| 1. |
- Guo, Ying, et al.
(författare)
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Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum
- 2023
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:12
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Tidskriftsartikel (refereegranskat)abstract
- Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.
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| 2. |
- Guo, Zhiming, et al.
(författare)
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Identification of the apple spoilage causative fungi and prediction of the spoilage degree using electronic nose
- 2021
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Ingår i: Journal of food process engineering. - : John Wiley & Sons. - 0145-8876 .- 1745-4530. ; 44:10
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Tidskriftsartikel (refereegranskat)abstract
- Apple is resistant to storage, but it is susceptible to fungal infection during transportation and storage, resulting in serious losses after harvest. A convenient and nondestructive monitoring method for fungi-inoculated apples was proposed in this research. Four dominant spoilage fungi, including Aspergillus niger, Penicillium expansum, Penicillium chrysogenum, and Alternaria alternata, were inoculated on apple samples. The volatile information of samples with different degrees of spoilage was obtained by gas sensors. The pattern recognition methods were compared to classify the fungi and degrees of spoilage. Back propagation-artificial neural networks (BP-ANN) had the best identification model result with the highest recognition rates of 95.62 and 99.58% for fungi and spoilage degrees, respectively. The variable selection methods were employed, and variables of the gas sensors data for the prediction of apple spoilage area were optimized. The best prediction models of Aspergillus niger, Penicillium expansum, Penicillium chrysogenum, and Alternaria alternata were 0.854, 0.939, 0.909, and 0.918, respectively. The results show that the gas sensors can be used as a nondestructive technique in apple fungi infection evaluation. This proposed fruit spoilage detection technology is expected to provide a reference for the early detection of apple spoilage to promote food quality and safety inspection.Practical ApplicationsThis research used gas sensors to identify the four main spoilage fungi of apples and predicted the spoilage degree of apples using established prediction models. The apple spoilage detection method adopted in this research provides a reference for the early detection of fruit spoilage, which is helpful for apple storage and reduces the economic loss caused by corruption. It is an important measure to help ensure the economic benefits of apple and provide consumers with a large number of high-quality apple products.
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| 3. |
- Shi, Feng, et al.
(författare)
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Interdecadal to Multidecadal Variability of East Asian Summer Monsoon Over the Past Half Millennium
- 2022
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Ingår i: Journal of Geophysical Research - Atmospheres. - : American Geophysical Union (AGU). - 2169-897X .- 2169-8996. ; 127:20
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Tidskriftsartikel (refereegranskat)abstract
- The East Asian summer monsoon (EASM) plays a crucial role for ecosystems and societies in East Asia past, present, and future. However, substantial uncertainties remain regarding EASM variability on interdecadal to multidecadal timescales because of the short length of instrumental data in East Asia. This study extended the EASM circulation index in the modern meteorological studies to the paleoclimate over the past half-millennium (1470–1998 CE) to reconcile the understanding of the EASM variability in paleoclimate and modern meteorological studies. The EASM index is reconstructed based on the common signal from the three main types of the proxy records (the tree rings, speleothems, and historical documentary data) related to EASM. The reconstructed EASM index captures the simultaneous changes of the “Meiyu precipitation” and the southwesterly anomalies in South China on interdecadal to multidecadal timescales, which is a dynamic pattern visible and well-documented in the modern meteorology. Analysis of the reconstructed EASM index suggests that the interdecadal to multidecadal EASM variability is closely associated with the Pacific-Japan teleconnection pattern, which acts as a bridge between the negative phase of the Pacific Decadal Oscillation and the anomalous anticyclonic circulation over the western North Pacific. It also indicates that the EASM variability over the recent 30 years (1992–2021 CE) falls within the range of natural variability over the past half-millennium.
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| 4. |
- Guo, Ying, et al.
