| 1. |
- Wang, Shi Zhi, et al.
(författare)
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Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds
- 2024
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 41:7
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Tidskriftsartikel (refereegranskat)abstract
- The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3′UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
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| 2. |
- Sun, Jia, et al.
(författare)
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Leaf pigment retrieval using the PROSAIL model : Influence of uncertainty in prior canopy-structure information
- 2022
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Ingår i: Crop Journal. - : Elsevier BV. - 2095-5421 .- 2214-5141. ; 10:5, s. 1251-1263
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Tidskriftsartikel (refereegranskat)abstract
- Leaf pigments are critical indicators of plant photosynthesis, stress, and physiological conditions. Inversion of radiative transfer models (RTMs) is a promising method for robustly retrieving leaf biochemical traits from canopy observations, and adding prior information has been effective in alleviating the “ill-posed” problem, a major challenge in model inversion. Canopy structure parameters, such as leaf area index (LAI) and average leaf inclination angle (ALA), can serve as prior information for leaf pigment retrieval. Using canopy spectra simulated from the PROSAIL model, we estimated the effects of uncertainty in LAI and ALA used as prior information for lookup table-based inversions of leaf chlorophyll (Cab) and carotenoid (Car). The retrieval accuracies of the two pigments were increased by use of the priors of LAI (RMSE of Cab from 7.67 to 6.32 μg cm−2, Car from 2.41 to 2.28 μg cm−2) and ALA (RMSE of Cab from 7.67 to 5.72 μg cm−2, Car from 2.41 to 2.23 μg cm−2). However, this improvement deteriorated with an increase of additive and multiplicative uncertainties, and when 40% and 20% noise was added to LAI and ALA respectively, these priors ceased to increase retrieval accuracy. Validation using an experimental winter wheat dataset also showed that compared with Car, the estimation accuracy of Cab increased more or deteriorated less with uncertainty in prior canopy structure. This study demonstrates possible limitations of using prior information in RTM inversions for retrieval of leaf biochemistry, when large uncertainties are present.
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| 3. |
- Shi, Tian-Le, et al.
(författare)
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Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
- 2024
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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| 4. |
- Wang, Juan, et al.
(författare)
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Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut
- 2024
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Ingår i: Plants. - 2223-7747. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- The cultivated peanut (Arachis hypogaea L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide association study (GWAS) for nine fatty acid traits using the whole genome sequences of 160 representative Chinese peanut landraces and identified 6-1195 significant SNPs for different fatty acid contents. Particularly for oleic acid and linoleic acid, two peak SNP clusters on Arahy.09 and Arahy.19 were found to contain the majority of the significant SNPs associated with these two fatty acids. Additionally, a significant proportion of the candidate genes identified on Arahy.09 overlap with those identified in early studies, among which three candidate genes are of special interest. One possesses a significant missense SNP and encodes a known candidate gene FAD2A. The second gene is the gene closest to the most significant SNP for linoleic acid. It codes for an MYB protein that has been demonstrated to impact fatty acid biosynthesis in Arabidopsis. The third gene harbors a missense SNP and encodes a JmjC domain-containing protein. The significant phenotypic difference in the oleic acid/linoleic acid between the genotypes at the first and third candidate genes was further confirmed with PARMS analysis. In addition, we have also identified different candidate genes (i.e., Arahy.ZV39IJ, Arahy.F9E3EA, Arahy.X9ZZC1, and Arahy.Z0ELT9) for the remaining fatty acids. Our findings can help us gain a better understanding of the genetic foundation of peanut fatty acid contents and may hold great potential for enhancing peanut quality in the future.
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| 5. |
- Xie, Z., et al.
