1
|
Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
Collapse
Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| |
Collapse
|
2
|
Cabras S, Nueda MEC. Transfer Learning in Multiple Hypothesis Testing. ENTROPY (BASEL, SWITZERLAND) 2024; 26:49. [PMID: 38248175 DOI: 10.3390/e26010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
In this investigation, a synthesis of Convolutional Neural Networks (CNNs) and Bayesian inference is presented, leading to a novel approach to the problem of Multiple Hypothesis Testing (MHT). Diverging from traditional paradigms, this study introduces a sequence-based uncalibrated Bayes factor approach to test many hypotheses using the same family of sampling parametric models. A two-step methodology is employed: initially, a learning phase is conducted utilizing simulated datasets encompassing a wide spectrum of null and alternative hypotheses, followed by a transfer phase applying this fitted model to real-world experimental sequences. The outcome is a CNN model capable of navigating the complex domain of MHT with improved precision over traditional methods, also demonstrating robustness under varying conditions, including the number of true nulls and dependencies between tests. Although indications of empirical evaluations are presented and show that the methodology will prove useful, more work is required to provide a full evaluation from a theoretical perspective. The potential of this innovative approach is further illustrated within the critical domain of genomics. Although formal proof of the consistency of the model remains elusive due to the inherent complexity of the algorithms, this paper also provides some theoretical insights and advocates for continued exploration of this methodology.
Collapse
Affiliation(s)
- Stefano Cabras
- Department of Statistics, University Carlos III of Madrid, 28903 Madrid, Spain
| | | |
Collapse
|
3
|
Guo L, DaoLema, Liu B, Dai L, Wang X, Wang X, Cao J, Zhang W. Identification of milk-related genes and regulatory networks in Bactrian camel either supplemented or under grazing. Trop Anim Health Prod 2023; 55:342. [PMID: 37776405 DOI: 10.1007/s11250-023-03749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
Using gene co-expression networks to understand dynamic characterizations in lactating animals becomes a common method. However, there are rarely reporters focusing on milk traits in Bactrian camel by high-throughput sequencing. We used RNA-seq to generate the camel transcriptome from the blood of 16 lactating Alxa Bactrian camel in different feeding groups. In total, we obtained 1185 milk-related genes correlated with milk yield, milk protein, milk fat, and milk lactose across the WGCNA analysis. Moreover, 364 milk-related genes were differentially expressed between supplementation and grazing feeding groups. The differential expression-camel milk-related genes CMRGs (DE-CMRGs) in supplement direct an intensive gene co-expression network to improve milk performance in lactating camels. This study provides a non-invasive method to identify the camel milk-related genes in camel blood for four primary milk traits and valuable theoretical basis and research ideas for the study of the milk performance regulation mechanism of camelid animals.
Collapse
Affiliation(s)
- Lili Guo
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Inner Mongolia Agricultural University, Hohhot, China
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - DaoLema
- Bactrian Camel Institute of Alsha, Inner Mongolia, 16 Tuerhute Road, Bayanhot, Inner Mongolia, China
| | - Bin Liu
- Inner Mongolia Bionew Technology Co., Ltd., Hohhot, China
| | - Lingli Dai
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Inner Mongolia Agricultural University, Hohhot, China
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xue Wang
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Inner Mongolia Agricultural University, Hohhot, China
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaoshan Wang
- Bactrian Camel Institute of Alsha, Inner Mongolia, 16 Tuerhute Road, Bayanhot, Inner Mongolia, China
| | - Junwei Cao
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
| | - Wenguang Zhang
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Inner Mongolia Agricultural University, Hohhot, China.
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
| |
Collapse
|
4
|
Siurana A, Cánovas A, Casellas J, Calsamiglia S. Transcriptome Profile in Dairy Cows Resistant or Sensitive to Milk Fat Depression. Animals (Basel) 2023; 13:ani13071199. [PMID: 37048455 PMCID: PMC10093643 DOI: 10.3390/ani13071199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
Feeding linseed to dairy cows results in milk fat depression (MFD), but there is a wide range of sensitivity among cows. The objectives of this study were to identify target genes containing SNP that may play a key role in the regulation of milk fat synthesis in cows resistant or sensitive to MFD. Four cows were selected from a dairy farm after a switch from a control diet to a linseed-rich diet; two were resistant to MFD with a high milk fat content in the control (4.06%) and linseed-rich (3.90%) diets; and two were sensitive to MFD with the milk fat content decreasing after the change from the control (3.87%) to linseed-rich (2.52%) diets. Transcriptome and SNP discovery analyses were performed using RNA-sequencing technology. There was a large number of differentially expressed genes in the control (n = 1316) and linseed-rich (n = 1888) diets. Of these, 15 genes were detected as key gene regulators and harboring SNP in the linseed-rich diet. The selected genes MTOR, PDPK1, EREG, NOTCH1, ZNF217 and TGFB3 may form a network with a principal axis PI3K/Akt/MTOR/SREBP1 involved in milk fat synthesis and in the response to diets that induced MFD. These 15 genes are novel candidate genes to be involved in the resistance or sensitivity of dairy cows to milk fat depression.
Collapse
|
5
|
Fan X, Qiu L, Huang L, Zhu W, Zhang Y, Miao Y. MiR-190a regulates milk protein biosynthesis through the mTOR and JAK2–STAT5 signaling pathways by targeting PTHLH in buffalo mammary epithelial cells. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
|
6
|
Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs. Int J Mol Sci 2023; 24:ijms24043947. [PMID: 36835359 PMCID: PMC9960057 DOI: 10.3390/ijms24043947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.
Collapse
|
7
|
Ojo OE, Kreuzer-Redmer S. MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology. Vet Sci 2023; 10:vetsci10010057. [PMID: 36669058 PMCID: PMC9867202 DOI: 10.3390/vetsci10010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The knowledge of how diet choices, dietary supplements, and feed intake influence molecular mechanisms in ruminant nutrition and physiology to maintain ruminant health, is essential to attain. In the present review, we focus on the role of microRNAs in ruminant health and disease; additionally, we discuss the potential of circulating microRNAs as biomarkers of disease in ruminants and the state of technology for their detection, also considering the major difficulties in the transition of biomarker development from bench to clinical practice. MicroRNAs are an inexhaustible class of endogenous non-protein coding small RNAs of 18 to 25 nucleotides that target either the 3' untranslated (UTR) or coding region of genes, ensuring a tight post-transcriptionally controlled regulation of gene expression. The development of new "omics" technologies facilitated a fresh perspective on the nutrition-to-gene relationship, incorporating more extensive data from molecular genetics, animal nutrition, and veterinary sciences. MicroRNAs might serve as important regulators of metabolic processes and may present the inter-phase between nutrition and gene regulation, controlled by the diet. The development of biomarkers holds the potential to revolutionize veterinary practice through faster disease detection, more accurate ruminant health monitoring, enhanced welfare, and increased productivity. Finally, we summarize the latest findings on how microRNAs function as biomarkers, how technological paradigms are reshaping this field of research, and how platforms are being used to identify novel biomarkers. Numerous studies have demonstrated a connection between circulating microRNAs and ruminant diseases such as mastitis, tuberculosis, foot-and-mouth disease, fasciolosis, and metabolic disorders. Therefore, the identification and analysis of a small number of microRNAs can provide crucial information about the stage of a disease, etiology, and prognosis.
