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

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 genetics 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 farming.Revealing the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific ewes.Hu sheep,a high-quality Chinese sheep breed,is known for its high fecundity and is often used as a model to study prolificacy traits.In 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 sequencing.Results A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each group.Noticeably,the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa cells.Furthermore,four granulosa cell subtypes were identified.GeneSwitches analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112291 expression could lead to different evolutionary directions of the granulosa cells.Additionally,the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly higher.These genes inhibit necroptosis and ferroptosis of mural granulosa cells,which helps prevent follicular atresia.Conclusions This study provides insights into the molecular mechanisms underlying the high fecundity of Hu sheep.The differences in gene expression profiles,particularly in the granulosa cells,suggest that these cells play a critical role in female prolificacy.The findings also highlight the importance of genes such as JPH1,LOC101112291,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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Hepatic steatosis is associated with dysregulated cholesterol metabolism and altered protein acetylation dynamics in chickens

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Journal of animal Science and Biotechnology 2024年第1期15卷 53-67页

作者： Xiaoli Guo Qianqian Zhou Jiaming Jin Fangren Lan Chaoliang Wen Junying Li Ning Yang Congjiao Sun National Engineering Laboratory for animal Breeding and Key Laboratory of animal genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsChina Agricultural UniversityBeijing 100193China

Background Hepatic steatosis is a prevalent manifestation of fatty liver, that has detrimental effect on the health and productivity of laying hens, resulting in economic losses to the poultry industry. Here, we aimed to systematically investigate the genetic regulatory mechanisms of hepatic steatosis in laying hens.Methods Ninety individuals with the most prominent characteristics were selected from 686 laying hens according to the accumulation of lipid droplets in the liver, and were graded into three groups, including the control, mild hepatic steatosis and severe hepatic steatosis groups. A combination of transcriptome, proteome, acetylome and lipidome analyses, along with bioinformatics analysis were used to screen the key biological processes, modifications and lipids associated with hepatic steatosis.Results The rationality of the hepatic steatosis grouping was verified through liver biochemical assays and RNA-seq. Hepatic steatosis was characterized by increased lipid deposition and multiple metabolic abnormalities. Integration of proteome and acetylome revealed that differentially expressed proteins(DEPs) interacted with differentially acetylated proteins(DAPs) and were involved in maintaining the metabolic balance in the liver. Acetylation alterations mainly occurred in the progression from mild to severe hepatic steatosis, i.e., the enzymes in the fatty acid oxidation and bile acid synthesis pathways were significantly less acetylated in severe hepatic steatosis group than that in mild group(P < 0.05). Lipidomics detected a variety of sphingolipids(SPs) and glycerophospholipids(GPs) were negatively correlated with hepatic steatosis(r ≤-0.5, P < 0.05). Furthermore, the severity of hepatic steatosis was associated with a decrease in cholesterol and bile acid synthesis and an increase in exogenous cholesterol transport.Conclusions In addition to acquiring a global and thorough picture of hepatic steatosis in laying hens, we were able to reveal the role of acetylation in hepatic steatosis and depict the ch

关键词： Acetylation Cholesterol metabolism Hepatic steatosis Laying hens Multiomics

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Dietary copper requirement of broilers fed a corn-soybean meal diet during 22—42 d of age

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animal Nutrition 2024年第1期16卷 96-104页

作者： Ling Zhu Wei Wu Bingxin Wu Yun Hu Liyang Zhang Weiyun Zhang Tingting Li Xiaoyan Cui Feiyu Gao Ding Li Xugang Luo Shengchen Wang Poultry Mineral Nutrition Laboratory College of Animal Science and TechnologyYangzhou University Mineral Nutrition Research division State Key Laboratory of Animal NutritionInstitute of Animal ScienceChinese Academy of Agricultural Sciences