(författare)
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A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens
- 2016
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 12:6
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Tidskriftsartikel (refereegranskat)abstract
- Muffs and beard (Mb) is a phenotype in chickens where groups of elongated feathers gather from both sides of the face (muffs) and below the beak (beard). It is an autosomal, incomplete dominant phenotype encoded by the Muffs and beard (Mb) locus. Here we use genome-wide association (GWA) analysis, linkage analysis, Identity-by-Descent (IBD) mapping, array-CGH, genome re-sequencing and expression analysis to show that the Mb allele causing the Mb phenotype is a derived allele where a complex structural variation (SV) on GGA27 leads to an altered expression of the gene HOXB8. This Mb allele was shown to be completely associated with the Mb phenotype in nine other independent Mb chicken breeds. The Mb allele differs from the wild-type mb allele by three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27. The duplications contain total seven annotated genes and their expression was tested during distinct stages of Mb morphogenesis. A continuous high ectopic expression of HOXB8 was found in the facial skin of Mb chickens, strongly suggesting that HOXB8 directs this regional feather-development. In conclusion, our results provide an interesting example of how genomic structural rearrangements alter the regulation of genes leading to novel phenotypes. Further, it again illustrates the value of utilizing derived phenotypes in domestic animals to dissect the genetic basis of developmental traits, herein providing novel insights into the likely role of HOXB8 in feather development and differentiation.
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| 5. |
- Guo, Ying, et al.
(författare)
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Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history
- 2021
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571.
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Tidskriftsartikel (refereegranskat)abstract
- Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current com-mercial stocks bred for efficient meat and egg production. In-depth characteriza-tions of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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| 6. |
- Guo, Ying, et al.
(författare)
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Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens
- 2024
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Ingår i: Poultry Science. - : Elsevier. - 0032-5791 .- 1525-3171. ; 103:1
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Tidskriftsartikel (refereegranskat)abstract
- We compared the genomes of multiple domestic chicken breeds with red and white earlobes to identify the differentiated regions between groups of breeds differing in earlobe color. This was done using a selective sweep mapping approach based on whole-genome sequence data. The most significant selective sweep was identified on chromosome 11, where the white earlobe chicken breeds originated from Mediterranean share a common haplotype, and where multiple candidate genes are located. The most plausible functional candidate gene is the Melanocor-tin 1 Receptor (MC1R), a receptor known to regulate pigmentation in the skin and hair, and it is also the gene with the strongest positional support from the haplotype-based analyses. It, however, still needs to be explored experimentally to identify effects also on chicken earlobe color variation. Our study is the first exploration of the genetic basis of white earlobe color in Mediterranean chickens using a selective sweep mapping method based on whole-genome sequencing data and shows its value for identifying likely func-tional genes mediating the pigmentation in earlobe. It also indicates a potential novel role of MC1R in birds and exemplifies how selection on fancy traits has influenced the genome during formation of the modern chicken breeds.
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| 7. |
- Li, Tiewei, et al.
(författare)
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Increasing Sensitivity of Tree Radial Growth to Precipitation
- 2024
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Ingår i: Geophysical Research Letters. - 1944-8007 .- 0094-8276. ; 51:16
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Tidskriftsartikel (refereegranskat)abstract
- The sensitivity of tree growth to precipitation regulates their responses to drought, and is a crucial metric for predicting ecosystem dynamics and vulnerability. Sensitivity may be changing with continuing climate change, yet a comprehensive assessment of its change is still lacking. We utilized tree ring measurements from 3,044 sites, climate data and CO2 concentrations obtained from monitoring stations, combined with dynamic global vegetation models to investigate spatiotemporal changes in the sensitivity over the past century. We observed an increasing sensitivity since around 1950. This increased sensitivity was particularly pronounced in arid biomes due to the combined effect of increased precipitation and elevated CO2. While elevated CO2 reduced the sensitivity of the humid regions, the intensified water pressure caused by decreased precipitation still increased the sensitivity. Our findings suggest an escalating vulnerability of tree growth to precipitation change, which may increase the risk of tree mortality under future intensified drought.
