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Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers

Journal of animal Science and Biotechnology 2024年第5期15卷 1851-1865页

作者： Shuang Gu Qiang Huang Yuchen Jie Congjiao Sun Chaoliang Wen Ning Yang State Key laboratory of animal Biotech {2. and Frontier Science Center for Molecular Design {2. China Agricultural UniversityBeijing 100193China National Engineering laboratory for animal {2. and Key laboratory of animal genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsDepartment of Animal Genetics and BreedingCollege of Animal Science and Technology China Agricultural UniversityBeijing 100193China. Sanya Institute of China Agricultural University Hainan 572025China

Background Broilers stand out as one of the fastest-growing livestock globally,making a substantial contribution to animal meat ***,the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still *** study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing *** measured the growth performance of Cornish(CC)and White Plymouth Rock(RR)over a 42.d *** muscle samples from both CC and RR were randomly collected at day 2. after hatching(D2.)and D42.for RNA-seq and ATAC-seq library *** The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured,with CC outpacing RR in terms of weight at each stage of *** expression analysis identified 398 and 1,12. genes in the two dimensions of breeds and ages,respectively.A total of 75,149 ATAC-seq peaks were annotated in promoter,exon,intron and intergenic regions,with a higher number of peaks in the promoter and intronic *** age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent *** results spotlighted the upregulation of ACTC1 and FDPS at D2.,which were primarily associated with muscle structure development by gene cluster ***,a noteworthy upregulation of MUSTN1,FOS and TGFB3 was spotted in broiler chickens at D42.which were involved in cell differentiation and muscle regeneration after injury,suggesting a regulatory role of muscle growth and *** This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and *** findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent *** findings provide a foundation for future research to i

关键词： ATAC-seq Broiler Pectoral muscle development Rapid growth RNA-seq

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Multi-omics revealed the mechanism of feed efficiency in sheep by the combined action of the host and rumen microbiota

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animal Nutrition 2024年第3期18卷 367-379页

作者： Guangchen Zhou Junda Li Xuhui Liang Bohua Yang Ximeng He Hongyu Tang Hongran Guo Gongwei Liu Wenyuan Cui Yulin Chen Yuxin Yang Key laboratory of animal {2. Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China

This study was conducted to investigate potential regulatory mechanisms of feed efficiency(FE)in sheep by linking rumen microbiota with its host by the multi-omics *** hundred and ninety-eight hybrid female sheep(initial body weight=30.88±4.57 kg;4-month-old)were selected as candidate *** test sheep was fed in an individual pen for 60 days,and the residual feed intake(RFI)was *** ten candidate sheep with the highest RFI were divided into the Low-FE group,and the ten with the lowest RFI were divided into the High-FE group,all selected for sample *** RFI,average daily gain and average daily feed intake were highly significantly different between the two experimental groups(P2..The relative expression levels of insulin-like growth factor-1 and apolipoprotein A4 genes were significantly up-regulated in the liver of High-FE group(P<0.05),but relative expression level of monoacylglycerol O-acyltransferase 3 gene was significantly down-regulated(P¼0.037).These findings provide the mechanism by which the collaborative interaction between rumen microbiota fermentation and host uptake and metabolism of fermentation products impacts feed efficiency tr

关键词： Residual feed intake Sheep Microbial composition Rumen proteome Liver transcriptome Metabolite

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Single‑cell sequencing reveals the reproductive variations between primiparous and multiparous Hu ewes

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Journal of animal Science and Biotechnology 2024年第2期15卷 614-631页

作者： Ting Ge Yifan Wen Bo Li Xiaoyu Huang Shaohua Jiang Enping Zhang Key laboratory of animal {2. Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China

Background In the modern sheep production systems,the reproductive performance of ewes determines the economic profitability of *** the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific *** sheep,a high-quality Chinese sheep breed,is known for its high fecundity and is often used as a model to study prolificacy *** the current study,animals were divided into two groups according to their delivery rates in three consecutive lambing seasons(namely,the high and low reproductive groups with≥3 lambs and one lamb per season,n=3,respectively).The ewes were slaughtered within 12.h of estrus,and unilateral ovarian tissues were collected and analyzed by 10×Genomics single-cell RNA *** A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each ***,the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa ***,four granulosa cell subtypes were *** analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112.91 expression could lead to different evolutionary directions of the granulosa ***,the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly *** genes inhibit necroptosis and ferroptosis of mural granulosa cells,which helps prevent follicular *** This study provides insights into the molecular mechanisms underlying the high fecundity of Hu *** differences in gene expression profiles,particularly in the granulosa cells,suggest that these cells play a critical role in female *** findings also highlight the importance of genes such as JPH1,LOC101112.91,FTH1,and FTL in regulating granulosa cell function and follicular development.