Collapse
|
8
|
Jia R, Xu L, Sun D, Han B. Genetic marker identification of SEC13 gene for milk production traits in Chinese holstein. Front Genet 2023; 13:1065096. [PMID: 36685890 PMCID: PMC9846039 DOI: 10.3389/fgene.2022.1065096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
SEC13 homolog, nuclear pore and COPII coat complex component (SEC13) is the core component of the cytoplasmic COPII complex, which mediates material transport from the endoplasmic reticulum to the Golgi complex. Our preliminary work found that SEC13 gene was differentially expressed in dairy cows during different stages of lactation, and involved in metabolic pathways of milk synthesis such as citric acid cycle, fatty acid, starch and sucrose metabolisms, so we considered that the SEC13 might be a candidate gene affecting milk production traits. In this study, we detected the polymorphisms of SEC13 gene and verified their genetic effects on milk yield and composition traits in a Chinese Holstein cow population. By sequencing the whole coding and partial flanking regions of SEC13, we found four single nucleotide polymorphisms (SNPs). Subsequent association analysis showed that these four SNPs were significantly associated with milk yield, fat yield, protein yield or protein percentage in the first and second lactations (p ≤.0351). We also found that two SNPs in SEC13 formed one haplotype block by Haploview4.2, and the block was significantly associated with milk yield, fat yield, fat percentage, protein yield or protein percentage (p ≤ .0373). In addition, we predicted the effect of SNP on 5'region on transcription factor binding sites (TFBSs), and found that the allele A of 22:g.54362761A>G could bind transcription factors (TFs) GATA5, GATA3, HOXD9, HOXA10, CDX1 and Hoxd13; and further dual-luciferase reporter assay verified that the allele A of this SNP inhibited the fluorescence activity. We speculate that the A allele of 22:g.54362761A>G might inhibit the transcriptional activity of SEC13 gene by binding the TFs, which may be a cause mutation affecting the formation of milk production traits in dairy cows. In summary, we proved that SEC13 has a significant genetic effect on milk production traits and the identified significant SNPs could be used as candidate genetic markers for GS SNP chips development; on the other hand, we verified the transcriptional regulation of 22:g.54362761A>G on SEC13 gene, providing research direction for further function validation tests.
Collapse
Affiliation(s)
- Ruike Jia
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Lingna Xu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China,National Dairy Innovation Center, Hohhot, China
| | - Bo Han
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China,*Correspondence: Bo Han,
| |
Collapse
|
9
|
Bta-miR-106b Regulates Bovine Mammary Epithelial Cell Proliferation, Cell Cycle, and Milk Protein Synthesis by Targeting the CDKN1A Gene. Genes (Basel) 2022; 13:genes13122308. [PMID: 36553575 PMCID: PMC9777812 DOI: 10.3390/genes13122308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Our previous studies found that bta-miR-106b and its corresponding target gene, CDKN1A, were differentially expressed between the mammary epithelium of lactating Holstein cows with extremely high and low milk protein and fat percentage, implying the potential role of bta-miR-106b in milk composition synthesis. In this study, with luciferase assay experiment, bta-miR-106b was validated to target the 3'-untranslated region (UTR) of bovine CDKN1A, thereby regulating its expression. Moreover, in bovine mammary epithelial cells (BMECs), over-expression of bta-miR-106b significantly down-regulated the CDKN1A expression at both mRNA and protein levels, and inhibitors of bta-miR-106b increased CDKN1A expression. Of note, we observed that bta-miR-106b accelerated cell proliferation and cell cycle, and changed the expressions of protein synthesis related pathways such as JAK-STAT and PI3K/AKT/mTOR through regulating CDKN1A expression. Our findings highlight the important regulatory role of bta-miR-106b in milk protein synthesis by targeting CDKN1A in dairy cattle.
Collapse
|
10
|
Li X, Yuan L, Wang W, Zhang D, Zhao Y, Chen J, Xu D, Zhao L, Li F, Zhang X. Whole genome re-sequencing reveals artificial and natural selection for milk traits in East Friesian sheep. Front Vet Sci 2022; 9:1034211. [PMID: 36330154 PMCID: PMC9623881 DOI: 10.3389/fvets.2022.1034211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 08/23/2023] Open
Abstract
The East Friesian sheep is one of the important high-yielding dairy sheep breeds, but still little is known about their genetic and genomic variation during domestication. Therefore, we analyzed the genomic data of 46 sheep with the aim of identifying candidate genes that are closely related to milk production traits. Our genomic data consisted of 20 East Friesian sheep and 26 Asian Mouflon wild sheep. Finally, a total of 32590241 SNPs were identified, of which 0.61% (198277) SNPs were located in exonic regions. After further screening, 122 shared genomic regions in the top 1% of F ST and top 1% of Nucleotide diversity ratio were obtained. After genome annotation, these 122 candidate genomic regions were found to contain a total of 184 candidate genes. Finally, the results of KEGG enrichment analysis showed four significantly enriched pathways (P < 0.05): beta-Alanine metabolism (SMOX, HIBCH), Pathways in cancer (GLI2, AR, TXNRD3, TRAF3, FGF16), Non-homologous end-joining (MRE11), Epstein-Barr virus infection (TRAF3, PSMD13, SIN3A). Finally, we identified four important KEGG enrichment pathways and 10 candidate genes that are closely related to milk production in East Friesian sheep. These results provide valuable candidate genes for the study of milk production traits in East Friesian sheep and lay an important foundation for the study of milk production traits.