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| 8. |
- Liebsch, Daniela, et al.
(författare)
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Metabolic control of arginine and ornithine levels paces the progression of leaf senescence
- 2022
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Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 189:4, s. 1943-1960
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Tidskriftsartikel (refereegranskat)abstract
- Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.
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| 9. |
- Liu, Xiuyu, et al.
(författare)
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Functional characterization of (S)–N-methylcoclaurine 3′-hydroxylase (NMCH) involved in the biosynthesis of benzylisoquinoline alkaloids in Corydalis yanhusuo
- 2021
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Ingår i: Plant Physiology and Biochemistry. - : Elsevier BV. - 0981-9428. ; 168, s. 507-515
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Tidskriftsartikel (refereegranskat)abstract
- Benzylisoquinoline alkaloids (BIAs) are compounds naturally found in plants and can have significant value in clinical settings. Metabolic engineering and synthetic biology are both promising approaches for the heterologous acquisition of benzylisoquinoline alkaloids. (S)–N-methylcoclaurine 3′-hydroxylase (NMCH), a member of the CYP80 family of CYP450, is the penultimate catalytic enzyme that forms the central branch-point intermediate (S)-reticuline and plays a key role in the biosynthesis of BIAs. In this study, an NMCH gene was cloned from Corydalis yanhusuo, while in vitro reactions demonstrated that CyNMCH can catalyze (S)–N-methylcoclaurine to produce (S)-3′-hydroxy-N-methylcoclaurine. The Km and Kcat of CyNMCH were estimated and compared with those identified in Eschscholzia californica and Coptis japonica. This newly discovered CyNMCH will provide alternative genetic resources for the synthetic biological production of benzylisoquinoline alkaloids and provides a foundation to help analyze the biosynthetic pathway of BIAs biosynthesis in C. yanhusuo.
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| 10. |
- Wang, Chunyu, et al.
(författare)
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Co-regulation of temperature and moisture in the irrigated agricultural ecosystem productivity
- 2023
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Ingår i: Agricultural Water Management. - : Elsevier BV. - 0378-3774. ; 275
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Tidskriftsartikel (refereegranskat)abstract
- Agroecosystem photosynthesis is key to coping with global climate change. In farmland where human activities are highly involved, the interaction between environmental factors and their influences on gross primary productivity (GPP) are insufficiently understood. Particularly, the irrigation and mulching in water-saving agriculture can alter the crop responses to environmental change. Based on eddy covariance measurements of maize fields under mulched drip irrigation (DM) and mulched border irrigation (BM) in arid areas of Northwest China from 2014 to 2018, we systematically studied the interaction between multiple environmental factors and their independent effects on GPP using structural equation modeling, partial correlation coefficient and decoupling analysis by bins. The top three factors exerting the largest total effects on the GPP were soil temperature (Ts), canopy temperature (Tc) and vapor pressure deficit (VPD), among which Ts (0.75) and Tc (0.66) had the largest total effect on GPP under DM and BM, respectively. The independent effects of Ts, soil water content (SWC) and VPD on GPP were different under the two irrigation methods. SWC after excluding the influence of Ts showed a negative effect on GPP under DM (−1.24 g Cm−2d−1), while a positive effect under BM (0.02 g Cm−2d−1). By contrast, SWC after excluding the influence of VPD showed a positive effect on GPP under DM (0.59 g Cm−2d−1), while a negative effect under BM (−0.05 g Cm−2d−1). Interestingly, higher Ts, lower SWC and higher VPD had the potential to increase GPP under the two irrigation methods. We also found that the total effects of irrigation and VPD as well as the indirect effects of environmental factors on GPP should not be ignored. Our study will provide important reference for dealing with the effect of high temperature and drought stress on agro-ecosystem GPP and evaluating the response of vegetation to environmental factors.
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