This research was to assess the dietary copper(Cu) requirement of broiler chickens fed a practical cornsoybean meal diet during 22—42 d of age. A total of 288 numbered Arbor Acres male broilers at 22 d of age were randomly allotted 6 treatments with 8 replicate cages(6 broilers per cage) per treatment.Broilers were fed a Cu-unsupplemented corn-soybean meal basal diet(control, containing 7.36 mg Cu/kg) or the basal diet added with 3, 6, 9, 12, or 15 mg Cu/kg from CuSO4·5H2O for 21 d. Quadratic,asymptotic and broken-line models were fitted and the best fitted models were selected to determine dietary Cu requirements. The results revealed that the contents of Cu in serum and liver, m RNA expression levels of Cu-and zinc-containing superoxide dismutase(CuZnSOD) in liver and monoamine oxidase b(MAO B) in heart, as well as protein expression level of CuZnSOD in liver were affected(P < 0.05) by supplemental Cu levels, and the above indices varied linearly and quadratically(P < 0.05)with increasing Cu levels. Dietary Cu requirements assessed according to the best fitted broken-line models(P < 0.05) of the above indexes were 10.45—13.81 mg/kg. It was concluded that mRNA expression levels of CuZnSOD in liver and MAO B in heart, as well as liver CuZnSOD protein expression level were new specific sensitive biomarkers for estimating dietary Cu requirements, and the dietary Cu requirement was recommended to be 14 mg/kg to support Cu metabolic needs related to key Cucontaining enzymes in broilers fed the corn-soybean meal diet during 22—42 d of age, which was higher than the dietary Cu requirement(8 mg/kg) for broilers at the corresponding stage suggested by the Chinese Feeding Standard of Chicken.

关键词： Copper Copper content Gene expression of copper-containing enzyme Requirement Broiler

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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 immunoprecipitation.However,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science research.Here,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 days.Meanwhile,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 information.Our 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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The chemical characteristics of different sodium iron ethylenediaminetetraacetate sources and their relative bioavailabilities for broilers fed with a conventional corn‑soybean meal diet

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Journal of animal Science and Biotechnology 2024年第2期15卷 826-843页

作者： Shengchen Wang Bingxin Wu Ling Zhu Weiyun Zhang Liyang Zhang We Wu Jiaqi Wu Yun Hu Tingting Li Xiaoyan Cui Xugang Luo College of animal Science and Technology Yangzhou UniversityYangzhou 225000People’s Republic of China Mineral Nutrition Research division State Key Laboratory of Animal NutritionInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China

Background Our previous studies demonstrated that divalent organic iron(Fe)proteinate sources with higher complexation or chelation strengths as expressed by the greater quotient of formation(Qf)values displayed higher Fe bioavailabilities for broilers.Sodium iron ethylenediaminetetraacetate(NaFeEDTA)is a trivalent organic Fe source with the strongest chelating ligand EDTA.However,the bioavailability of Fe when administered as NaFeEDTA in broilers and other agricultural animals remains untested.Herein,the chemical characteristics of 12 NaFeEDTA products were determined.Of these,one feed grade NaFeEDTA(Qf=2.07×10^(8)),one food grade NaFeEDTA(Qf=3.31×10^(8)),and one Fe proteinate with an extremely strong chelation strength(Fe-Prot ES,Qf value=8,590)were selected.Their bioavailabilities relative to Fe sulfate(FeSO_(4)·7H_(2)O)for broilers fed with a conventional corn-soybean meal diet were evaluated during d 1 to 21 by investigating the effects of the above Fe sources and added Fe levels on the growth performance,hematological indices,Fe contents,activities and gene expressions of Fe-containing enzymes in various tissues of broilers.Results NaFeEDTA sources varied greatly in their chemical characteristics.Plasma Fe concentration(PI),transferrin saturation(TS),liver Fe content,succinate dehydrogenase(SDH)activities in liver,heart,and kidney,catalase(CAT)activity in liver,and SDH mRNA expressions in liver and kidney increased linearly(P<0.05)with increasing levels of Fe supplementation.However,differences among Fe sources were detected(P<0.05)only for PI,liver Fe content,CAT activity in liver,SDH activities in heart and kidney,and SDH mRNA expressions in liver and kidney.Based on slope ratios from multiple linear regressions of the above indices on daily dietary analyzed Fe intake,the average bioavailabilities of Fe-Prot ES,feed grade NaFeEDTA,and food grade NaFeEDTA relative to the inorganic FeSO_(4)·7H_(2)O(100%)for broilers were 139%,155%,and 166%,respectively.Conclusions The bioavailabilities of organic Fe sources