Collapse
Affiliation(s)
- Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lvfeng Yuan
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jiangbo Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
11
|
Krishna N, Vishwakarma S, Katara P. Identification and annotation of milk associated genes from milk somatic cells using expression and RNA-seq data. Bioinformation 2022; 18:703-709. [PMID: 37323558 PMCID: PMC10266364 DOI: 10.6026/97320630018703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 09/20/2023] Open
Abstract
It is of interest to identify and annotate milk associated genes using expression profiling and RNA-Seq data from milk somatic cells. RNA-Seq data was pre-processed and mapping was done to identify differentially expressed genes (DEG). The functional insights about the up and down regulated genes were gleaned using the protein-protein interaction Network in the STRING database followed by CytoHubba analysis in Cytoscope. Gene ontology, annotation and pathway enrichment was completed using ShinyGO, David tool and QTL analysis. These analysis shows that 21 genes are linked with the secretion of milk.
Collapse
Affiliation(s)
- Neelam Krishna
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj - 211002, India
| | - Shraddha Vishwakarma
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj - 211002, India
| | - Pramod Katara
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj - 211002, India
| |
Collapse
|
12
|
Mohammadi A, Alijani S, Rafat S, Abdollahi-Arpanahi R. Single-step genome-wide association study and candidate genes networks affecting reproductive traits in Iranian Holstein cattle. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
13
|
Raza SHA, Liang C, Alshammari AM, Aloufi BH, Gui L, Khan R, Zan L. Genetic variants in the serum amyloid A2 (SAA2) gene as a potential marker for milk production traits in Chinese Holstein cows. Vet Med Sci 2022; 8:1835-1840. [PMID: 35470977 PMCID: PMC9297766 DOI: 10.1002/vms3.796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background This study was conducted to detect potential polymorphisms of the serum amyloid A2 (SAA2) gene and explore their relationships with milk production traits in Chinese Holstein cows. Objectives: This study used sequencing technology conducted in 532 Chinese Holstein cows. Methods Three single nucleotide polymorphisms (SNPs) were identified within intron 1, named g.14061A>G, g.14072G>C and g.14819C>T. Eight estimated haplotypes were identified, of which three major haplotypes had a frequency of Hap3 (‐ACC‐), Hap5 (‐GCC‐) and Hap2 (‐AGT‐), with 17.9%, 12.30% and 8.10%, respectively. Results The association analysis of single markers (g.14061A>G and g.14819C>T) and combined genotypes (Hap1/5) revealed prominent effects on milk production traits in Chinese Holstein cows (p < 0.05). Conclusions Our results suggest that the SAA2 gene is associated with economic traits in Chinese Holstein cows and may be used as candidate gene for marker‐assisted selection and management in breeding programs.
Collapse
Affiliation(s)
- Sayed Haidar Abbas Raza
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingP. R. China
- National Beef Cattle Improvement CenterNorthwest A&F UniversityYanglingP. R. China
| | - Chengcheng Liang
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingP. R. China
- National Beef Cattle Improvement CenterNorthwest A&F UniversityYanglingP. R. China
| | | | - Bandar H. Aloufi
- Faculty of Science, Biology DepartmentUniversity of HailHailSaudi Arabia
| | - Linsheng Gui
- State Key Laboratory of Plateau Ecology and AgricultureQinghai UniversityXiningP. R. China
| | - Rajwali Khan
- Department of Livestock Management, Breeding and GeneticsThe University of AgriculturePeshawarPakistan
| | - Linsen Zan
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingP. R. China
- National Beef Cattle Improvement CenterNorthwest A&F UniversityYanglingP. R. China
| |
Collapse
|
14
|
Song X, Zhao M, Cao Q, Wang S, Li R, Zhang X, Zhang L, Shi K. Transcriptome provides insights into bovine mammary regulatory mechanisms during the lactation cycle. JOURNAL OF APPLIED ANIMAL RESEARCH 2022. [DOI: 10.1080/09712119.2022.2064865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Xuyang Song
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Meng Zhao
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Qiaoqiao Cao
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Shengxuan Wang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Ranran Li
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Xuan Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Letian Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Kerong Shi
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| |
Collapse
|
15
|
The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep. Noncoding RNA 2021; 7:ncrna7040078. [PMID: 34940759 PMCID: PMC8708473 DOI: 10.3390/ncrna7040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.
Collapse
|
16
|
Yang X, Liu G, Wang Q, Gao X, Xia T, Zhao C, Dou H, Zhang H. Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes. Ecol Evol 2021; 11:13475-13486. [PMID: 34646484 PMCID: PMC8495804 DOI: 10.1002/ece3.8071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/30/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
The silver fox and blue fox are economically important fur species and were domesticated by humans from their wild counterparts, the arctic fox and red fox, respectively. Farmed foxes show obvious differences from their wild counterparts, including differences in physiology, body size, energy metabolism, and immunity. However, the molecular mechanisms underlying these differences are presently unclear. In this study, we built transcriptome libraries from multiple pooled tissues for each species of farmed fox, used RNA-seq to obtain a comprehensive dataset, and performed selection analysis and sequence-level analyses of orthologous genes to identify the genes that may be influenced by human domestication. More than 153.3, 248.0, 81.6, and 65.8 million clean reads were obtained and assembled into a total of 118,577, 401,520, 79,900, and 186,988 unigenes with an average length range from 521 to 667 bp for AF, BF, RF, and SF, respectively. Selective pressure analysis showed that 11 and 14 positively selected genes were identified, respectively, in the two groups (AF vs. BF and RF vs. SF). Several of these genes were associated with natural immunity (CFI and LRRFIP1), protein synthesis (GOLGA4, CEP19 and SLC35A2), and DNA damage repair (MDC1). Further functional enrichment analyses demonstrated that two positively selected genes (ACO1 and ACAD10) were involved in metabolic process (GO:0008152, p-value = .032), representing a significant enrichment. Sequence analysis of 117 orthologous genes shared by the two groups showed that the LEMD2, RRBP1, and IGBP1 genes might be affected by artificial selection in farmed foxes, with mutation sites located within sequences that are otherwise highly conserved across most mammals. Our results provide a valuable transcriptomic resource for future genetic studies and improvement in the assisted breeding of foxes and other farmed animals.
