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An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs

Science China(Life Sciences) 2024年第6期67卷 1133-1154页

作者： Yang Zhang Mengyao Wang Zhenguo Li Xuan Yang Keqin Li Ao Xie Fang Dong Shihan Wang Jianbing Yan Jianxiao Liu National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Smart Farming for agricultural Animals Huazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of agricultural Bioinformatics Huazhong Agricultural UniversityWuhan 430070China College of Informatics Huazhong Agricultural UniversityWuhan 430070China College of Life Sciences Nankai UniversityTianjin 300071China

Detecting genes that affect specific traits(such as human diseases and crop yields)is important for treating complex diseases and improving crop quality.A genome-wide association study(GWAS)provides new insights and directions for understanding complex traits by identifying important single nucleotide polymorphisms.Many GWAS summary statistics data related to various complex traits have been gathered recently.Studies have shown that GWAS risk loci and expression quantitative trait loci(e QTLs)often have a lot of overlaps,which makes gene expression gradually become an important intermediary to reveal the regulatory role of GWAS.In this review,we review three types of gene-trait association detection methods of integrating GWAS summary statistics and e QTLs data,namely colocalization methods,transcriptome-wide association study-oriented approaches,and Mendelian randomization-related methods.At the theoretical level,we discussed the differences,relationships,advantages,and disadvantages of various algorithms in the three kinds of gene-trait association detection methods.To further discuss the performance of various methods,we summarize the significant gene sets that influence highdensity lipoprotein,low-density lipoprotein,total cholesterol,and triglyceride reported in 16 studies.We discuss the performance of various algorithms using the datasets of the four lipid traits.The advantages and limitations of various algorithms are analyzed based on experimental results,and we suggest directions for follow-up studies on detecting gene-trait associations.

关键词： gene-trait association GWAS eQTL colocalization transcriptome-wide association study(TWAS) Mendelian randomization(MR)

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Weak Graph Map Homotopy and Its Applications

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Chinese Annals of Mathematics,Series B 2024年第2期45卷 235-252页

作者： Conglei ZHANG Yanying WANG Zhiguo ZHANG Yan ZHAO School of Mathematical Sciences Hebei Normal UniversityShijiazhuang 050024China Department of Basic Science Shanxi Agricultural UniversityJinzhang 030801ShanxiChina Center for Topology and Geometry based Technology School of Mathematical SciencesHebei Normal UniversityShijiazhuang 050024China School of Mathematical Sciences Hebei Normal UniversityTaiyuan 030031China School of Mathematics and Computer Science Shanxi Normal UniversityShijiazhuang 050024China School of Mathematics and Science Hebei GEO UniversityShijiazhuang 050031China

The authors introduce a notion of a weak graph map homotopy(they call it M-homotopy),discuss its properties and applications.They prove that the weak graph map homotopy equivalence between graphs coincides with the graph homotopy equivalence defined by Yau et al in 2001.The difference between them is that the weak graph map homotopy transformation is defined in terms of maps,while the graph homotopy transformation is defined by means of combinatorial operations.They discuss its advantages over the graph homotopy transformation.As its applications,they investigate the mapping class group of a graph and the 1-order M P-homotopy group of a pointed simple graph.Moreover,they show that the 1-order M P-homotopy group of a pointed simple graph is invariant up to the weak graph map homotopy equivalence.

关键词： Weak graph map homotopy Trivial vertex Strong deformation retract Mapping class group MP-Homotopy group

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Autophagy receptor ZmNBR1 promotes the autophagic degradation of ZmBRI1a and enhances drought tolerance in maize

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Journal of Integrative Plant Biology 2024年第6期66卷 1068-1086页

作者： Yang Xiang Guangdong Li Qian Li Yingxue Niu Yitian Pan Yuan Cheng Xiangli Bian Chongyang Zhao Yuanhong Wang Aying Zhang College of Life Sciences Nanjing Agricultural UniversityNanjing210095 China State Key Laboratory of Crop Genetics&Germplasm Enhancement and Utilization Nanjing Agricultural UniversityNanjing210095 China Sanya Institute of Nanjing agricultural university Nanjing Agricultural UniversitySanya572025 China