关键词： Broilers Chelation strengths Fe-containing enzymes NaFeEDTA Relative bioavailabilities

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miR-24-3p promotes proliferation and inhibits apoptosis of porcine granulosa cells by targeting P27

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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 genetics Breeding and Reproduction of Shaanxi ProvinceYangling 712100China

Ovarian follicle development is associated with the physiological functions of granulosa cells(GCs),including proliferation and apoptosis.The level of miR-24-3p in ovarian tissue of high-yielding Yorkshire×Landrace sows was significantly higher than that of low-yielding sows.However,the functions of miR-24-3p on GCs are unclear.In this study,using flow cytometry,5-ethynyl-2′-de-oxyuridine(EdU)staining,and cell count,we showed that miR-24-3p promoted the proliferation of GCs increasing the proportion of cells in the S phase and upregulating the expression of cell cycle genes,moreover,miR-24-3p inhibited GC apoptosis.Mechanistically,on-line prediction,bioinformatics analysis,a luciferase reporter assay,RT-qPCR,and Western blot results showed that the target gene of miR-24-3p in proliferation and apoptosis is cyclin-dependent kinase inhibitor 1B(P27/CDKN1B).Furthermore,the effect of miR-24-3p on GC proliferation and apoptosis was attenuated by P27 overexpression.These findings suggest that miR-24-3p regulates the physiological functions of GCs.

关键词： miR-24-3p granulosa cells proliferation apoptosis

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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 genetics 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 adipocytes.Results Here, we constructed the largest transcriptomic dataset of porcine mammary gland cells thus far. The dataset captured 126,829 high-quality nuclei from physiological mammary glands across five developmental stages(d 90 of gestation, G90;d 0 after lactation, L0;d 20 after lactation, L20;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 L20), 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 CCL21-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 populations dedifferentiate into mesenchymal stem cells t

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

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Importance of dietary supplementation of soluble and insoluble fibers to sows subjected to high ambient temperatures during late gestation and effects on lactation performance

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animal Nutrition 2024年第1期16卷 73-83页

作者： Seung Min Oh Abdolreza Hosseindoust Sang Hun Ha Jun Young Mun Joseph Moturi Habeeb Tajudeen Yo Han Choi Su Hyup Lee Jin Soo Kim Gyeongbuk Livestock Research Institute Department of animal Industry Convergence Kangwon National University Swine division National Institute of Animal Science Rural Development Administration Department of Swine Science Korea National University of Agriculture and Fisheries

Heat stress adversely affects sows' performance, which can be improved by applying proper nutritional strategies. This study was conducted to investigate the interactive effects of dietary fiber levels and sources on sows' reproductive performance, metabolic response during gestation, and the carry-over influence on litter performance in the lactation period during heat stress(average room temperature of 27.1°C). Fifty-four multiparous sows(Landrace × Yorkshire; initial body weight of 236.3 ± 16 kg; 2, 3and 4 parities) at d 90 of gestation were assigned to a 2 × 3 factorial arrangement(9 sows/treatment),involving 2 dietary fiber levels(4.5% and 6% crude fiber) and 3 dietary fiber sources(wheat bran [WB],palm kernel meal [PK], and beet pulp [BP]). Sows fed the BP diet had highest(P < 0.01) feed intake and constipation index and lowest(P < 0.01) farrowing duration. Piglet weight(P = 0.041) and litter weight(P < 0.01) at weaning were higher in sows in the BP treatment compared to PK treatment. Sows in the BP treatment showed the greatest(P < 0.01) digestibility of crude protein and neutral detergent fiber. The fecal concentration of acetate was the lowest(P < 0.01) in the PK treatment. Total short-chain fatty acid production was increased in the WB and BP treatments compared with the PK. Sows in the BP treatment showed the lowest(P = 0.036) hair cortisol. The blood insulin concentration of sows was higher(P = 0.026) in the high fiber(6%) treatment compared with the low fiber(4.5%) treatment at 90 min and120 min after the meal. The concentration of phthalic acid, succinic acid, phenylethylamine, hydrocinnamic acid, iron, linoleic acid, glycerol, ketone, and formamide were increased(P < 0.05) in the BP treatment compared with the WB. The BP treatment with high soluble fiber content improved the constipation index, farrowing duration, and litter performance, while high insoluble fibers increased sows comfort and reduced stress factors including respiratory rate and rectal temperature. Therefore,both soluble and insolub