Collapse
Affiliation(s)
- Xiufeng Yang
- College of Life ScienceQufu Normal UniversityQufuChina
| | | | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid AreasHulunbuirChina
| | - Xiaodong Gao
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Tian Xia
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Chao Zhao
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid AreasHulunbuirChina
| | - Honghai Zhang
- College of Life ScienceQufu Normal UniversityQufuChina
| |
Collapse
|
17
|
Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens. Animals (Basel) 2021; 11:ani11092606. [PMID: 34573572 PMCID: PMC8470203 DOI: 10.3390/ani11092606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The slow-growing Korat chicken (KR) is economically attractive, as KR meat has a high selling price and has thus been used in Thailand to support smallholder farmers. However, low feed efficiency in KR stockbreeding makes the product less competitive and improving KR feed efficiency is central to increasing KR profitability. Using RNA sequencing, we compared the jejunal transcriptomic profiles of low- and high-feed conversion ratio (FCR) KR chickens, to identify FCR-related transcriptional variation and biological pathways. Gene Ontology and Kyoto Encyclopedia of Gene and Genome analysis revealed that the main pathways involved in KR FCR variation are related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and neuronal and cardiac maturation, development, and growth. This is the first study to investigate, in the jejunum, the molecular genetic mechanisms affecting the FCR of slow-growing chickens. These findings will be useful in line-breeding programs to improve feed efficiency and profitability in slow-growing chicken stockbreeding. Abstract Improving feed efficiency is an important breeding target for the poultry industry; to achieve this, it is necessary to understand the molecular basis of feed efficiency. We compared the jejunal transcriptomes of low- and high-feed conversion ratio (FCR) slow-growing Korat chickens (KRs). Using an original sample of 75 isolated 10-week-old KR males, we took jejunal samples from six individuals in two groups: those with extremely low FCR (n = 3; FCR = 1.93 ± 0.05) and those with extremely high FCR (n = 3; FCR = 3.29 ± 0.06). Jejunal transcriptome profiling via RNA sequencing revealed 56 genes that were differentially expressed (p < 0.01, FC > 2): 31 were upregulated, and 25 were downregulated, in the low-FCR group relative to the high-FCR group. Functional annotation revealed that these differentially expressed genes were enriched in biological processes related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and neuronal and cardiac maturation, development, and growth, suggesting that these are important mechanisms governing jejunal feed conversion. These findings provide an important molecular basis for future breeding strategies to improve slow-growing chicken feed efficiency.
Collapse
|
18
|
Marina H, Pelayo R, Suárez-Vega A, Gutiérrez-Gil B, Esteban-Blanco C, Arranz JJ. Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds. J Dairy Sci 2021; 104:11850-11866. [PMID: 34454756 DOI: 10.3168/jds.2021-20510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
Abstract
This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.
Collapse
Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain.
| |
Collapse
|
19
|
Hao M, Jiang J, Zhang Y, Wang S, Fu G, Zou F, Xie Y, Zhao S, Li W. Transcriptional profiling of buffalo mammary gland with different milk fat contents. Gene 2021; 802:145864. [PMID: 34352300 DOI: 10.1016/j.gene.2021.145864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/08/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Milk fat is the most important energy substance in milk and contributes to its quality and health benefits. Water buffalo milk is well known for its high milk quality with higher fat contents compared with cattle milk. Dehong buffalo is a unique local swamp breed in Yunnan Province with higher milk fat and excellent milk quality which provides a good model for the investigation of the molecular mechanisms of milk fat deposition. In this study, we used RNA-seq to obtain mammary tissue transcriptomics of buffalo with different milk fat phenotypes including high(H), medium (M)and low (L) fat content groups. Comparative analyses of buffalo among three groups yielded differentially expressed genes (DEGs). Analyzing the number of different genes among H_VS_L, H_VS_M, and M_VS_L showed the same expression pattern between H_VS_M. The increasing expression levels of genes including CSN1S1, BTN1A1, LALBA, ALDH1L2, SCD and MUC15, and down-regulated expression levels of genes containing CCL2, CRABP2, ADTRP, CLU and C4A in H_VS_L and M_VS_L were found. GO and KEGG enriched pathways revealed these DEGs involved in milk protein and fat as well as immune response. The findings would enhance the understanding of the interplay between the milk composition and immune response, which suggests that the immune capacity should be considered when we tried to improve the milk quality.
Collapse
Affiliation(s)
- Meilin Hao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi 563006, China
| | - Juncai Jiang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, China
| | - Yongyun Zhang
- Teaching Demonstration Center of the Basic Experiments of Agricultural Majors, Yunnan Agricultural University, Kunming 650201, China
| | - Shaoqing Wang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Guowen Fu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Fengcai Zou
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuxiao Xie
- College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi 563006, China
| | - Sumei Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
| |
Collapse
|
20
|
Michailidou S, Gelasakis A, Banos G, Arsenos G, Argiriou A. Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds. Front Genet 2021; 12:700489. [PMID: 34349787 PMCID: PMC8326974 DOI: 10.3389/fgene.2021.700489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
In dairy sheep industry, milk production dictates the value of a ewe. Milk production is directly related to the morphology and physiology of the mammary gland; both being designated targets of breeding strategies. Although within a flock breeding parameters are mutual, large differences in milk production among individual ewes are usually observed. In this work, we tested two of the most productive dairy sheep breeds reared intensively in Greece, one local the Chios breed and one foreign the Lacaune breed. We used transcriptome sequencing to reveal molecular mechanisms that render the mammary gland highly productive or not. While highly expressed genes (caseins and major whey protein genes) were common among breeds, differences were observed in differentially expressed genes. ENSOARG00000008077, as a member of ribosomal protein 14 family, together with LPCAT2, CCR3, GPSM2, ZNF131, and ASIP were among the genes significantly differentiating mammary gland's productivity in high yielding ewes. Gene ontology terms were mainly linked to the inherent transcriptional activity of the mammary gland (GO:0005524, GO:0030552, GO:0016740, GO:0004842), lipid transfer activity (GO:0005319) and innate immunity (GO:0002376, GO:0075528, GO:0002520). In addition, clusters of genes affecting zinc and iron trafficking into mitochondria were highlighted for high yielding ewes (GO:0071294, GO:0010043). Our analyses provide insights into the molecular pathways involved in lactation between ewes of different performances. Results revealed management issues that should be addressed by breeders in order to move toward increased milk yields through selection of the desired phenotypes. Our results will also contribute toward the selection of the most resilient and productive ewes, thus, will strengthen the existing breeding systems against a spectrum of environmental threats.
Collapse
Affiliation(s)
- Sofia Michailidou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Georgios Banos
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Scotland’s Rural College, Easter Bush, Edinburgh, United Kingdom
| | - George Arsenos
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Department of Food Science and Nutrition, University of the Aegean, Lemnos, Greece
| |
Collapse
|
21
|
Liu R, Tearle R, Low WY, Chen T, Thomsen D, Smith TPL, Hiendleder S, Williams JL. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. BMC Genomics 2021; 22:410. [PMID: 34082698 PMCID: PMC8176687 DOI: 10.1186/s12864-021-07667-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses. Results In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. Conclusions These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07667-2.