Drought stress is a crucial environmental factor that limits plant growth,development,and productivity.Autophagy of misfolded proteins can help alleviate the damage caused in plants experiencing drought.However,the mechanism of autophagy-mediated drought tolerance in plants remains largely unknown.Here,we cloned the gene for a maize(Zea mays)selective autophagy receptor,NEXT TO BRCA1GENE 1(ZmNBR1),and identified its role in the response to drought stress.We observed that drought stress increased the accumulation of autophagosomes.RNA sequencing and reverse transcriptionquantitative polymerase chain reaction showed that ZmNBR1 is markedly induced by drought stress.ZmNBR1 overexpression enhanced drought tolerance,while its knockdown reduced drought tolerance in maize.Our results established that ZmNBR1 mediates the increase in autophagosomes and autophagic activity under drought stress.ZmNBR1 also affects the expression of genes related to autophagy under drought stress.Moreover,we determined that BRASSINOSTEROID INSENSITIVE1A(ZmBRI1a),a brassinosteroid receptor of the BRI1-like family,interacts with ZmNBR1.Phenotype analysis showed that ZmBRI1a negatively regulates drought tolerance in maize,and genetic analysis indicated that ZmNBR1 acts upstream of ZmBRI1a in regulating drought tolerance.Furthermore,ZmNBR1facilitates the autophagic degradation of ZmBRI1a under drought stress.Taken together,our results reveal that ZmNBR1 regulates the expression of autophagy-related genes,thereby increasing autophagic activity and promoting the autophagic degradation of ZmBRI1a under drought stress,thus enhancing drought tolerance in maize.These findings provide new insights into the autophagy degradation of brassinosteroid signaling components by the autophagy receptor NBR1 under drought stress.

关键词： autophagy receptor drought tolerance Zea mays ZmBRI1a ZmNBR1

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Selenium-oxidizing Agrobacterium sp.T3F4 decreases arsenic uptake by Brassica rapa L.under a native polluted soil

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Journal of Environmental Sciences 2024年第4期138卷 506-515页

作者： Lijin An Chunzhi Zhou Lipeng Zhao Ao Wei Yiting Wang Huimin Cui Shixue Zheng State Key Laboratory of agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China

Toxic arsenic(As)and trace element selenium(Se)are transformed by microorganisms but their complex interactions in soil-plant systems have not been fully understood.An Asand Se-oxidizing bacterium,Agrobacterium sp.T3F4,was applied to a native seleniferous As-polluted soil to investigate As/Se uptake by the vegetable Brassica rapa L.and As-Se interaction as mediated by strain T3F4.The Se content in the aboveground plants was significantly enhanced by 34.1%,but the As content was significantly decreased by 20.5% in the T3F4-inoculated pot culture compared to the control(P<0.05).Similar result was shown in treatment with additional 5 mg/kg of Se(IV)in soil.In addition,the As contents in roots were significantly decreased by more than 35% under T3F4 or Se(IV)treatments(P<0.05).Analysis of As-Se-bacterium interaction in a soil simulation experiment showed that the bioavailability of Se significantly increased and As was immobilized with the addition of the T3F4strain(P<0.05).Furthermore,an As/Se co-exposure hydroponic experiment demonstrated that As uptake and accumulation in plants was reduced by increasing Se(IV)concentrations.The 50% growth inhibition concentration(IC50)values for As in plants were increased about one-fold and two-fold under co-exposure with 5 and 10μmol/L Se(IV),respectively.In conclusion,strain T3F4 improves Se uptake but decreases As uptake by plants via oxidation of As and Se,resulting in decrease of soil As bioavailability and As/Se competitive absorption by plants.This provides a potential bioremediation strategy for Se biofortification and As immobilization in As-polluted soil.