关键词： Granulosa cells Hu sheep Lambing number Ovarian somatic cells Single-cell RNA sequencing

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Nutrition strategies to control post-weaning diarrhea of piglets: From the perspective of feeds

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animal Nutrition 2024年第2期17卷 297-311页

作者： Qingsong Tang Tianyi Lan Chengyu Zhou Jingchun Gao Liuting Wu Haiyang Wei Wenxue Li Zhiru Tang Wenjie Tang Hui Diao Yetong Xu Xie Peng Jiaman Pang Xuan Zhao Zhihong Sun laboratory for Bio-Feed and Molecular Nutrition College of Animal Science and Technology Southwest University animal breeding and {2. Key laboratory of Sichuan Province Sichuan Animal Science Academy Yibin Academy of Southwest University

Post-weaning diarrhea(PWD) is a globally significant threat to the swine industry. Historically, antibiotics as well as high doses of zinc oxide and copper sulfate have been commonly used to control ***, the development of bacterial resistance and environmental pollution have created an interest in alternative strategies. In recent years, the research surrounding these alternative strategies and the mechanisms of piglet diarrhea has been continually updated. Mechanically, diarrhea in piglets is a result of an imbalance in intestinal fluid and electrolyte absorption and secretion. In general, enterotoxigenic Escherichia coli(ETEC) and diarrheal viruses are known to cause an imbalance in the absorption and secretion of intestinal fluids and electrolytes in piglets, resulting in diarrhea when Cl secretion-driven fluid secretion surpasses absorptive capacity. From a perspective of feedstuffs, factors that contribute to imbalances in fluid absorption and secretion in the intestines of weaned piglets include high levels of crude protein(CP), stimulation by certain antigenic proteins, high acid-binding capacity(ABC), and contamination with deoxynivalenol(DON) in the diet. In response, efforts to reduce CP levels in diets,select feedstuffs with lower ABC values, and process feedstuffs using physical, chemical, and biological approaches are important strategies for alleviating PWD in piglets. Additionally, the diet supplementation with additives such as vitamins and natural products can also play a role in reducing the diarrhea incidence in weaned piglets. Here, we examine the mechanisms of absorption and secretion of intestinal fluids and electrolytes in piglets, summarize nutritional strategies to control PWD in piglets from the perspective of feeds, and provide new insights towards future research directions.

关键词： Post-weaning diarrhea Fluid secretion Feed Nutritional regulation strategies Piglet

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Hi-Tag:a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

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Science China(Life Sciences) 2024年第5期67卷 1027-1034页

作者： Xiaolong Qi Lu Zhang Qiulin Zhao Peng Zhou Sai Xian Zhang Jingjin Li Zhuqing Zheng Yue Xiang Xueting Dai Zhe Jin Yaobang Jian Xinyun Li Liangliang Fu Shuhong Zhao Key Lab of Agricultural animal genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China The Cooperative Innovation Center for Sustainable Pig Production Wuhan 430070China Hubei Hongshan laboratory Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhan 430070China

Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin ***,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science ***,we develop a novel method,Hi-Tag,that identifies high-resolution,long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation(with a phosphorothioate-modified linker).Hi-Tag can be implemented using as few as 100,000 cells,involving simple experimental procedures that can be completed within 1.5 ***,Hi-Tag is capable of using its own data to identify the binding sites of specific proteins,based on which,it can acquire accurate interaction *** results suggest that Hi-Tag has great potential for advancing chromatin interaction studies,particularly in the context of limited cell availability.

关键词： Hi-Tag chromatin interactions transposase tagmentation chromatin proximity ligation low cell numbers

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miR-2.-3p promotes proliferation and inhibits apoptosis of porcine granulosa cells by targeting P2.