Collapse
Affiliation(s)
- Ruijie Liu
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Tong Chen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Dana Thomsen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Timothy P L Smith
- USMARC, USDA-ARS-US Meat Animal Research Center, Clay Center, NE, USA
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Present address: Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| |
Collapse
|
22
|
Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle. Funct Integr Genomics 2021; 21:393-404. [PMID: 33963462 DOI: 10.1007/s10142-021-00786-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Lipid metabolism in bovine mammary epithelial cells has been the primary focus of the research of milk fat percentage of dairy cattle. Functional microRNAs can affect lipid metabolism by regulating the expression of candidate genes. The purpose of the study was to screen and identify differentially expressed miRNAs, candidate genes, and co-regulatory pathways related to the metabolism of milk fat. To achieve this aim, we used miRNA and transcriptome data from the mammary epithelial cells of dairy cattle with high (H, 4.85%) and low milk fat percentages (L, 3.41%) during mid-lactation. One hundred ninety differentially expressed genes and 33 differentially expressed miRNAs were significantly enriched in related regulatory networks, of which 27 candidate genes regulated by 18 differentially expressed miRNAs significantly enriched in pathways related to lipid metabolism (p < 0.05). Target relationships between PDE4D and bta-miR-148a, PEG10 and bta-miR-877, SOD3 and bta-miR-2382-5p, and ADAMTS1 and bta-miR-2425-5p were verified using luciferase reporter assays and quantitative RT-PCR. The detection of triglyceride production in BMECs showed that bta-miR-21-3p and bta-miR-148a promote triglyceride synthesis, whereas bta-miR-124a, bta-miR-877, bta-miR-2382-5p, and bta-miR-2425-5p inhibit triglyceride synthesis. The conjoint analysis could identify functional miRNAs and regulatory candidate genes involved in lipid metabolism within the co-expression networks of the dairy cattle mammary system, which contributes to the understanding of potential regulatory mechanisms of genetic element and gene signaling networks involved in milk fat metabolism.
Collapse
|
23
|
Dong W, Yang J, Zhang Y, Liu S, Ning C, Ding X, Wang W, Zhang Y, Zhang Q, Jiang L. Integrative analysis of genome-wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle. J Anim Breed Genet 2021; 138:562-573. [PMID: 33620112 DOI: 10.1111/jbg.12530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/17/2020] [Accepted: 12/04/2020] [Indexed: 02/03/2023]
Abstract
Epigenetic modification plays a critical role in establishing and maintaining cell differentiation, embryo development, tumorigenesis and many complex diseases. However, little is known about the epigenetic regulatory mechanisms for milk production in dairy cattle. Here, we conducted an epigenome-wide study, together with gene expression profiles to identify important epigenetic candidate genes related to the milk production traits in dairy cattle. Whole-genome bisulphite sequencing and RNA sequencing were employed to detect differentially methylated genes (DMG) and differentially expressed genes (DEG) in blood samples in dry period and lactation period between two groups of cows with extremely high and low milk production performance. A total of 10,877 and 6,617 differentially methylated regions were identified between the two groups in the two periods, which corresponded to 3,601 and 2,802 DMGs, respectively. Furthermore, 156 DEGs overlap with DMGs in comparison of the two groups, and 131 DEGs overlap with DMGs in comparison of the two periods. By integrating methylome, transcriptome and GWAS data, some potential candidate genes for milk production traits in dairy cattle were suggested, such as DOCK1, PTK2 and PIK3R1. Our studies may contribute to a better understanding of epigenetic modification on milk production traits of dairy cattle.
Collapse
Affiliation(s)
- Wanting Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenwen Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Li Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
24
|
Cui X, Zhang S, Zhang Q, Guo X, Wu C, Yao M, Sun D. Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages. Front Genet 2020; 11:548268. [PMID: 33343617 PMCID: PMC7744623 DOI: 10.3389/fgene.2020.548268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/05/2020] [Indexed: 12/27/2022] Open
Abstract
A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3'UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.
Collapse
Affiliation(s)
- Xiaogang Cui
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Key Lab of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangyu Guo
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Changxin Wu
- Key Lab of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Mingze Yao
- Key Lab of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
25
|
Wu X, Zhou X, Xiong L, Pei J, Yao X, Liang C, Bao P, Chu M, Guo X, Yan P. Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period. Front Cell Dev Biol 2020; 8:579708. [PMID: 33324637 PMCID: PMC7723986 DOI: 10.3389/fcell.2020.579708] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
The mammary gland is a remarkably dynamic organ of milk synthesis and secretion, and it experiences drastic structural and metabolic changes during the transition from dry periods to lactation, which involves the expression and regulation of numerous genes and regulatory factors. Long non-coding RNA (lncRNA) has considered as a novel type of regulatory factors involved in a variety of biological processes. However, their role in the lactation cycle of yak is still poorly understood. To reveal the involved mechanism, Ribo-zero RNA sequencing was employed to profile the lncRNA transcriptome in mammary tissue samples from yak at two physiological stages, namely lactation (LP) and dry period (DP). Notably, 1,599 lncRNA transcripts were identified through four rigorous steps and filtered through protein-coding ability. A total of 59 lncRNAs showed significantly different expression between two stages. Accordingly, the results of qRT-PCR were consistent with that of the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that target genes of differentially expressed lncRNAs (DELs) were involved in pathways related to lactation, such as ECM-receptor interaction, PI3K-Akt signaling pathway, biosynthesis of amino acids and focal adhesion etc. Finally, we constructed a lncRNA-gene regulatory network containing some well known candidate genes for milk yield and quality traits. This is the first study to demonstrate a global profile of lncRNA expression in the mammary gland of yak. These results contribute to a valuable resource for future genetic and molecular studies on improving milk yield and quality, and help us to gain a better understanding of the molecular mechanisms underlying lactogenesis and mammary gland development of yak.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Xian Guo
- Key Lab of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Lab of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|
26
|
Xin J, Chai Z, Zhang C, Zhang Q, Zhu Y, Cao H, Yangji C, Chen X, Jiang H, Zhong J, Ji Q. Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production. BMC Genomics 2020; 21:731. [PMID: 33081725 PMCID: PMC7576800 DOI: 10.1186/s12864-020-07151-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptations to high-altitude environment, including strong blood oxygen transportation capabilities and high metabolism. The roles of DNA methylation and gene expression in milk production and high-altitudes adaptation need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle tissues from yaks of different ages. We identified 432,350 differentially methylated regions (DMRs) across the age groups within each tissue. The post-mature breast tissue had considerably more differentially methylated regions (155,957) than that from the three younger age groups. Hypomethylated genes with high expression levels might regulate milk production by influencing protein processing in the endoplasmic reticulum. According to weighted gene correlation network analysis, the “hub” gene ZGPAT was highly expressed in the post-mature breast tissue, indicating that it potentially regulates the transcription of 280 genes that influence protein synthesis, processing, and secretion. The tissue network analysis indicated that high expression of HIF1A regulates energy metabolism in the lung. Conclusions This study provides a basis for understanding the epigenetic mechanisms underlying milk production in yaks, and the results offer insight to breeding programs aimed at improving milk production. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07151-3.