关键词： Selenium oxidation Selenium biofortification Arsenite-oxidizing bacteria Arsenic immobilization Brassica rapa L

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养分回收加剧了氮沉降背景下盐渍化草地优势植物内在氮磷的失衡

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Journal of Plant Ecology 2024年第1期17卷 111-120页

作者： Yuan Su Shuaikai Wu Jie Hao Huajie Diao Kuanhu Dong Changhui Wang shanxi Key Laboratory of Grassland Ecological Protection and Native Grass Germplasm Innovation College of Grassland ScienceShanxi Agricultural UniversityTaigu 030801China Youyu Loess Plateau Grassland Ecosystem National Research Station Shanxi Agricultural UniversityTaigu 030801China

在落叶之前,从衰老组织中重新吸收养分被认为是植物适应养分缺乏的一种策略。然而,养分重吸收如何调节植物体内氮(N)和磷(P)的平衡仍不清楚,特别是在土壤氮有效性增加的情况下。本文研究了不同速率(0、1、2、4、8、16、24和32 g N m^(-2... 详细信息

在落叶之前,从衰老组织中重新吸收养分被认为是植物适应养分缺乏的一种策略。然而,养分重吸收如何调节植物体内氮(N)和磷(P)的平衡仍不清楚,特别是在土壤氮有效性增加的情况下。本文研究了不同速率(0、1、2、4、8、16、24和32 g N m^(-2)yr^(-1))氮添加对中国北方盐渍化草地优势植物赖草(Leymus secalinus)叶片和茎秆养分回收的影响,以及养分回收在调控植物内部氮磷平衡的作用。研究结果表明:氮添加6年后,随着施氮量的增加,绿色和衰老组织(叶和茎)的N浓度和氮磷比均呈上升趋势。随着施氮量的增加,绿色组织中P浓度降低,而衰老组织中P浓度无显著变化。N重吸收效率(NRE)、P重吸收效率(PRE)和NRE:PRE比值沿N添加梯度显著降低。此外,我们发现衰老组织(叶和茎)氮磷比比绿色组织(叶和茎)氮磷比对氮素添加的响应更敏感,植物内在氮磷失衡的加剧主要是由于不成比例的减少养分重吸收,尤其是NRE。总的来说,我们的研究表明,NRE和PRE的差异进一步加剧了植物凋落物内部氮磷的失衡。

关键词：生态化学计量学氮添加氮磷失衡重吸收效率重吸收能力重吸收比盐渍化草地

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Retinoic acid alleviates rotavirus-induced intestinal damage by regulating redox homeostasis and autophagic flux in piglets

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Animal Nutrition 2024年第1期16卷 409-421页

作者： Xin Lai Aimin Wu Bing Yu Hui Yan Junqiu Luo Ping Zheng Jie Yu Daiwen Chen Institute of Animal Nutrition Sichuan Agricultural University Key Laboratory for Animal Disease-resistance Nutrition of China Ministry of Education Sichuan Agricultural University

Rotaviruses(RV) are a major cause of severe gastroenteritis, particularly in neonatal piglets. Despite the availability of effective vaccines, the development of antiviral therapies for RV remains an ongoing challenge. Retinoic acid(RA), a metabolite of vitamin A, has been shown to have anti-oxidative and antiviral properties. However, the mechanism by which RA exerts its intestinal-protective and antiviral effects on RV infection is not fully understood. The study investigates the effects of RA supplementation in Duroc × Landrace × Yorkshire(DLY) piglets challenged with RV. Thirty-six DLY piglets were assigned into six treatments, including a control group, RA treatment group with two concentration gradients(5and 15 mg/d), RV treatment group, and RV treatment group with the addition of different concentration gradients of RA(5 and 15 mg/d). Our study revealed that RV infection led to extensive intestinal architecture damage, which was mitigated by RA treatment at lower concentrations by increasing the villus height and villus height/crypt depth ratio(P < 0.05), enhancing intestinal stem cell signaling and promoting intestinal barrier functions. In addition, 15 mg/d RA supplementation significantly increased NRF2 and HO-1 protein expression(P < 0.05) and GSH content(P < 0.05), indicating that RA supplementation can enhance anti-oxidative signaling and redox homeostasis after RV challenge. Additionally,the research demonstrated that RA exerts a dual impact on the regulation of autophagy, both stimulating the initiation of autophagy and hindering the flow of autophagic flux. Through the modulation of autophagic flux, RA influence the progression of RV infection. These findings provide new insights into the regulation of redox hemostasis and autophagy by RA and its potential therapeutic application in RV infection.

