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Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle

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Journal of Animal Science and Biotechnology 2024年第2期15卷 733-748页

作者： Jianmin Chai Caleb P.Weiss Paul A.Beck Wei Zhao Ying Li Jiangchao Zhao Guangdong Provincial key laboratory of Animal Molecular Design and Precise breeding College of Life Science and EngineeringFoshan UniversityFoshanChina Division of Agriculture Department of Animal ScienceUniversity of ArkansasFayettevilleARUSA Department of Animal and Food Sciences Oklahoma State UniversityStillwaterOKUSA Institute of Feed Research of Chinese Academy of Agricultural Sciences Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural AffairsBeijing 100193China

Background Stocker cattle diet and management influence beef cattle performance during the finishing stage,but knowledge of the dynamics of the rumen microbiome associated with the host are lacking.A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota.During the stocker phase,either dry hay or wheat pasture were provided,and three levels of monensin were administrated.All calves were then transported to a feedlot and received similar finishing diets with or without monensin.Rumen microbial samples were collected on d 0,28,85 during the stocker stage(S0,S28 and S85)and d 0,14,28,56,30 d before slaughter and the end of the trial during the finishing stage(F0,F14,F28,F56,Pre-Ba,and Final).The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced.Results Higher alpha diversity,including the number of observed bacterial features and the Shannon index,was observed in the stocker phase compared to the finishing phase.The bacterial amplicon sequence variants(ASVs)differentiating different sampling time points were identified.Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota.For example,shared bacteria,including Bacteroidales(ASV19)and Streptococcus infantarius(ASV94),were significantly higher in hay rumen on S28,S85,and F0,while Bacteroidaceae(ASV11)and Limivicinus(ASV15)were more abundant in wheat.Monensin affected rumen microbial composition at a specific time.Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves.Bacterial taxa associated with body weight were classified,and core microbiotas interacted with each other during the trial.Conclusions In summary,the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy.Diet at the stocker phase may temporarily affect the microbial composition duri

关键词： beef cattle Diet Feedlot phase Monensin Next-generation sequencing Rumen microbiota Stocker

Prescreening of large-effect markers with multiple strategies improves the accuracy of genomic prediction

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Journal of Integrative Agriculture 2024年第5期23卷 1634-1643页

作者： Keanning Li Bingxing An Mang Liang Tianpeng Chang Tianyu Deng Lili Du Sheng Cao Yueying Du Hongyan Li Lingyang Xu Lupei Zhang Xue Gao Junya LI Huijiang Gao laboratory of Molecular Biology and Bovine breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China Shaanxi key laboratory of Molecular Biology for Agriculture College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China College of Computer and Information Engineering Tianjin Agricultural UniversityTianjin 300384China College of Animal Science and Technology Qingdao Agricultural UniversityQingdao 266109China Tongliao Animal Agriculture Development Service Center Tongliao 028000China

Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for SF.These methods also captured more genetic variance than GBLUP.Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.

关键词： multi-omics data features prescreening eQTL mapping Huaxi cattle genomic selection

Characteristics of genetic basis copy number variation in production and adaptation traits of Chinese indigenous sheep

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Journal of genetics and Genomics 2024年第5期51卷 566-569页

作者： Meilin Jin Gang Liu Jian Lu Zhiqiang Chen Huihua Wang Taotao Li Caihong Wei State key laboratory of Animal Biotech breeding Institute of Animal SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China College of Animal Science and Technology China Agricultural UniversityBeijing100193China National Animal Husbandry Service National Center of Preservation&Utilization of Animal Genetic ResourcesBeijing 100125China Glbizzia Biosciences Beijing 102629China

Copy number variations(CNVs)range in size from 50 base pairs(bp)to several megabases(Mb)and encompass various types of structural variations,such as insertions,deletions,duplications,and complex multiallelic events(MacDonald et al.,2014).These genomic alterations modulate phenotype by altering gene dosage and transcriptional regulation,and are key drivers of biological evolution and determinants of genetic diversity and phenotypic variation.In recent years,CNVs have been detected in the genomes of various livestock species(Yuan et al.,2021;Chen et al.,2022).Upadhyay et al.(2017)conducted a comprehensive analysis of CNV distribution in the European cattle genome and determined that the Kit gene is associated with color-sidedness in English longhorn cattle.Another study presented extensive genome-wide information on CNVs in wild,commercial,and local chicken breeds to gain an integrated understanding of the domestication process and exclusively identified the genes involved(Chen et al.,2022).