Collapse
Affiliation(s)
- Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Cidan Yangji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Xiaoying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China.
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China. .,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China.
| |
Collapse
|
27
|
Huang J, Feng X, Zhu R, Guo D, Wei Y, Cao X, Ma Y, Shi D. Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo. BMC Genomics 2020; 21:710. [PMID: 33045988 PMCID: PMC7552535 DOI: 10.1186/s12864-020-07120-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition. RESULTS To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the longissimus dorsi muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 (PCK1) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the PCK1 promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of PCK1 in buffalo promoter is higher than that in cattle. CONCLUSIONS These results indicate the important role of PCK1 in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive PCK1 expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.
Collapse
Affiliation(s)
- Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China. .,College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.,School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| |
Collapse
|
28
|
Quercetin Improving Lipid Metabolism by Regulating Lipid Metabolism Pathway of Ileum Mucosa in Broilers. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8686248. [PMID: 33014279 PMCID: PMC7520004 DOI: 10.1155/2020/8686248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 02/06/2023]
Abstract
This study is aimed at evaluating the regulatory mechanism of quercetin on lipid metabolism in the ileum of broilers to better understand these pathways decreasing abdominal fat. 480 chickens were randomly divided into 4 groups (control, 0.02% quercetin, 0.04% quercetin, and 0.06% quercetin). Breast muscle, thigh muscle, and abdominal fat pad were removed and weighed at 42 d of age. Serum was obtained by centrifuging blood samples from the jugular vein (10 ml) to determine high-density lipoprotein (HDL), total cholesterol (TC), low-density lipoprotein (LDL), triglyceride (TG), leptin, and adiponectin using ELISA. About 5 g of the ileum was harvested and immediately frozen in liquid nitrogen for RNA-seq. Then, the confirmation of RNA-seq results by the Real-Time Quantitative PCR (RT-qPCR) method was evaluated using Pearson's correlation. Compared with control, abdominal fat percentage was significantly decreased with increasing quercetin supplementation, and the best result was obtained at 0.06% dietary quercetin supplementation (P < 0.01). Breast muscle percentage was significantly decreased at 0.02% quercetin (P < 0.01), and thigh muscle percentage tended to increase (P = 0.078). Meanwhile, 0.04% and 0.06% quercetin significantly decreased TG (P < 0.01), TC (P < 0.01), and LDL content (P < 0.05) in serum. Serum leptin and adiponectin contents were significantly increased by 0.04% and 0.06% dietary quercetin supplementation, compared with the control (P < 0.01). Analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to identify differently expressed genes and lipid metabolism pathways. Quercetin decreased abdominal fat percentage through regulating fat digestion and absorption, glycerophospholipid metabolism, AMPK signaling pathway, fatty acid degradation, and cholesterol metabolism.
Collapse
|
29
|
Devani K, Plastow G, Orsel K, Valente TS. Genome-wide association study for mammary structure in Canadian Angus cows. PLoS One 2020; 15:e0237818. [PMID: 32853245 PMCID: PMC7451565 DOI: 10.1371/journal.pone.0237818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022] Open
Abstract
Functional and enduring mammary structure is pivotal for producer profitability, and animal health and welfare in beef production. Genetic evaluations for teat and udder score in Canadian Angus cattle have previously been developed. The aim of this study was to identify genomic regions associated with teat and udder structure in Canadian Angus cows thereby enhancing knowledge of the biological architecture of these traits. Thus, we performed a weighted single-step genome wide association study (WssGWAS) to identify candidate genes for teat and udder score in 1,582 Canadian Angus cows typed with the GeneSeek® Genomic Profiler Bovine 130K SNP array. Genomically enhanced estimated breeding values (GEBVs) were converted to SNP marker effects using unequal variances for markers to calculate weights for each SNP over three iterations. At the genome wide level, we detected windows of 20 consecutive SNPs that explained more than 0.5% of the variance observed in these traits. A total of 35 and 28 windows were identified for teat and udder score, respectively, with two SNP windows in common for both traits. Using Ensembl, the SNP windows were used to search for candidate genes and quantitative trait loci (QTL). A total of 94 and 71 characterized genes were identified in the regions for teat and udder score, respectively. Of these, 7 genes were common for both traits. Gene network and enrichment analysis, using Ingenuity Pathway Analysis (IPA), signified key pathways unique to each trait. Genes of interest were associated with immune response and wound healing, adipose tissue development and morphology, and epithelial and vascular development and morphology. Genetic architecture from this GWAS confirms that teat and udder score are distinct, polygenic traits involving varying and complex biological pathways, and that genetic selection for improved teat and udder score is possible.
Collapse
Affiliation(s)
- Kajal Devani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tiago S. Valente
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
| |
Collapse
|
30
|
Li Q, Liang R, Li Y, Gao Y, Li Q, Sun D, Li J. Identification of candidate genes for milk production traits by RNA sequencing on bovine liver at different lactation stages. BMC Genet 2020; 21:72. [PMID: 32646377 PMCID: PMC7346489 DOI: 10.1186/s12863-020-00882-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 07/01/2020] [Indexed: 11/23/2022] Open
Abstract
Background RNA-sequencing was performed to explore the bovine liver transcriptomes of Holstein cows to detect potential functional genes related to lactation and milk composition traits in dairy cattle. The bovine transcriptomes of the nine liver samples from three Holstein cows during dry period (50-d prepartum), early lactation (10-d postpartum), and peak of lactation (60-d postpartum) were sequenced using the Illumina HiSeq 2500 platform. Results A total of 204, 147 and 81 differentially expressed genes (DEGs, p < 0.05, false discovery rate q < 0.05) were detected in early lactation vs. dry period, peak of lactation vs. dry period, and peak of lactation vs. early lactation comparison groups, respectively. Gene ontology and KEGG pathway analysis showed that these DEGs were significantly enriched in specific biological processes related to metabolic and biosynthetic and signaling pathways of PPAR, AMPK and p53 (p < 0.05). Ten genes were identified as promising candidates affecting milk yield, milk protein and fat traits in dairy cattle by using an integrated analysis of differential gene expression, previously reported quantitative trait loci (QTL), data from genome-wide association studies (GWAS), and biological function information. These genes were APOC2, PPP1R3B, PKLR, ODC1, DUSP1, LMNA, GALE, ANGPTL4, LPIN1 and CDKN1A. Conclusion This study explored the complexity of the liver transcriptome across three lactation periods in dairy cattle by performing RNA sequencing. Integrated analysis of DEGs and reported QTL and GWAS data allowed us to find ten key candidate genes influencing milk production traits.
