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Improving the accuracy of genomic prediction in dairy cattle using the biologically annotated neural networks framework

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Journal of Animal Science and Biotechnology 2024年第6期15卷 2216-2228页

作者： Xue Wang Shaolei Shi Md.Yousuf Ali Khan Zhe Zhang Yi Zhang State Key Laboratory of Animal Biotech Breeding National Engineering Laboratory for Animal BreedingKey Laboratory of Animal GeneticsBreeding and Reproduction of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Bangladesh Livestock Research Institute Dhaka 1341Bangladesh Guangdong Laboratory of Lingnan Modern Agriculture National Engineering Research Center for Breeding Swine IndustryGuangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular BreedingCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China

Background Biologically annotated neural networks(BANNs)are feedforward Bayesian neural network models that utilize partially connected architectures based on SN P-set *** an interpretable neural network,BANNs model SNP and SNP-set effects in their input and hidden layers,***,the weights and connections of the network are regarded as random variables with prior distributions reflecting the manifestation of genetic effects at various genomic ***,its application in genomic prediction has yet to be *** This study extended the BANNs framework to the area of genomic selection and explored the optimal SN P-set partitioning strategies by using dairy cattle *** SN P-sets were partitioned based on two strategiesgene annotations and 100 kb windows,denoted as BANN_gene and BANN_100kb,*** BANNs model was compared with GBLU P,random forest(RF),BayesB and BayesCπthrough five replicates of five-fold cross-validation using genotypic and phenotypic data on milk production traits,type traits,and one health trait of 6,558,6,210and 5,962 Chinese Holsteins,*** showed that the BANNs framework achieves higher genomic prediction accuracy compared to GBLU P,RF and Bayesian ***,the BANN_100kb demonstrated superior accuracy and the BANN_gene exhibited generally suboptimal accuracy compared to GBLUP,RF,BayesB and BayesCrr across all *** average accuracy improvements of BANN_100kb over GBLU P,RF,BayesB and BayesCrr were 4.86%,3.95%,3.84%and 1.92%,and the accuracy of BANN_gene was improved by3.75%,2.86%,2.73%and 0.85%compared to GBLUP,RF,BayesB and BayesCπ,respectively across all seven ***,both BANN_100kb and BANN_gene yielded lower overall mean square error values than GBLUP,RF and Bayesian *** Our findings demonstrated that the BANNs framework performed better than traditional genomic prediction methods in our tested scenarios,and might serve as a p

关键词： Biologically annotated neural networks Dairy cattle Genomic prediction

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Mikania micrantha Kunth and its derived biochar impacts on heavy metal bioavailability and siderophore-related genes during chicken manure composting

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Biochar 2024年第1期6卷 989-1009页

作者： Yousif Abdelrahman Yousif Abdellah Hong-Yu Chen Shi-Wen Deng Wan-Ting Li Rong-Jie Ren Xi Yang Muhammad Shoaib Rana Shan-Shan Sun Jia-Jie Liu Rui-Long Wang Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture Department of EcologyCollege of Natural Resources and EnvironmentSouth China Agricultural UniversityGuangzhou 510642China. The Germplasm Bank of Wild Species Yunnan Key Laboratory for Fungal Diversity and Green DevelopmentKunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina. Key Laboratory of Agro-Environment in the Tropics Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510642China. Faculty of Public and Environmental Health University of KhartoumKhartoum 11111Sudan. Engineering Research Center of Agricultural Microbiology Technology Ministry of Education and Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region and Key Laboratory of MicrobiologyCollege of Heilongjiang Province and School of Life SciencesHeilongjiang UniversityHarbin 150080China.

