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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 {1. and Frontier Science Center for Molecular Design {1. China Agricultural UniversityBeijing 100193China National Engineering Laboratory for animal {1. 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 21.after hatching(D21.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 1.1.9 genes in the two dimensions of breeds and ages,respectively.A total of 75,1.9 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 D21.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 {1. 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(P1.and very low-density lipoprotein in serum and the propionate in rumen significantly increased in High-FE group(P1.,but the acetate:propionate ratio in rumen significantly decreased in High-FE group(P¼0.034).Metagenomics revealed Selenomonas ruminantium,Selenomonas *** Faecalibacterium prausnitzii were key bacteria,and increased abundance of the genes encoding the enzymes for cellulose degradation and production of propionate in High-FE *** results of proteomics and section showed the rumen papilla length and expression of carbonic anhydrase and Na^(+)/K^(+)-ATPase were significantly higher in High-FE group(P1.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 {1. 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,{1.s 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 1. h of estrus,and unilateral ovarian tissues were collected and analyzed by 1.×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 LOC1.1.1.291.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.LOC1.1.1.291.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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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 {1. 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-24-3p in ovarian tissue of high-yielding Yorkshire×Landrace sows was significantly higher than that of low-yielding ***,the functions of miR-24-3p on GCs are *** 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 ***,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 1.(P27/CDKN1.).Furthermore,the effect of miR-24-3p on GC proliferation and apoptosis was attenuated by P27 *** 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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Dynamic transcriptome profiles and novel markers in bovine spermatogenesis revealed by single-cell sequencing

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Journal of Integrative Agriculture 2024年第7期23卷 2362-2378页

作者： Yuan Gao Fuxia Bai Qi Zhang Xiaoya An Zhaofei Wang Chuzhao Lei Ruihua Dang Key Laboratory of animal {1. Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China College of Life Sciences Northwestern Polytechnical UniversityXi’an 710072China

Testicular development is an important biological process in male and requires interaction between the male germ cells and somatic ***,the mechanisms of testicular development in livestock,particularly in cattle,are poorly ***,cellular heterogeneity hinders the profiling of different cell types at different developmental *** this study,we first performed a single-cell transcriptomic study of the bovine testis development during puberty by using 1.×genomics single-cell RNA sequencing(scRNA-seq).By collecting the scRNA-seq data from 1.,083 cells from prepubertal and pubertal bovine testes,a high-resolution scRNA-seq atlas was described,identifying 9 somatic and 1. spermatogenic *** also distinguished several stage-specific marker genes for bovine germ cells and somatic cells,such as GRAF2 and MORC1.for SSC(spermatogonial stem cells),HJURP and TCF1. for differentiating spermatogonia,ARSE for immature Sertoli,CLEC1.B for mature Sertoli,LOC1.2441.70 for *** conclusion,we have examined the transcription levels and constructed the single-cell developmental maps of germ cells and somatic cells during testicular development in Angus *** datasets provided new insights into spermatogenesis and testicular somatic cell development in cattle.

关键词： scRNA-seq cattle spermatogenesis testis development

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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 {1. 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 {1. 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 1. sheep remains in 6 Chinese sites and 1.Uzbekistan site dated 4429–31.0 years before present(BP).By obtaining the mitogenomes from the sheep(4429–3556 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 4429–3556 *** 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 4429 BP to 2500 ***,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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Genome-wide identification,characterization and functional prediction of the SRS gene family in sesame(Sesamum indicum L.)

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Oil Crop Science 2024年第2期9卷 69-80页

作者： Farjana Afroz Susmi Tasmina Islam Simi Md Nahid Hasan Md Abdur Rahim department of {1. and Plant breeding Sher-e-Bangla Agricultural UniversityDhaka1207Bangladesh

Sesame(Sesamum indicum L.)is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health *** RELATED SEQUENCE(SRS)proteins are the transcription factors(TFs)specific to plants that contain RING-like zinc finger domain and are associated with the regulation of several physiological and biochemical *** also play vital roles in plant growth and development such as root formation,leaf development,floral development,hormone biosynthesis,signal transduction,and biotic and abiotic stress ***,the SRS gene family was not reported in sesame *** this study,identification,molecular characterization,phylogenetic relationship,cis-acting regulatory elements,protein-protein interaction,syntenic relationship,duplication events and expression pattern of SRS genes were analyzed in *** identified total six SiSRS genes on seven different linkage groups in the *** genome by comparing with the other species,including the model plant Arabidopsis *** SiSRS genes showed variation in their structure like2–5 exons and 1.4 *** other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1.***,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of ***,***,and some other plant *** cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4(SIN_1.1.561.showed the highest 1. and 1. elements for light-and phytohormone-responses whereas,SiSRS1.SIN_1.1.1.7)showed the highest 1. elements for *** ABREs,or ABA-responsive elements,were found in a maximum of 8 copies in the SiSRS3(SIN 1.091.0).Moreover,the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples,especially in drought and salinity conditions *** SiSRS genes like SiSRS1.SIN_1.1.1.7)and SiSRS5(SIN_1.21.65),also exhibited variabl