Collapse
Affiliation(s)
- Qian Li
- College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street, Baoding, 071001, China.,Hebei Animal Husbandry and Veterinary Institute, Baoding, 071000, China
| | - Ruobing Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yan Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Yanxia Gao
- College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street, Baoding, 071001, China
| | - Qiufeng Li
- College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street, Baoding, 071001, China
| | - Dongxiao Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Jianguo Li
- College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street, Baoding, 071001, China.
| |
Collapse
|
31
|
Khan MZ, Khan A, Xiao J, Dou J, Liu L, Yu Y. Overview of Folic Acid Supplementation Alone or in Combination with Vitamin B12 in Dairy Cattle during Periparturient Period. Metabolites 2020; 10:metabo10060263. [PMID: 32630405 PMCID: PMC7344520 DOI: 10.3390/metabo10060263] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/19/2022] Open
Abstract
The periparturient period is the period from three weeks before calving to three weeks post-calving. This period is important in terms of health, productivity and profitability, and is fundamental to successful lactation. During this period, the animal experiences stress because of hormonal changes due to pregnancy and the significant rise in milk production. In addition, a negative energy balance usually occurs, because the demand for nutrients to sustain milk production increases by more than the nutrient supply during the periparturient period. The immunity of dairy cattle is suppressed around parturition, which increases their susceptibility to infections. Special care regarding nutrition can reduce the risks of metabolism and immunity depression, which dairy cattle face during the periparturient span. Folic acid is relevant in this regard because of its critical role in the metabolism to maintain lactational performance and to improve health. Being a donor of one-carbon units, folic acid has a vital role in DNA and RNA biosynthesis. Generally, the folic acid requirements of dairy cattle can be met by the microbial synthesis in the rumen; however, in special cases, such as during the periparturient period, the requirement for this vitamin strictly increases. Vitamin B12 also has a critical role in the metabolism as a coenzyme of the enzyme methionine synthase for the transfer of a methyl group from folic acid to homocysteine for the regeneration of methionine. In the current review, we highlight the issues facing periparturient dairy cattle, and relevant knowledge and practices, and point out future research directions for utilization of the associated vitamins in ruminants, especially during the periparturient period.
Collapse
Affiliation(s)
- Muhammad Zahoor Khan
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (A.K.); (J.D.); (L.L.)
| | - Adnan Khan
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (A.K.); (J.D.); (L.L.)
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research, Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Jinhuan Dou
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (A.K.); (J.D.); (L.L.)
| | - Lei Liu
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (A.K.); (J.D.); (L.L.)
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.Z.K.); (A.K.); (J.D.); (L.L.)
- Correspondence: ; Tel.: +86-10-627324611
| |
Collapse
|
32
|
Golan Y, Assaraf YG. Genetic and Physiological Factors Affecting Human Milk Production and Composition. Nutrients 2020; 12:E1500. [PMID: 32455695 PMCID: PMC7284811 DOI: 10.3390/nu12051500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Human milk is considered the optimal nutrition for infants as it provides additional attributes other than nutritional support for the infant and contributes to the mother's health as well. Although breastfeeding is the most natural modality to feed infants, nowadays, many mothers complain about breastfeeding difficulties. In addition to environmental factors that may influence lactation outcomes including maternal nutrition status, partner's support, stress, and latching ability of the infant, intrinsic factors such as maternal genetics may also affect the quantitative production and qualitative content of human milk. These genetic factors, which may largely affect the infant's growth and development, as well as the mother's breastfeeding experience, are the subject of the present review. We specifically describe genetic variations that were shown to affect quantitative human milk supply and/or its qualitative content. We further discuss possible implications and methods for diagnosis as well as treatment modalities. Although cases of nutrient-deficient human milk are considered rare, in some ethnic groups, genetic variations that affect human milk content are more abundant, and they should receive greater attention for diagnosis and treatment when necessary. From a future perspective, early genetic diagnosis should be directed to target and treat breastfeeding difficulties in real time.
Collapse
Affiliation(s)
| | - Yehuda G. Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel;
| |
Collapse
|
33
|
Wang J, Zhou H, Hickford JGH, Hao Z, Shen J, Luo Y, Hu J, Liu X, Li S. Comparison of the Transcriptome of the Ovine Mammary Gland in Lactating and Non-lactating Small-Tailed Han Sheep. Front Genet 2020; 11:472. [PMID: 32508880 PMCID: PMC7253648 DOI: 10.3389/fgene.2020.00472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Small-Tailed Han (STH) sheep are known for their high fecundity, but the survival of lambs is compromised and influences the commercial return from farming these sheep, with this being attributed in part to starvation from insufficient milk production by the ewes. In this study, the transcriptome profiles of the mammary gland of lactating and non-lactating STH ewes were investigated using paired-end RNA sequencing (RNA-Seq). An average of 14,447 genes were found to be expressed at peak-lactation in the STH sheep, while 15,146 genes were expressed in non-lactating ewes. A total of 4,003 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the DEGs were associated with a wide range of cellular components, biological processes and metabolic pathways, including binding activities, signaling pathways, cellular structures, and immune responses. The most highly expressed genes at peak-lactation included CSN2, LGB, LALBA, CSN1S1, CSN1S2, and CSN3, and the 10 most highly expressed genes accounted for 61.37% of the total Reads Per Kilobase of transcript, per Million mapped reads (RPKM). The most highly expressed genes in the mammary gland of non-lactating ewes included IgG, THYMB4X, EEF1A1, IgA, and APOE, and the 10 most highly expressed genes accounted for only 12.97% of the total gene RPKM values. This suggests that the sheep mammary gland undergoes a substantial development in milk protein synthesis infrastructure and promotion of protein transportation during lactation.