关键词： Rotavirus Piglet Retinoic acid Intestinal barrier Redox hemostasis Autophagic flux

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Comprehensive DNA barcode reference library and optimization of genetic divergence threshold facilitate the exploration of species diversity of green lacewings (Neuroptera: Chrysopidae)

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Insect Science 2024年第2期31卷 613-632页

作者： Yan Lai Kaiyu Li Xingyue Liu Deparment of Entomology Cllege of Plant ProtectionChina Agricultural UniversityBejingChina College of Bioogical Sciencs China Agricultural UniversityBeijingChina

Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae.Currently,the taxonomy of Chrysopidae lacks a comprehensive revision,which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents.We have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling(95.63%)in 25 of the 34 provincial regions in China,comprising 1119 barcodes of 25 genera and 197 species(representing 85%genera and 43.62%species from China).Combining other 1049 high quality green lacewing DNA barcodes,we first inferred the optimal threshold of interspecific genetic divergence(1.87%)for successful species identification in multiple simulated scenarios based on present data.We further inferred the threshold of genetic divergence(7.77%)among genera with biocontrol significance.The inference and performance of the threshold appears to be mainly associated with the completeness of sampling,the proportion of closely related species,and the analytical approaches.Six new combinations,Apertochrysa platypa(Yang&Yang,1991)comb.nov.,Apertochrysa shennongana(Yang&Wang,1990)comb.nov.,Apertochrysa pictifacialis(Yang,1988)comb.nov.,Apertochrysa helana(Yang,1993)comb.nov.,Plesiochrysa rosulata(Yang&Yang,2002)comb.nov.,and Signochrysa hainana(Yang&Yang,1991),are proposed according to integrative species delimitation.Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings.Our study also provides a methodological reference in molecular delimitation of other insects.

关键词： Chrysopidae DNA barcode genetic distance optimal threshold species delimitation

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Essential oils improve nursery pigs' performance and appetite via modulation of intestinal health and microbiota

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Animal Nutrition 2024年第1期16卷 174-188页

作者： Bi-Chen Zhao Tian-Hao Wang Jian Chen Bai-Hao Qiu Ya-Ru Xu Jin-Long Li College of Veterinary Medicine Northeast Agricultural University Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine Northeast Agricultural University Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment Northeast Agricultural University

Optimal intestinal health and functionality are essential for animal health and performance,and simultaneously intestinal nutrient transporters and intestinal peptides are also involved in appetite and feed intake control mechanisms.Given the potential of essential oil (EO) in improving animal performance and improving feed palatability,we hypothesized that dietary supplementation of cinnamaldehyde and carvacrol could improve performance and appetite of nursery pigs by modulating intestinal health and microbiota.Cinnamaldehyde (100 mg/kg),carvacrol (100 mg/kg),and their mixtures(including 50 mg/kg cinnamaldehyde and 50 mg/kg carvacrol) were supplemented into the diets of 240 nursery pigs for 42 d,and data related to performance were measured.Thereafter,the influence of EO on intestinal health,appetite and gut microbiota and their correlations were explored.EO supplementation increased (P<0.05) the body weight,average daily gain (ADG) and average daily feed intake (ADFI) of piglets,and reduced (P<0.05) diarrhea rates in nursery pigs.Furthermore,EO increased (P<0.05) the intestinal absorption area and the abundance of tight junction proteins,and decreased (P<0.05) intestinal permeability and local inflammation.In terms of intestinal development and the mucus barrier,EO promoted intestinal development and increased (P<0.05) the number of goblet cells.Additionally,we found that piglets in the EO-supplemented group had upregulated (P<0.05) levels of transporters and digestive enzymes in the intestine,which were significantly associated with daily gain and feed utilization.In addition,EO supplementation somewhat improved appetite in nursery pigs,increased the diversity of the gut microbiome and the abundance of beneficial bacteria,and there was a correlation between altered bacterial structure and appetite-related hormones.These findings indicate that EO is effective in promoting growth performance and nutrient absorption as well as in regulating appetite by improving intestinal health and bacterial structure.