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Journal of Integrative Agriculture 2024年第4期23卷 1315-1328页

作者： Shengjie Shi Lutong Zhang Liguang Wang Huan Yuan Haowei Sun Mielie Madaniyati Chuanjiang Cai Weijun Pang Lei Gao Guiyan Chu College of animal Science and Technology Northwest A&F UniversityYangling 712100China Key laboratory of animal {2. Breeding and Reproduction of Shaanxi ProvinceYangling 712100China

Ovarian follicle development is associated with the physiological functions of granulosa cells(GCs),including proliferation and *** level of miR-2.-3p in ovarian tissue of high-yielding Yorkshire×Landrace sows was significantly higher than that of low-yielding ***,the functions of miR-2.-3p on GCs are *** this study,using flow cytometry,5-ethynyl-2.-de-oxyuridine(EdU)staining,and cell count,we showed that miR-2.-3p promoted the proliferation of GCs increasing the proportion of cells in the S phase and upregulating the expression of cell cycle genes,moreover,miR-2.-3p inhibited GC ***,on-line prediction,bioinformatics analysis,a luciferase reporter assay,RT-qPCR,and Western blot results showed that the target gene of miR-2.-3p in proliferation and apoptosis is cyclin-dependent kinase inhibitor 1B(P2./CDKN1B).Furthermore,the effect of miR-2.-3p on GC proliferation and apoptosis was attenuated by P2. *** findings suggest that miR-2.-3p regulates the physiological functions of GCs.

关键词： miR-2.-3p granulosa cells proliferation apoptosis

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Transcriptome analysis reveals steroid hormones biosynthesis pathway involved in abdominal fat deposition in broilers

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Journal of Integrative Agriculture 2024年第9期23卷 3118-3128页

作者： Yuting Zhu Yongli Wang Yidong Wang Guiping Zhao Jie Wen Huanxian Cui State Key laboratory of animal Nutrition/Key laboratory of animal(Poultry)genetics breeding and Reproduction Ministry of Agriculture and Rural Affairs/Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China

Excessive abdominal fat deposition reduces the feed efficiency and increase the cost of production in ***,it is an important task for poultry breeders to breed broilers with low abdominal *** fat deposition is a highly complex biological process,and its molecular basis remains *** this study,we performed transcriptome analysis to compare gene expression profiles at different stages of abdominal fat deposition to identify the key genes and pathways involved in abdominal fat *** found that abdominal fat weight(AFW)increased gradually from day 35(D35)to 91(D91),and then decreased at day 119(D119).Accordingly,after detecting differentially expressed genes(DEGs)by comparing gene expression profiles at D35 vs.D63 and D35 vs.D91,and identifying gene modules associated with fat deposition by weighted gene co-expression network analysis(WGCNA),we performed intersection analysis of the detected DEGs and WGCNA gene modules and identified 394 and 435 intersecting genes,*** results of the Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses showed that the steroid hormone biosynthesis and insulin signaling pathways were co-enriched in all intersecting genes,steroid hormones have been shown that regulated insulin signaling pathway,indicating the importance of the steroid hormone biosynthesis pathway in the development of broiler abdominal *** then identified 6 hub genes(ACTB,SOX9,RHOBTB2.PDLIM3,NEDD9,and DOCK4)related to abdominal fat *** analysis also revealed that there were direct interactions between 6 hub ***9 has been shown to bind to proteins required for steroid hormone receptor binding,and RHOBTB2.indirectly regulates the steroid hormones biosynthesis through cyclin factor,and ultimately affect fat *** results suggest that the genes RHOBTB2.and SOX9 play an important role in fat deposition in broilers,by regul

关键词： broilers abdominal fat deposition transcriptome analysis hub genes steroid hormones biosynthesis pathway

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A cell transcriptomic profile p ovides insights into adipocytes of porcine mammary gland across development

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Journal of animal Science and Biotechnology 2024年第1期15卷 182-200页

作者： Yongliang Fan Long Jin Zhiping He Tiantian Wei Tingting Luo Jiaman Zhang Can Liu Changjiu Dai Chao A Yan Liang Xuan Tao Xuebin Lv Yiren Gu Mingzhou Li State Key laboratory of Swine and Poultry breeding Industry College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China Key laboratory of Qinghai‑Tibetan Plateau animal Genetic Resource Reservation and Utilization Southwest Minzu UniversityChengdu 610041China animal breeding and {2. Key laboratory of Sichuan Province Sichuan Animal Science AcademyChengdu 610000China