关键词： SiSRS gene family SHI Transcription factor Characterization Sesamum indicum

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ChMYB1.ChbHLH42-ChTTG1.module regulates abscisic acidinduced anthocyanin biosynthesis in Cerasus humilis

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Horticultural Plant Journal 2024年第1期10卷 51-65页

作者： Xiaolong Ji Zhe Li Mingyu Zhang Shaoyu Lang Xingshun Song State Key Laboratory of Tree genetics and {1. Northeast Forestry UniversityHarbinHeilongjiang 150040China department of {1. College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiang 150040China

Cerasus humilis is a kind of economic fruit tree peculiar to China,which is widely used in the food,landscape,and pharmaceutical *** are a phenolic metabolite that plays an essential role in fruit ***,the regulatory network of *** in anthocyanin biosynthesis is still *** this study,the R2R3-MYB transcription factor ChMYB1.was isolated from the full genome of the *** one-hybrid,dual-luciferase assays,and GUS staining showed that ChMYB1.significantly increased anthocyanin contents in *** fruit by promoting the expression of ChCHS and ChUFGT by binding MBS(MYB-binding elements).ChMYB1.interacted with ChbHLH42and ChTTG1.to form the MBW complex and further enhanced the expression of *** addition,abscisic acid(ABA)treatment promoted the expression of ChMYB1.and anthocyanin accumulation in *** ***,ABA treatment enhanced the interaction between ChMYB1.and ***,ChABI5 inhibited the interaction between ChMYB1.and *** data elucidated the primary molecular mechanism of anthocyanin biosynthesis in *** fruit,deepening the understanding of the regulatory network affecting anthocyanin metabolism in edible fruit crops.

关键词： Cerasus humilis Anthocyanin ChMYB1 Fruit ABA

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DNA methylation in poultry:a review

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Journal of animal Science and Biotechnology 2024年第2期15卷 509-518页

作者： Xing Ju Zhijun Wang Danfeng Cai Semiu Folaniyi Bello Qinghua Nie State Key Laboratory for Conservation and Utilization of Subtropical Agro‑Bioresources Lingnan Guangdong Laboratory of AgricultureCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangdong Provincial Key Lab of Agro‑animal Genomics and Molecular {1. and Key Lab of Chicken genetics Breeding and ReproductionMinistry of AgricultureGuangzhouGuangdong 510642China College of animal Science and Technology Zhejiang Agriculture and Forestry University666 Wusu RoadLin’an 311300China

As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome *** DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological *** paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry.

关键词： CpG islands Differentially methylated genes Differentially methylated regions DNA methylation Poultry

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Hypoxia activates autophagy by Akt/FoxO1.pathway in fish cells

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Aquaculture and Fisheries 2024年第4期9卷 557-565页

作者： Kang Chen Linlin Shi Hong Liu Huanling Wang Key Lab of Freshwater animal {1. Key Laboratory of Agricultural Animal GeneticsBreeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhan430070China Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt Ministry of EducationWuhan430070China

Hypoxia,a common environmental condition,can affect cell survival and physiological function by triggering oxidative ***/FoxO pathway has been proven to play a non-negligible role in the regulation of ***,the role of Akt/FoxO pathway in hypoxia-induced autophagy is unclear in ***,in this study,grass carp hepatocyte cells(L8824)were treated by CoCl2 to simulate hypoxia,and the results showed that CoCl2 can increase the expression of Hif-1.protein at different concentrations or different treatment *** study found that hypoxia increased intracellular reactive oxygen species(ROS)level,and the expression of autophagy-related genes(LC3-II,pink1.beclin-1.and p62)and foxO1./*** mitochondrial membrane potential(Δψm)was also depolarized,and autophagosomes were intriguingly detected by transmission electron microscope(TEM)after the treatment of ***,hypoxia inhibited Akt phosphorylation,while PI3K/Akt pathway inhibitor,LY294002 significantly up-regulated the expression of foxO1./1. and autophagy-related ***,silencing foxo1. also resulted in down-regulation of autophagy-related *** was demonstrated that hypoxia induced autophagy via Akt/FoxO1.*** results will provide a new light on further understanding the role of Akt/FoxO pathway in the response to hypoxia in fish.

关键词： Hypoxia Autophagy Fish cells Akt FoxO

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