(författare)
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Physiological responses to salinity change and diel-cycling hypoxia in gills of Hong Kong oyster Crassostrea hongkongensis
- 2023
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486. ; 570
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Tidskriftsartikel (refereegranskat)abstract
- Global climate change is a frequent cause of salinity fluctuation in seawater, especially in aquaculture sites. Moreover, anthropologic activities often cause seawater eutrophication with the consequence that hypoxia ap-pears often during nighttime. The Hong Kong oyster Crassostrea hongkongensis, as a species that inhabits estuarine and coastal waters, is faced with such challenges. In this study, oyster physiological changes were considered to be closely related to hypoxia and salinity changes. Physiological indices were examined in Hong Kong oysters by employing six treatments to shed light into the effects of diel-cycling hypoxia (periodical hypoxia) and salinity change. Three salinities (10%o, low salinity; 25%o, normal salinity; and 35%o, high salinity) and two types of dissolved oxygen (normoxia, 6 mg/L throughout the day) and periodical hypoxic condition (6 mg/L at daytime for 12 h and 2 mg/L at nighttime for 12 h) were set. After 14-and 28-day exposures, gill tissues were sampled to detect changes in gill ATP production, mitochondrial membrane potential (MMP), mitochondrial reactive oxygen species production (ROS), and gill respiratory metabolic enzymes. Results indicated that periodical hypoxia and salinity change led to increased hexokinase (HK) and pyruvate kinase (PK) (p < 0.05). By contrast, they had no significant effect on mitochondrial number (MN). Adenosine-triphosphate (ATP) production only increased in the early exposure. In addition, low salinity with periodical hypoxia resulted in decreased MMP, lactate dehy-drogenase (LDH), and succinate dehydrogenase (SDH, p < 0.05). On the contrary, periodical hypoxia with high salinity led to increases in ATP and ROS and decreases in SDH, MMP, and LDH (p < 0.05). These results revealed that when diel-cycling hypoxia occurs with salinity change, the gill metabolism of Hong Kong oysters are gradually dominated by glycolysis while aerobic respiration decreases. Moreover, gill functions could be affected although energy accumulation exists during early exposure. Therefore, long-term exposure to periodical hypoxia with salinity change poses risk to the health and growth of Hong Kong oysters, impairing oyster aquaculture and coastal ecosystem health.
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| 6. |
- Zhang, Tongyu, et al.
(författare)
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Genome-wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep
- 2019
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Ingår i: Journal of Animal Breeding and Genetics. - : WILEY. - 0931-2668 .- 1439-0388. ; 136:5, s. 362-370
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Tidskriftsartikel (refereegranskat)abstract
- Fat-tailed sheep have a unique characteristic of depositing fat in their tails. In the present study, we conducted genome-wide association studies (GWAS) on traits related to tail fat deposition and body size in the Hulun Buir sheep. A total number of 300 individuals belonging to two fat-tailed lines of the Hulun Buir sheep breed genotyped with the Ovine Infinium HD SNP BeadChip were included in the current study. Two mixed models, one for continuous and one for binary phenotypic traits, were employed to analyse ten traits, that is, body length (BL), body height (BH), chest girth (CG), tail length (TL), tail width (TW), tail circumference (TC), carcass weight (CW), tail fat weight (TF), ratio of CW to TF (RCT) and tail type (TT). We identified 7, 6, 7, 2, 10 and 1 SNPs significantly associated with traits TF, CW, RCT, TW, TT and CG, respectively. Their associated genomic regions harboured 42 positional candidate genes. Out of them, 13 candidate genes including SMURF2, FBF1, DTNBP1, SETD7 and RBM11 have been associated with fat metabolism in sheep. The RBM11 gene has already been identified in a previous study on signatures of selection in this specific sheep population. Two more genes, that is, SMARCA5 and GAB1 were associated with body size in sheep. The present study has identified candidate genes that might be implicated in tail fat deposition and body size in sheep.
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| 7. |
- Guo, Zhiming, et al.
(författare)
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Nondestructive monitoring storage quality of apples at different temperatures by near-infrared transmittance spectroscopy
- 2020
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Ingår i: Food Science & Nutrition. - : WILEY. - 2048-7177. ; 8:7, s. 3793-3805
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Tidskriftsartikel (refereegranskat)abstract
- Apple is the most widely planted fruit in the world and is popular in consumers because of its rich nutritional value. In this study, the portable near-infrared (NIR) transmittance spectroscopy coupled with temperature compensation and chemometric algorithms was applied to detect the storage quality of apples. The postharvest quality of apples including soluble solids content (SSC), vitamin C (VC), titratable acid (TA), and firmness was evaluated, and the portable spectrometer was used to obtain near-infrared transmittance spectra of apples in the wavelength range of 590-1,200 nm. Mixed temperature compensation method (MTC) was used to reduce the influence of temperature on the models and to improve the adaptability of the models. Then, variable selection methods, such as uninformative variable elimination (UVE), competitive adaptive reweighted sampling (CARS), and successive projections algorithm (SPA), were developed to improve the performance of the models by determining characteristic variables and reducing redundancy. Comparing the full spectral models with the models established on variables selected by different variable selection methods, the CARS combined with partial least squares (PLS) showed the best performance with prediction correlation coefficient (R-p) and residual predictive deviation (RPD) values of 0.9236, 2.604 for SSC; 0.8684, 2.002 for TA; 0.8922, 2.087 for VC; and 0.8207, 1.992 for firmness, respectively. Results showed that NIR transmittance spectroscopy was feasible to detect postharvest quality of apples during storage.