Biochar can potentially reduce heavy metals(HMs)mobility and bioavailability during ***,siderophores secreted by functional microbes might lead to the re-mobilization of metals like Cu and ***,this study intended to explore the impacts of Mikania micrantha Kunth(MM)and MM-derived biochar(MMB)in the reduction of Cu and Zn bioavailability,and siderophore-related gene abundances during *** with MM and corn straw(CS)composts,a significant decline was noticed in the extractable and reducible Cu[(2.3 mg kg^(−1)+12.1 mg kg^(−1)),and(3.3 mg kg^(−1)+14.6 mg kg^(−1))],and Zn[(103.1 mg kg^(−1)+110.1 mg kg^(−1)),and(109.6 mg kg^(−1)+117.2 mg kg^(−1))]in MMB and corn straw biochar(CSB)composts,***,the lowest relative abundance of HMs-resistant bacteria particularly Corynebacterium(0.40%),Pseudomonas(0.46%),and Enterobacter(0.47%),was noted in MMB ***,a significant increase in sesquiterpenoid and triterpenoid biosynthesis abundance(5.77%)accompanied by a reduction in the abundance of clusters related to siderophore transport,and siderophore transmembrane transporter activity was detected in MMB *** analysis labeled temperature,moisture content,total organic carbon,Corynebacterium,and Bacillus as the primary factors significantly correlated with the Cu and Zn bioavailability(−0.90≤r≤0.90,P<0.05).The structural equation model revealed that physicochemical parameters,microbial abundance,and siderophores exert a substantial influence on Cu and Zn ***,MM and its derived biochar are recommended as an effective approach for accelerating Cu and Zn bioavailability reduction and managing the growth and distribution of invasive plants.

关键词： Mikania micrantha Kunth Biochar Heavy metals Mikania micrantha Kunth-related phytochemicals Siderophore-related genes

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Clock component OsPRR59 delays heading date by repressing transcription of Ehd3 in rice

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The Crop Journal 2022年第6期10卷 1570-1579页

作者： Yupeng Wang Fuqing Wu Shirong Zhou Weiwei Chen Chenyan Li Erchao Duan Jiachang Wang Zhijun Cheng Xin Zhang Qibing Lin Yulong Ren Cailin Lei Xiuping Guo Ziming Wu Shanshan Zhu Jianmin Wan National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China National Key Laboratory for Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095JiangsuChina Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of EducationJiangxi Agricultural UniversityNanchang 330045JiangxiChina

Heading date(or flowering time),an important agronomic trait in crop species,is closely associated with regional adaptation and *** of the Pseudo-Response Regulator(PRR)family play key roles in regulating ***,their role and molecular mechanism controlling heading date in rice is not very ***,we identified rice OsPRR protein,OsPRR59,which delayed heading under longday ***59 positively regulates yield by affecting plant height,secondary branches number per panicle,grain number per panicle,seed setting rate,and grain weight per ***59 is expressed in most tissues and its protein is localized to the *** also found that OsPRR59 directly binds to the promoter of Ehd3 to inhibit its *** with the WT,osprr59 ehd3 showed a significantly delayed heading phenotype,as did the ehd3 *** was opposite to the phenotype of the osprr59 mutant,confirming that Ehd3 acted downstream of OsPRR59 in regulating rice *** results identified a direct regulator of Ehd3,and revealed a novel molecular mechanism of clock component OsPRR proteins in regulating heading date and provide a new genetic resource for fine-tuning heading date in rice.

关键词： Circadian clock Ehd3 Heading date Oryza sativa Pseudo-response regulator

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Melittin analog p5RHH enhances recombinant adeno-associated virus transduction efficiency

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Journal of Integrative Medicine 2024年第1期22卷 72-82页

作者： Jing-shun Meng Yun He Heng-bin Yang Li-ping Zhou Si-yuan Wang Xi-lin Feng Omar Yahya Al-shargi Xiao-min Yu Li-qing Zhu Chang-quan Ling Shanghai University of Traditional Chinese Medicine Shanghai 201203China Oncology Department of Traditional Chinese Medicine Changhai HospitalNaval Medical UniversityShanghai 200433China Faculty of Traditional Chinese Medicine Naval Medical UniversityShanghai 200043China State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology(Ministry of Education) School of Life SciencesZhongshan HospitalFudan UniversityShanghai 200438China Yantai Fuheng Biological Technology Co. Ltd.YantaiShandong Province 264006China. Department of Clinical Laboratory the First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000Zhejiang ProvinceChina

