, and their emission is of great concern. Herein, we discovered abundant dioxin formation in soil and various organic carbon-containing matrices after digestion with aqua regia. Sigma 17PCDD/Fs concentrations were in the range of 66.6-142,834 pg/g dw (5.6-17,021 pg WHO2005-TEQ/g dw) in 19 soil samples after digestion with aqua regia for 6 h. Sigma 17PCDD/Fs concentration was significantly and positively correlated with soil organic carbon content (R-2 = 0.89; p < 0.01). Compared with cellulose and lignin, humic acid served as an important organic matter component that was converted to PCDD/Fs during soil digestion. Strong oxidation and production of reactive chlorine by aqua regia may be the key factors in the formation of PCDD/Fs. The yearly emission of PCDD/Fs due to digestion with strong acids by the inspection and testing industry was estimated to be 83.8 g TEQ in China in 2021 based on the highest level, which was similar to 0.9% of the total dioxin inventory in China. Great attention should be paid to unexpected dioxin formation during digestion processes considering the potential risk of release from laboratories and enterprises.
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