关键词： sided number dosage

MED4 gene positively affects preadipocyte differentiation in Chinese red steppe cattle

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生物细胞(英文) 2023年第9期47卷 2115-2123页

作者： MINGHONG WEI CHENG XIAO JIAN WU LIHONG QIN HONGLIANG LIU YANG CAO YUMIN ZHAO Institute of Animal Biotechnology Jilin Academy of Agricultural SciencesGongzhuling136100China Institute of Muscle Biology and Growth Research Institute for Farm Animal Biology(FBN)Dummerstorf18196Germany key laboratory of beef cattle genetics and breeding Ministry of Agriculture and Rural AffairsGongzhuling136100China

Background:The regulatory genes related to lipid metabolism affect the intramuscular fat(IMF)content and improve meat quality traits.Mediator Complex Subunit 4(MED4),a vitamin D receptor protein,affects vitamin D,livestock growth,carcass traits,and triglyceride deposition.However,the physiological function of the MED4 gene on bovine adipocyte differentiation remains unknown.Methods:This study explored the function of the MED4 gene in preadipocyte differentiation in Chinese Red Steppe cattle.The overexpression plasmid and the interference sequences of the MED4 gene were constructed to detect the effects of the MED4 gene on adipogenesis and biomakers using quantitative polymerase chain reaction and western blotting.Results:The MED4 gene had significantly high expression during preadipocyte differentiation(pcattle by regulating the PPARγgene.

关键词： Chinese red steppe cattle MED4 PPARγ Predipocyte differentiation Lipid metabolism Meat quality trait

Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez Laura M.Jensen Raluca G.Mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied Systems Biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production.Results Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were identified.Conclusions In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the develo

关键词： beef cattle Fertility GWAS QTL

Building a cattle pan-genome using more de novo assemblies

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Journal of genetics and Genomics 2022年第9期49卷 906-908页

作者： Mian Gong Peng Yang Wenwen Fang Ran Li Yu Jiang key laboratory of Animal genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China

A reference genome assembled from a single individual cannot capture the complex population level of polymorphism,especially for genetically divergent or admixed populations(Sherman et al.,2019).A complete genome data representative of a species rather than one individual,termed as pan-genome,can recover the genomic diversity and variations that are absent in the reference genome.

关键词： genome cattle assembled

RNA-seq analysis reveals the critical role of the novel lnc RNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

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Journal of Animal Science and Biotechnology 2023年第3期14卷 917-935页

作者： Xinhao Ma Xinran Yang Dianqi Zhang Wenzhen Zhang Xiaoyu Wang Kuncheng Xie Jie He Chugang Mei Linsen Zan College of Animal Science and Technology Northwest A&F UniversityYanglingShaanxi 712100People’s Republic of China Xi’an Dairy Cow breeding Center Xi’an Agriculture and Rural BureauXi’anShaanxi 712100People’s Republic of China National beef cattle Improvement Center Northwest A&F UniversityYanglingShaanxi 712100People’s Republic of China

Background Long non-coding RNAs(lncRNAs)regulate numerous biological processes,including adipogenesis.Research on adipogenesis will assist in the treatment of human metabolic diseases and improve meat quality in livestock,such as the content of intramuscular fat(IMF).However,the significance of lncRNAs in intramuscular adipogenesis remains unclear.This research aimed to reveal the lncRNAs transcriptomic profiles in the process of bovine intramuscular adipogenesis and to identify the lncRNAs involved in the adipogenesis of bovine intramuscular adipocytes.Results In this research,a landscape of lncRNAs was identified with RNA-seq in bovine intramuscular adipocytes at four adipogenesis stages(0 d,3 d,6 d,and 9 d after differentiation).A total of 7035 lncRNAs were detected,including 3396 novel lncRNAs.Based on the results of differential analysis,co-expression analysis,and functional prediction,we focused on the bovine intramuscular adipogenesis-associated long non-coding RNA(BIANCR),a novel lncRNA that may have an important regulatory function.The knockdown of BIANCR inhibited proliferation and promoted apoptosis of intramuscular preadipocytes.Moreover,BIANCR knockdown inhibited intramuscular adipogenesis by regulating the ERK1/2 signaling pathway.Conclusion This study obtained the landscape of lncRNAs during adipogenesis in bovine intramuscular adipocytes.BIANCR plays a crucial role in adipogenesis through the ERK1/2 signaling pathway.The results are noteworthy for improving beef meat quality,molecular breeding,and metabolic disease research.

