| 1. |
- Chen, Zhi-Qiang, et al.
(författare)
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
- 2021
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.Results: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.Conclusion: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.
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| 2. |
- Du, Xinyu, et al.
(författare)
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Distribution, behavior, and risk assessment of chlorinated paraffins in paddy plants throughout whole growth cycle
- 2022
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 167
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Tidskriftsartikel (refereegranskat)abstract
- Paddy plants provide staple food for 3 billion people worldwide. This study explores the environmental fate and behavior of a high-volume production emerging contaminants chlorinated paraffins (CPs) in the paddy ecosystem. Very-short-, short-, medium-, and long-chain CPs (vSCCPs, SCCPs, MCCPs, and LCCPs, respectively) were analyzed in specific tissue of paddy plants at four main growth stages and soils from the Yangtze River Delta, China throughout a full rice growing season. The total CP concentrations in the paddy roots, stalks, leaves, panicles, hulls, rice, and soils ranged from 181 to 1.74 × 103, 21.7–383, 19.6–585, 108–332, 245–470, 59.6–130, and 99.6–400 ng/g dry weight, respectively. The distribution profile indicated the translocation of SCCPs and MCCPs from soils to paddy tissue, highlighting their elevated bioaccumulative potential. The evolution of CP level/mass/pattern during the whole growth cycle suggested atmospheric CPs deposition on leaves and hulls, as well as stalk-rice transfer. CSOIL plant uptake model well predicted the level, distribution pattern, and bioconcentration factors (BCFs) of SCCPs and MCCPs in paddy shoot and recognized the soil-air-shoot pathway as the major contributor. Moreover, risk evaluation indicated that MCCPs intake and subsequent risks dominated the total exposure to CPs via rice ingestion. This is the first report on the occurrence, fate and risk assessment of all CPs classes in paddy ecosystems, and the results underline the potential health effects caused by the in-use MCCPs via rice ingestion.
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| 3. |
- Drager, Luciano F., et al.
(författare)
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Intermittent hypoxia inhibits clearance of triglyceride-rich lipoproteins and inactivates adipose lipoprotein lipase in a mouse model of sleep apnoea
- 2012
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Ingår i: European Heart Journal. - Oxford : Oxford University Press. - 0195-668X .- 1522-9645. ; 33:6, s. 783-U33
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Tidskriftsartikel (refereegranskat)abstract
- Delayed lipoprotein clearance is associated with atherosclerosis. This study examined whether chronic intermittent hypoxia (CIH), a hallmark of obstructive sleep apnoea (OSA), can lead to hyperlipidaemia by inhibiting clearance of triglyceride rich lipoproteins (TRLP). Male C57BL/6J mice on high-cholesterol diet were exposed to 4 weeks of CIH or chronic intermittent air (control). FIO2 was decreased to 6.5 once per minute during the 12 h light phase in the CIH group. After the exposure, we measured fasting lipid profile. TRLP clearance was assessed by oral gavage of retinyl palmitate followed by serum retinyl esters (REs) measurements at 0, 1, 2, 4, 10, and 24 h. Activity of lipoprotein lipase (LpL), a key enzyme of lipoprotein clearance, and levels of angiopoietin-like protein 4 (Angptl4), a potent inhibitor of the LpL activity, were determined in the epididymal fat pads, skeletal muscles, and heart. Chronic intermittent hypoxia induced significant increases in levels of total cholesterol and triglycerides, which occurred in TRLP and LDL fractions (P 0.05 for each comparison). Compared with control mice, animals exposed to CIH showed increases in REs throughout first 10 h after oral gavage of retinyl palmitate (P 0.05), indicating that CIH inhibited TRLP clearance. CIH induced a 5-fold decrease in LpL activity (P 0.01) and an 80 increase in Angptl4 mRNA and protein levels in the epididymal fat, but not in the skeletal muscle or heart. CIH decreases TRLP clearance and inhibits LpL activity in adipose tissue, which may contribute to atherogenesis observed in OSA.
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| 4. |
- 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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| 5. |
- Liu, Jun, et al.