Objective Melittin and its derivatives have been characterized to establish effective gene delivery *** capability of facilitating endosomal release enhances the nanoparticles-based gene ***,little investigation has been conducted to explore its potential application in the context of viral *** Various melittin-derived peptides were inserted into the loop VIII of the capsid proteins of recombinant adeno-associated virus *** vectors carrying either gfp or fluc genes were subjected to qPCR assays and transduction assays of HEK293T cells to investigate the efficiency of vector production and gene *** addition,the ability of a specific p5RHH-rAAV vector to deliver genes was examined through in vitro transduction of different cultured cells and in vivo tail vein administration to C57BL/6 ***,the intricate details of the vector-mediated transduction mechanisms were revealed by specific pharmacological inhibitors of every stage of the rAAV2 intracellular life *** A total of 76 melittin-related peptides were compiled from existing *** them,cMA2,Melt13,p5RHH and aAR3 were found to significantly enhance the gene delivery efficiency of rAAV2 *** p5RHH-rAAV2 vectors efficiently transduced not only rAAV-potent cell lines but also cell lines previously considered resistant to ***,bafilomycin A1,a vacuolar endosome acidification inhibitor,completely inhibited the transgene expression mediated by the p5RHH-rAAV2 *** importantly,p5RHH-rAAV8 vectors also demonstrated increased hepatic transduction in vivo in C57BL/6 *** The incorporation of melittin analogues into the rAAV capsids results in a significant improvement in rAAV-mediated transgene *** further modifications remain an area of interest,our studies have substantially broadened the pharmacological prospects of melittin in the context of viral vector-mediated gene delivery.

关键词： Melittin Recombinant adeno-associated virus Capsid engineering Transduction efficiency

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Nuclear encoded elongation factor EF-Tu is required for chloroplast development in rice grown under low-temperature conditions

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Journal of genetics and Genomics 2022年第5期49卷 502-505页

作者： Liang Cai Zongkai Liu Long Cai Xiaofeng Yan Yuan Hu Benyuan Hao Zhuang Xu Yunlu Tian Xi Liu Linglong Liu Ling Jiang Shirong Zhou Jianmin Wan State Key Laboratory for Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingJiangsu 210095China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

As a thermophilic crop that originated in tropical and subtropical areas, rice is sensitive to low temperatures, particularly during the early seedling stage. Cold stress at the seedling stage inhibits chlorophyll biosynthesis and causes oxidative damage, resulting in death(Zhao et al., 2020). Investigation of the mechanism of chloroplast development in rice seedlings under low-temperature conditions is important for breeding varieties with increased cold resistance.

关键词： seedling breeding originated

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Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

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Molecular Plant 2023年第12期16卷 1893-1910页

作者： Jizeng Jia Guangyao Zhao Danping Li Kai Wang Chuizheng Kong Pingchuan Deng Xueqing Yan Xueyong Zhang Zefu Lu Shujuan Xu Yuannian Jiao Kang Chong Xu Liu Dangqun Cui Guangwei Li Yijing Zhang Chunguang Du Liang Wu Tianbao Li Dong Yan Kehui Zhan Feng Chen Zhiyong Wang Lichao Zhang Xiuying Kong Zhengang Ru Daowen Wang Lifeng Gao College of Agronomy Collaborative Innovation Center of Henan Grain CropsState Key Laboratory of Wheat and Maize Crop Scienceand Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhou 450046HenanChina State Key Laboratory of Crop Gene Resources and Breeding the National Key Facility for Crop Gene Resources and Genetic ImprovementInsttute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China School of Life Science and Technology Henan Institute of Science and TechnologyXinxiangHenan 453003China xi'An Shansheng Biosciences Co. Ltd.Xi'an 71000China Zhejang Provincial Key Laboratory of Crop Genetic Resources College of Agriculture and BiotechnologyZhejang UniversityHangzhouZhejiang 310058China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Bejing 100049China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBejing 100093China State Key Laboratory of Genetic Engineering Colaborative Innovation Centerof Genetics and DevelopmentDeparment of BiochemistryInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China Hainan Yazhou Bay Seed Laboratory Hainan Institute of Zhejiang UniversitySanyaHainan 56200China State Key Laboratory of Crop Stress Biology in Arid Areas College of AgronomyNorthwest&F UniversityYanglingShaanxi 612100China

Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal *** also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and *** homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related *** built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run *** work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.