Background Studying the composition and developmental mechanisms in mammary gland is crucial for healthy growth of newborns. The mammary gland is inherently heterogeneous, and its physiological function dependents on the gene expression of multiple cell types. Most studies focused on epithelial cells, disregarding the role of neighboring *** Here, we constructed the largest transcriptomic dataset of porcine mammary gland cells thus far. The dataset captured 12.,82. high-quality nuclei from physiological mammary glands across five developmental stages(d 90 of gestation, G90;d 0 after lactation, L0;d 2. after lactation, L2.;2.d post natural involution, PI2.7 d post natural involution, PI7). Seven cell types were identified, including epithelial cells, adipocytes, endothelial cells, fibroblasts cells, immune cells, myoepithelial cells and precursor cells. Our data indicate that mammary glands at different developmental stages have distinct phenotypic and transcriptional signatures. During late gestation(G90), the differentiation and proliferation of adipocytes were inhibited. Meanwhile, partly epithelial cells were completely differentiated. Pseudo-time analysis showed that epithelial cells undergo three stages to achieve lactation, including cellular differentiation, hormone sensing, and metabolic activation. During lactation(L0 and L2.), adipocytes area accounts for less than 0.5% of mammary glands. To maintain their own survival, the adipocyte exhibited a poorly differentiated state and a proliferative capacity. Epithelial cells initiate lactation upon hormonal stimulation. After fulfilling lactation mission, their undergo physiological death under high intensity lactation. Interestingly, the physiological dead cells seem to be actively cleared by immune cells via CCL2.-ACKR4 pathway. This biological process may be an important mechanism for maintaining homeostasis of the mammary gland. During natural involution(PI2.and PI7), epithelial cell populatio

关键词： Adipocytes Cell–cell interaction Development Mammary gland snRNA-seq

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Proteo-transcriptomic profiles reveal key regulatory pathways and functions of LDHA in the ovulation of domestic chickens(Gallus gallus)

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Journal of animal Science and Biotechnology 2024年第4期15卷 1449-1465页

作者： Ruixue Nie Wenhui Zhang Haoyu Tian Junying Li Yao Ling Bo Zhang Hao Zhang Changxin Wu State Key laboratory of animal Biotech {2. Beijing Key Laboratory for Animal Genetic ImprovementCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Background In poultry, the smooth transition of follicles from the preovulatory-to-postovulatory phase impacts egg production in hens and can benefit the poultry industry. However, the regulatory mechanism underlying follicular ovulation in avians is a complex biological process that remains *** Critical biochemical events involved in ovulation in domestic chickens(Gallus gallus) were evaluated by transcriptomics, proteomics, and in vitro assays. Comparative transcriptome analyses of the largest preovulatory follicle(F1) and postovulatory follicle(POF1) in continuous laying(CL) and intermittent laying(IL) chickens indicated the greatest difference between CL_F1 and IL_F1, with 950 differentially expressed genes(DEGs), and the smallest difference between CL_POF1 and IL_POF1, with 14 DEGs. Additionally, data-independent acquisition proteomics revealed 2.2.differentially abundant proteins between CL_F1 and IL_F1. Perivitelline membrane synthesis, steroid biosynthesis, lysosomes, and oxidative phosphorylation were identified as pivotal pathways contributing to ovulation regulation. In particular, the regulation of zona pellucida sperm-binding protein 3, plasminogen activator, cathepsin A, and lactate dehydrogenase A(LDHA) was shown to be essential for ovulation. Furthermore, the inhibition of LDHA decreased cell viability and promoted apoptosis of ovarian follicles in *** This study reveals several important biochemical events involved in the process of ovulation, as well as crucial role of LDHA. These findings improve our understanding of ovulation and its regulatory mechanisms in avian species.

关键词： Chicken Data-independent acquisition proteomics LDHA Ovulation Regulatory mechanism Transcriptome

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Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia

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Journal of genetics and Genomics 2024年第1期51卷 87-95页

作者： Liu Yang Xing Zhang Yaning Hu Piao Zhu Hua Li Zhenyu Peng Hai Xiang Xinying Zhou Xingbo Zhao National Engineering laboratory for animal {2. Key Laboratory of AnimalGeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Guangdong Provincial Key laboratory of animal Molecular Design and Precise {2. School of Life Science and EngineeringFoshan UniversityFoshanGuangdong 528225China State Key laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China Key laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China

Sheep have been one of the most important groups of animals since ancient ***,the knowledge of their migration routes and genetic relationships is still poorly *** investigate sheep maternal migration histories alongside Eurasian communications routes,in this study,we obtain mitochondrial genomes(mitogenomes)from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 442.–3100 years before present(BP).By obtaining the mitogenomes from the sheep(442.–3556 BP)found in the Tongtian Cave site in Xinjiang,Altai region of northwest China,our results support the emergence of haplogroup C sheep in Xinjiang as early as 442.–3556 *** combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern *** least two migration events have taken place for sheep crossing Eurasia to China,one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 442. BP to 2.00 ***,this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.

关键词： Sheep Ancient DNA Eastern Asia Mitochondrial genome Migration Altai

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