关键词： Adipogenesis BIANCR Bovine Intramuscular adipocyte LncRNAs

Identification of single nucleotide polymorphisms of PIK3R1 and DUSP1 genes and their genetic associations with milk production traits in dairy cows

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Journal of Animal Science and Biotechnology 2020年第1期11卷 9-19页

作者： Bo Han Yuwei Yuan Lijun Shi Yanhua Li Lin Liu Dongxiao Sun Department of Animal genetics Breeding and ReproductionCollege of Animal Science and TechnologyKey Laboratory of Animal GeneticsBreeding and Reproduction of Ministry of Agriculture and Rural AffairsNational Engineering Laboratory for Animal BreedingChina Agricultural UniversityNo.2 Yuanmingyuan West RoadHaidian DistrictBeijing 100193China Beijing Dairy cattle Center Beijing 100192China.

Background:Previously,phosphoinositide-3-kinase regulatory subunit 1(PIK3R1)and dual specificity phosphatase 1(DUSP1)were identified as promising candidate genes for milk production traits due to their being differentially expressed between the dry period and the peak of lactation in livers of dairy cows.Hence,in this study,the single nucleotide polymorphisms(SNPs)of PIK3R1 and DUSP1 genes were identified and their genetic associations with milk yield,fat yield,fat percentage,protein yield,and protein percentage,were investigated using 1067 Chinese Holstein cows from 40 sire families.Results:By re-sequencing the entire coding region and 2000 bp of the 5′and 3′flanking regions of the two genes,one SNP in the 5′untranslated region(UTR),three in the 3′UTR,and two in the 3′flanking region of PIK3R1 were identified,and one in the 5′flanking region,one in the 3′UTR,and two in the 3′flanking region of DUSP1 were found.Subsequent single-locus association analyses showed that five SNPs in PIK3 R1,rs42590258,rs210389799,rs208819656,rs41255622,rs133655926,and rs211408208,and four SNPs in DUSP1,rs207593520,rs208460068,rs209154772,and rs210000760,were significantly associated with milk,fat and protein yields in the first or second lactation(P values≤0.0001 and 0.0461).In addition,by the Haploview 4.2 software,the six and four SNPs in PIK3R1 and DUSP1 respectively formed one haplotype block,and the haplotype-based association analyses showed significant associations between their haplotype combinations and the milk traits in both two lactations(P values≤0.0001 and 0.0364).One SNP,rs207593520(T/G),was predicted to alter the transcription factor binding sites(TFBSs)in the 5′flanking region of DUSP1.Further,the dual-luciferase assay showed that the transcription activity of allele T in rs207593520 was significantly higher than that of allele G,suggesting the activation of transcriptional activity of DUSP1 gene by allele T of rs207593520.Thus,the rs207593520 SNP was highlighted as a potential causal mutation that should be further

关键词： Chinese Holstein DUSP1 Genetic association Milk production PIK3R1 SNP

Molecular regulation mechanism of oocyte maturation in beef cattle

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BIOCELL 2023年第7期47卷 1509-1518页

作者： BINWU BAO JINPENG WANG YANXIA LI FEN FENG ZHONGXIANG JI ZHUOMA LUORENG XINGPING WANG Ningxia key laboratory of Ruminant Molecular and Cellular breeding College of AgricultureNingxia UniversityYinchuan750021China

Bovine oocytes are one of the indispensable cells in cattle reproduction and have become a research hot spot in cattle reproduction in recent years.The maturation process of oocytes is mainly regulated by enzymes,hormones,cytokines,and other molecules.The factors affecting cattle oocyte maturation have been previously studied to clarify the molecular mechanisms of cattle oocyte maturation.In this review article,phospholipid protein-3-kinase/protein kinase B,mitogen-activated protein kinase/extracellular signal-regulated kinase,Janus kinase/signal transducer and activator of transcription,epidermal growth factor receptor/extracellular signal-regulated kinase,and other signaling pathways related to oocyte maturation are discussed.In addition,the molecular mechanisms of some coding genes(JY-1,FGF-10,CDC20,etc.)and non-coding genes(miRNA,lncRNA,and circRNA)regulating oocyte maturation have been reviewed to provide new ideas for high reproductive performance molecular breeding of high-quality cattle.

关键词： Signaling pathway Bovine reproduction Regulation mechanism Gene Oocyte