关键词： Soluble fiber Insoluble fiber Beet pulp Wheat bran Palm kernel Metabolites

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Imprinting at the KBTBD6 locus involves species-specific m ternal methylation and monoallelic expression in livestock animals

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Journal of animal Science and Biotechnology 2024年第1期15卷 127-145页

作者： Jinsoo Ahn In-Sul Hwang Mi-Ryung Park Seongsoo Hwang Kichoon Lee Department of animal Sciences The Ohio State UniversityColumbusOH 43210USA animal Biotechnology division Rural Development AdministrationNational Institute of Animal ScienceJeonbuk 55365Republic of Korea Columbia Center for Translational Immunology Columbia University Irving Medical CenterColumbia UniversityNew YorkNY 10032USA animal Welfare Research Team National Institute of Animal ScienceRDA1500Kongjwipatjwi‑roJeollabuk‑do 55365Republic of Korea

Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting.Results Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter Cp G island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter Cp G islands were methylated in oocytes and/or allelically methyl-ated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these Cp G islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting.Conclusions In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.

关键词： Differentially methylated region Domesticated mammal Imprinting KBTBD6 Parthenogenetic

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Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders

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Neural Regeneration Research 2024年第6期19卷 1256-1261页

作者： Helen M.Knight Merve Demirbugen ?z Adriana PerezGrovas-Saltijeral division of Cells Organisms and Molecular Genetics School of Life Sciences University of Notingham Department of Pharmaceutical Toxicology Faculty of Pharmacy Ankara University

The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying mechanisms. Methylation of N6 adenosine(m6A) and C5 cytosine(m5C) bases occur on mRNAs, tRNA, mt-tRNA, and rRNA species as well as non-coding RNAs. With emerging knowledge of RNA binding proteins that act as writer, reader, and eraser effector proteins, comes a new understanding of physiological processes controlled by these systems. Such processes when spatiotemporally disrupted within cellular nanodomains in highly specialized tissues such as the brain, give rise to different forms of disease. In this review, we discuss accumulating evidence that changes in the m6A and m5C methylation systems contribute to neurocognitive disorders. Early studies first identified mutations within FMR1 to cause intellectual disability Fragile X syndromes several years before FMR1 was identified as an m6A RNA reader protein. Subsequently, familial mutations within the m6A writer gene METTL5, m5C writer genes NSUN2, NSUN3, NSUN5, and NSUN6, as well as THOC2 and THOC6 that form a protein complex with the m5C reader protein ALYREF, were recognized to cause intellectual development disorders. Similarly, differences in expression of the m5C writer and reader effector proteins, NSUN6, NSUN7, and ALYREF in brain tissue are indicated in individuals with Alzheimer’s disease, individuals with a high neuropathological load or have suffered traumatic brain injury. Likewise, an abundance of m6A reader and anti-reader proteins are reported to change across brain regions in Lewy bodies diseases, Alzheimer’s disease, and individuals with high cognitive reserve. m6A-modified RNAs are also reported significantly more abundant in dementia with Lewy bodies brain tissue but significantly reduced in Parkinson’s disease tissue, whilst modified RNAs are misplaced within diseased cells, particularly where synapses are located. In parahippocampal brain tissue, m6A modification is enriched in transcripts associated with psychiatri

关键词： 5-methylcytosine methylation Alzheimer's disease cognitive diseases epitranscriptomics intellectual disability Lewy body diseases N6 adenosine RNA modification

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