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| 8. |
- Guo, Zhiming, et al.
(författare)
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Quantitative detection of apple watercore and soluble solids content by near infrared transmittance spectroscopy
- 2020
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Ingår i: Journal of Food Engineering. - : ELSEVIER SCI LTD. - 0260-8774 .- 1873-5770. ; 279
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Tidskriftsartikel (refereegranskat)abstract
- Near-infrared (NIR) spectroscopy as an emerging analytical technique was used for the first time to quantitatively detect the watercore degree and soluble solids content (SSC) in apple. To reduce the data processing time and meet the needs of practical application, the variable selection methods including synergy interval (SI), successive projections algorithm (SPA), genetic algorithm (GA) and competitive adaptive reweighted sampling (CARS) were used to identify the characteristic variables and simplify the models. The spectral variables closely related to the apple bioactive components were used for the establishment of the partial least squares (PLS) models. The predictive correlation coefficient (R-p), root mean square error of prediction (RMSEP), and residual predictive deviation (RPD) were used to estimate the performance of the models. The CARS-PLS models displayed the best prediction performance using 600-1000 nm spectra with R-p, RMSEP, and RPD values of 0.9562, 1.340% and 3.720 for apple watercore degree; 0.9808, 0.327 (o)Bx and 4.845 for apple SSC, respectively. These results demonstrate the potential of the NIR transmittance spectroscopy technology for quantitative detection of SSC and watercore degree in apple fruit.
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| 9. |
- Guo, Zhiming, et al.
(författare)
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Rapid enrichment detection of patulin and alternariol in apple using surface enhanced Raman spectroscopy with coffee-ring effect
- 2021
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Ingår i: Lebensmittel-Wissenschaft + Technologie. - : Elsevier. - 0023-6438 .- 1096-1127. ; 152
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Tidskriftsartikel (refereegranskat)abstract
- Patulin (PAT) and alternariol (AOH) are the main mycotoxin contaminants in fruits and their products, which have great toxic effects on human body due to their teratogenicity and carcinogenicity. This study proposed a surface enhanced Raman spectroscopy (SERS) technology combining chemometrics and coffee-ring effect to build high-throughput label-free detection models for PAT and AOH. A stable coffee ring structure was built by optimizing the drying temperature and droplet volume. Comparing the partial least squares (PLS) models grounded on variables selection method, the best performance was obtained by using synergy interval (Si) and genetic algorithm (GA) for PAT (R-c = 0.9905, R-p = 0.9759) and AOH (R-c = 0.9829, R-p = 0.9808), respectively. The limits of detection (LOD) for PAT and AOH were as low as 1 mu g L-1, and the recovery rates were 92.80%-114.83% with relative standard deviation (RSD) = 4.86 for PAT and 82.06%-108.13% with RSD <= 2.28% for AOH. The SERS technology combined with chemometrics and coffee-ring effect holds promise for high-throughput label-free detection of PAT and AOH in fruits and their products.
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| 10. |
- Huang, Yanqin, et al.
(författare)
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Humic Acids Combined with Dairy Slurry as Fertilizer Can Increase Alfalfa Yield and Reduce Nitrogen Losses
- 2024
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Ingår i: Agriculture. - : Multidisciplinary Digital Publishing Institute (MDPI). - 2077-0472. ; 14:8
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Tidskriftsartikel (refereegranskat)abstract
- Dairy slurry could be a significant source of nitrogen (N) for plants, but mismanagement can lead to atmospheric ammonia losses or nitrate leaching into groundwater. To make the use of dairy slurry efficient and reasonable, the loss of N pollution to the environment should be reduced. We used repacked lysimeters to comprehensively determine ammonia emission and N leaching losses in an alfalfa–soil system. The application of dairy slurry had no significant effect on alfalfa yield at the same rate of N application in comparison to chemical fertilizer, and adding humic acids significantly increased yield by about 12%. However, the application of dairy slurry increased the ammonia emission rate significantly, leading to an increase in the cumulative amount of ammonia emission, while the addition of humic acids reduced the ammonia emissions by 11%. Chemical fertilizer and dairy slurry application significantly increased nitrate leaching compared to the control treatment, while the addition of humic acids can significantly reduce ammonium N leaching. Dairy slurry was proven to be as effective as chemical N fertilizer in achieving the optimum biomass, and adding humic acids can significantly reduce N loss to the atmosphere and groundwater. This study showed the possibility of replacing chemical fertilizer with dairy slurry in alfalfa production and the advantages of humic acids’ addition to alfalfa to maintain production yield and improve environmental friendliness.
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