关键词： Nursery pig Essential oil Intestinal health Appetite Microbiota

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Remediation of di(2-ethylhexyl)phthalate(DEHP)contaminated black soil by freeze-thaw aging biochar

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Journal of Environmental Sciences 2024年第1期135卷 681-692页

作者： Lei Wang Zeyu Dou Chaoran Ma Xiaochen Jia Hongye Wang Wenjing Bao Lei Wang Jianhua Qu Ying Zhang School of Resources and Environment Northeast Agricultural UniversityHarbin 150030China

Di(2-ethylhexyl)phthalate(DEHP),a complex structure with high toxicity,is a common organic pollutant.This study investigated the effects of fresh biochar(FBC),and freeze-thaw cycled aged biochar(FTC-BC)on DEHP-contaminated soils using a pot experiment.The specific surface area of FBC increased from 145.20 to 303.50 m~2/g,and oxygen-containing functional groups increased from 1.26 to 1.48 mol/g after freeze-thaw cycles,greatly enhancing the adsorption of DEHP by biochar in the soil.The comprehensive radar chart evaluation showed that FBC and FTC-BC reduced DEHP growth stress and improved the soil properties.Compared with FBC,FTC-BC performed better in protecting the normal growth of pakchoi and improving soil properties.In addition,the application of biochar increased the diversity and abundance of bacteria in the DEHP-contaminated soil and changed the composition of the soil bacterial community.The partial least squares path model(PLS-PM)showed that adding biochar as a soil remediation agent significantly positively impacted soil nutrients and indirectly reduced the DEHP levels in soil and plants by increasing soil microbial diversity.Compared with FBC,FTC-BC creates a more satisfactory living environment for microorganisms and has a better effect on the degradation of DEHP in the soil.This study provides a theoretical basis for future biochar remediation of DEHP-contaminated soils in cold high-latitude regions.

关键词： DEHP Freeze-thaw cycles Biochar Soil restoration

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Ferroptosis contributes to JEV-induced neuronal damage and neuroinflammation

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Virologica Sinica 2024年第1期39卷 144-155页

作者： Wenjing Zhu Qi Li Yong Yin Huanchun Chen Youhui Si Bibo Zhu Shengbo Cao Zikai Zhao Jing Ye National Key Laboratory of agricultural Microbiology Huazhong Agricultural UniversityWuhan430070China Frontiers Science Center for Animal Breeding and Sustainable Production Huazhong Agricultural UniversityWuhan430070China The Cooperative Innovation Center for Sustainable Pig Production Huazhong Agricultural UniversityWuhan430070China Hubei Hongshan Laboratory Wuhan430070China

Ferroptosis is a newly discovered prototype of programmed cell death (PCD) driven by iron-dependent phospholipid peroxidation accumulation, and it has been linked to numerous organ injuries and degenerative pathologies. Although studies have shown that a variety of cell death processes contribute to JEV-induced neuroinflammation and neuronal injury, there is currently limited research on the specific involvement of ferroptosis. In this study, we explored the neuronal ferroptosis induced by JEV infection in vitro and in vivo. Our results indicated that JEV infection induces neuronal ferroptosis through inhibiting the function of the antioxidant system mediated by glutathione (GSH)/glutathione peroxidase 4 (GPX4), as well as by promoting lipid peroxidation mediated by yes-associated protein 1 (YAP1)/long-chain acyl-CoA synthetase 4 (ACSL4). Further analyses revealed that JEV E and prM proteins function as agonists, inducing ferroptosis. Moreover, we found that treatment with a ferroptosis inhibitor in JEV-infected mice reduces the viral titers and inflammation in the mouse brains, ultimately improving the survival rate of infected mice. In conclusion, our study unveils a critical role of ferroptosis in the pathogenesis of JEV, providing new ideas for the prevention and treatment of viral encephalitis.

关键词： Japanese encephalitisvirus(JEV) Ferroptosis Neuron Lipid peroxidation Inflammatory response

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