关键词： common wheat genome sequencing subgenome diploidization and divergence homoeologous Iocus-based GWAs homoeologous haplotypes polyploid crops

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A multi-objective design method for seismic retrofitting of existing reinforced concrete frames using pin-supported rocking walls

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Frontiers of Structural and Civil engineering 2022年第9期16卷 1089-1103页

作者： Yue CHEN Rong XU Hao WU Tao SHENG Institute of Engineering Mechanics China Earthquake AdministrationKey Laboratory of Earthquake Engineering and Engineering Vibration of China Earthquake AdministrationHarbin 150088China Research Center of Industrialization Construction Technology of Zhejiang Province Ningbo University of TechnologyNingbo 315106China State Key Laboratory of Disaster Reduction in Civil Engineering Tongji UniversityShanghai 200092China College of Civil and Environmental Engineering Ningbo UniversityNingbo 315211China

Over the past several decades,a variety of technical ways have been developed in seismic retrofitting of existing reinforced concrete frames(RFs).Among them,pin-supported rocking walls(PWs)have received much attentions to researchers ***,it is still a challenge that how to determine the stiffness demand of PWs and assign the value of the drift concentration factor(DCF)for entire systems rationally and *** this paper,a design method has been exploited for seismic retrofitting of existing RFs using PWs(RF-PWs)via a multi-objective evolutionary ***,the method has been investigated and verified through a practical ***,a parametric analysis was executed to exhibit the strengths and working mechanism of the multi-objective design *** sum up,the findings of this investigation show that the method furnished in this paper is feasible,functional and can provide adequate information for determining the stiffness demand and the value of the DCFfor ***,it can be applied for the preliminary design of these kinds of structures.

关键词： pin-supported rocking wall reinforced concrete frame seismic retrofit stiffness demand drift concentration factor multi-objective design genetic algorithm Pareto optimal solution

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Insight into microbial synthesis of metal nanomaterials and their environmental applications:Exploration for enhanced controllable synthesis

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Chinese Chemical Letters 2024年第11期35卷 6-15页

作者： Yuqing Liu Yu Yang Yuhan E Changlong Pang Di Cui Ang Li State Key Laboratory of Urban Water Resource and Environment School of EnvironmentHarbin Institute of TechnologyHarbin 150090China Zhixing Daohe(Jiangxi)Environmental Protection Industry Technology Research Institute Co. Ltd.Nanchang 330000China Engineering Research Center for Medicine College of PharmacyHarbin University of CommerceHarbin 150076China

Microbial fabrication of metal nanoparticles(MNPs)has received significant attention due to the advantages of low toxicity,energy efficiency and ecological *** groups of MNPs can be synthesized intracellularly or extracellularly by various wild-type microorganisms,including bacteria,fungi,algae and *** biology approaches,represented by genetic engineering,have been applied to overcome the shortcomings in productivity,stability,and controllability of biosynthetic *** electron microscope(SEM),transmission electron microscope(TEM)and other characterization techniques assist in deciphering their unique *** addition,biosynthetic MNPs have been widely explored for the utilization in environmental remediation and contaminant *** machine learning contains a great potential for designing targeted MNPs and predicting their *** review provides a comprehensive overview of the research progress in the microbial synthesis of *** outlook on the current challenges and future prospects in the biologically controllable synthesis and engineering environmental applications of MNPs is also provided in this review.