(författare)
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Application potential analysis of biochar as a carbon capture material in cementitious composites: A review
- 2022
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Ingår i: Construction and Building Materials. - : Elsevier BV. - 0950-0618. ; 350
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Forskningsöversikt (refereegranskat)abstract
- In recent years, emissions of carbon dioxide in the atmosphere have been increasing, leading to increasingly severe global warming. In the construction industry, the increase in cement production is one of the main sources of CO2 emissions. Cementitious composites can sequester CO2 in calcium carbonate precipitates through carbonation reactions, but their carbon sequestration efficiency is very low due to the slow diffusion rate of CO2 in the cement matrix. To reduce the net CO2 emissions during concrete production, a feasible option is to enhance its carbon capture performance through accelerated carbonation curing (ACC) and CO2 capture and storage (CCS) technologies. Biochar has a strong adsorption capacity for CO2, its production process is green and low-carbon, and its production cost is low, which has high economic benefits. Many studies have applied biochar as cementitious composites in the construction industry to improve the mechanical properties, durability and functionality of cementitious composites. Additionally, biochar is a potential carbon capture material that can effectively improve the carbon sequestration performance of cementitious composites. In this review, the latest research progress of biochar in cementitious composites in recent years is reviewed, and the mechanical properties, durability and carbon sequestration performance of biochar-cementitious composites were analyzed. Additionally, the mechanism of the synergistic effect of biochar and the carbonization reaction in concrete and the effect on the carbon capture ability of cementitious composites were also investigated.
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| 6. |
- Niimi, Jun, et al.
(författare)
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Wine consumers' subjective responses to wine mouthfeel and understanding of wine body
- 2017
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Ingår i: Food Research International. - : Elsevier Ltd. - 0963-9969 .- 1873-7145. ; 99, s. 115-122
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Tidskriftsartikel (refereegranskat)abstract
- Wine mouthfeel is considered important for wine quality by experts, while consumers understanding of mouthfeel and the role of wine body in their wine choice is unknown. One experiment determined the influence of intrinsic wine mouthfeel on consumers' wine liking and emotions, and the other, how consumers understand the term wine body. The first experiment used a 2 astringency level × 2 body level experimental design. The samples were base wine with; nothing added (control), added xanthan gum (for increased body), added grape seed extract (GSE, for increased astringency), and with both added xanthan gum and GSE. The consumer taste trial (n = 112) indicated that wine with increased body did not influence wine liking and emotions; while increased astringency decreased liking and elicited more intense negative emotions. The second experiment examined consumers' knowledge of wine body through an online survey (n = 136). Consumers described wine body most frequently using words such as flavour, fullness, and strength. Wine body was therefore understood by consumers predominantly as a holistic multi-sensory perception of flavour. Wine flavour was indicated by consumers to be the most important factor driving purchase decisions followed by balance of flavours and wine body. It is crucial that wine professionals carefully communicate wine characteristics to consumers to prevent possible misunderstandings such as the meaning of wine body and as a result better meet consumer expectations. In future, the term body may benefit from a clearer definition for academic research as well as industry.
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| 7. |
- Pang, Jun-Feng, et al.
(författare)
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mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves.
- 2009
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 1537-1719 .- 0737-4038. ; 26:12, s. 2849-64
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Tidskriftsartikel (refereegranskat)abstract
- There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analyzed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence that the dog has a single origin in time and space and an estimation of the time of origin, number of founders, and approximate region, which also gives potential clues about the human culture involved. The analyses showed that dogs universally share a common homogenous gene pool containing 10 major haplogroups. However, the full range of genetic diversity, all 10 haplogroups, was found only in southeastern Asia south of Yangtze River, and diversity decreased following a gradient across Eurasia, through seven haplogroups in Central China and five in North China and Southwest (SW)Asia, down to only four haplogroups in Europe. The mean sequence distance to ancestral haplotypes indicates an origin 5,400-16,300 years ago (ya) from at least 51 female wolf founders. These results indicate that the domestic dog originated in southern China less than 16,300 ya, from several hundred wolves. The place and time coincide approximately with the origin of rice agriculture, suggesting that the dogs may have originated among sedentary hunter-gatherers or early farmers, and the numerous founders indicate that wolf taming was an important culture trait.
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