关键词： Microbial synthesis Metal nanoparticles Controllable synthesis Synthetic biology Environmental applications

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Regulatory mechanisms of dopamine metabolism in a marine Meyerozyma guilliermondii GXDK6 under NaCl stress as revealed by integrative multi-omics analysis

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Synthetic and Systems Biotechnology 2024年第1期9卷 115-126页

作者： Huijie Sun Huashan Bai Yonghong Hu Sheng He Ruihang Wei Duotao Meng Qiong Jiang Hongping Pan Peihong Shen Qian Ou Chengjian Jiang State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources Guangxi Research Center for Microbial and Enzyme Engineering TechnologyCollege of Life Science and TechnologyGuangxi UniversityNanning530004China Guangxi Key Laboratory for Green Processing of Sugar Resources College of Biological and Chemical EngineeringGuangxi University of Science and TechnologyLiuzhou545006China Guangxi Key Laboratory of Birth Defects Research and Prevention Guangxi Key Laboratory of Reproductive Health and Birth Defect PreventionGuangxi Zhuang Autonomous Region Women and Children Health Care HospitalNanning530033China College of Food Science and Light Industry Nanjing Tech UniversityNo.30South Puzhu RoadNanjing211816China

Dopamine can be used to treat depression,myocardial infarction,and other ***,few reports are available on the de novo microbial synthesis of dopamine from low-cost *** this study,integrated omics technology was used to explore the dopamine metabolism of a novel marine multi-stress-tolerant aromatic yeast Meyerozyma guilliermondii ***6 was found to have the ability to biosynthesize dopamine when using glucose as the substrate.14 key genes for the biosynthesis of dopamine were identified by whole genome-wide *** and proteomic data showed that the expression levels of gene AAT2 encoding aspartate aminotransferase(regulating dopamine anabolism)were upregulated,while gene AO-I encoding copper amine oxidase(involved in dopamine catabolism)were downregulated under 10%NaCl stress compared with non-NaCl stress,thereby contributing to biosynthesis of ***,the amount of dopamine under 10%NaCl stress was 2.51-fold higher than that of zero NaCl,which was consistent with the multi-omics ***-time fluorescence quantitative PCR(RT-qPCR)and high-performance liquid chromatography(HPLC)results confirmed the metabolic model of ***,by overexpressing AAT2,AST enzyme activity was increased by 24.89%,the expression of genes related to dopamine metabolism was enhanced,and dopamine production was increased by 56.36%in recombinant *** conclusion,Meyerozyma guilliermondii GXDK6 could utilize low-cost carbon source to synthesize dopamine,and NaCl stress promoted the biosynthesis of dopamine.

关键词： Dopamine biosynthesis Multi-omics analysis NaCl stress Meyerozyma guilliermondii

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genetic modification of Gγ subunit AT1 enhances salt-alkali tolerance in main graminaceous crops

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National Science Review 2023年第6期10卷 54-57页

作者： Wenjing Sun Huili Zhang Sen Yang Lijing Liu Peng Xie Jian Li Yaoyao Zhu Yidan Ouyang Qi Xie Huawei Zhang Feifei Yu National Key Laboratory of Wheat Improvement Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agriculture Sciences in Weifang State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology The Innovative Academy of Seed Design Chinese Academy of Sciences The Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of Education School of Life Sciences Shandong University National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan) Hubei Hongshan Laboratory Huazhong Agricultural University National Center of Technology Innovation for Maize State Key Laboratory of Maize Germplasm Innovation and Molecular Breeding University of Chinese Academy of Sciences College of Grassland Science and Technology China Agricultural University

Soil s aline-alkalization is becoming a major constraint for agricultural production,seriously threatening global ecosystems and food *** estimated 50%of total agricultural land will be salinized by 2050 due to factors such as low precipitation,high surface evaporation,poor cultural practices,over application of chemical fertilizers and so on [1].It is important to note that approximately60%of the saline soil has concurrent alkalization problems,conferred by high amounts of sodium carbonate（Na2CO3） or sodium bicarbonate（NaHCO3）.Compared with pure neu-tral salt stress,

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