Collapse
Affiliation(s)
- Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Jon G H Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiyuan Shen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
34
|
Khan MZ, Liu L, Zhang Z, Khan A, Wang D, Mi S, Usman T, Liu G, Guo G, Li X, Wang Y, Yu Y. Folic acid supplementation regulates milk production variables, metabolic associated genes and pathways in perinatal Holsteins. J Anim Physiol Anim Nutr (Berl) 2020; 104:483-492. [PMID: 31994802 DOI: 10.1111/jpn.13313] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 02/01/2023]
Abstract
Perinatal period is the critical time in dairy cattle due to negative energy balance and high milk production stress. Being a key role in biosynthesis and methylation cycle, folic acid is considered essential for lactational and metabolic performance in dairy cattle. Thus, the current study was designed to evaluate the effect of folic acid supplementation on milk production phenotypic traits in periparturient cows. Transcriptomic screening was performed for milk production and metabolism-associated differentially expressed genes. The 123 cows having similar parity, weight and expected date of calving were randomly selected and divided into three groups; A (n = 41, folic acid 240 mg/500 kg cow/day), B (n = 40, FA 120 mg/500 kg cow/day) and C (Control, n = 42). Folic acid was supplemented for 21 days (14 days pre- and seven days post-calving), and three samples of blood lymphocytes were taken on day seven post-calving from each folic acid-treated and control group. In addition, the milk samples for each folic acid-treated group have been collected at 2nd, 3rd and 4th month of lactation. The increase in average milk yield noticed in group B were significantly (p-value < .05) higher than C and A. However, the data showed no noteworthy differences for milk fat and milk protein among the three groups. The transcriptomic analysis revealed that folic acid treatment regulated many key metabolic-related genes (DGAT2, ALOX5, LAP3, GPAT3, GGH, ALDOA, TKT) and pathways (glycolysis, folate biosynthesis, glutathione metabolism, etc.) in periparturient dairy cattle. It was concluded from the above findings that 120 mg/500 kg of folic acid quantity could be considered as a standard during the periparturient period to enhance the milk production performance of dairy cows. The transcriptomic profile revealed several metabolic and milk production-associated genes which could be a useful addition to the marker selection for the enhancement of metabolism and milk production of periparturient dairy cows.
Collapse
Affiliation(s)
- Muhammad Zahoor Khan
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Liu
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhichao Zhang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Adnan Khan
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Di Wang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Siyuan Mi
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tahir Usman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, Pakistan
| | - Gang Liu
- Hebei Shoulon Modern Agricultural Science and Technology Co. Ltd, Dingzhou, China
| | - Gang Guo
- Hebei Shoulon Modern Agricultural Science and Technology Co. Ltd, Dingzhou, China
| | - Xizhi Li
- Capital Agribusiness Group, Beijing Sanyuan Breeding Technology Co. Ltd, Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
35
|
Song S, Jiang M, Zhou J, Zhao F, Hou X, Lin Y. Nutrigenomic Role of Acetate and β-Hydroxybutyrate in Bovine Mammary Epithelial Cells. DNA Cell Biol 2020; 39:389-397. [PMID: 31905020 DOI: 10.1089/dna.2019.4783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Acetate and β-hydroxybutyrate (BHBA) are the predominant substrates for de novo fatty acid (FA) synthesis in mammary gland of dairy cow. To investigate the nutrigenomic role of acetate and BHBA in bovine mammary epithelial cells during milk fat production, RNA sequencing (RNA-seq) transcriptomic analysis was used to identify differentially expressed genes (DEGs) between acetate- and BHBA-treated cells (high-milk fat cells) and control cells. A total of 625 DEGs (358 upregulated and 267 downregulated) were identified between the high-milk fat cells and control cells. Gene ontology enrichment analysis revealed that the upregulated genes in high-milk fat cells were mainly involved in lipid biosynthetic process, steroid biosynthetic process, oxidation-reduction process, receptor binding, and vesicle and small molecule biosynthetic process. The downregulated genes were mainly associated with immune response, cytokine production, negative regulation of biological process, and peptidyl-threonine modification. Pathway analysis indicated that FA metabolism and steroid biosynthesis were significantly enriched for the upregulated genes in the high-milk fat cells, while apoptosis was enriched for the downregulated genes. This work provides a profile of gene expression changes that occur during acetate- and BHBA-induced milk fat synthesis in bovine mammary epithelial cells, which furthers our understanding of the molecular regulation of lipid metabolism.
Collapse
Affiliation(s)
- Shuyuan Song
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin, China
| | - Minghui Jiang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin, China
| | - Jinyu Zhou
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Feng Zhao
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Xiaoming Hou
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin, China
| | - Ye Lin
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| |
Collapse
|
36
|
Chen Z, Chu S, Liang Y, Xu T, Sun Y, Li M, Zhang H, Wang X, Mao Y, Loor JJ, Wu Y, Yang Z. miR-497 regulates fatty acid synthesis via LATS2 in bovine mammary epithelial cells. Food Funct 2020; 11:8625-8636. [DOI: 10.1039/d0fo00952k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Both mRNA and miRNA play an important role in the regulation of mammary fatty acid metabolism and milk fat synthesis.
Collapse
|
37
|
Guo X, Zhang W, Li M, Gao P, Hei W, He Z, Wu Y, Liu J, Cai C, Li B, Cao G. Transcriptome profile of skeletal muscle at different developmental stages in Large White and Mashen pigs. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2019-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
From the perspectives of promoting individual growth and development, increasing pork yield, and improving feed utilization, it is desirable to screen candidate genes underlying pig muscle growth and regulation. In this study, we investigated transcriptome differences at 1, 90, and 180 d of age in Large White and Mashen pigs, characterized differentially expressed genes (DEGs), and screened candidate genes affecting skeletal muscle growth and development. RNA-seq was applied to analyze the transcriptome of the longissimus dorsi (LD) in the two breeds. In LD samples from the two breeds at three growth stages, 7215, 6332, 237, 3935, 3404, and 846 DEGs were obtained for L01 vs. L90, L01 vs. L180, L90 vs. L180, MS01 vs. MS90, MS01 vs. MS180, and MS90 vs. MS180, respectively. Significant tendencies in DEG expression could be grouped into eight profiles. Based on the functional analysis of DEGs, 16 candidate genes related to skeletal muscle growth and development were identified, including PCK2, GNAS, ADCY2, PRKAB1, PRKAB2, PRKAG1, PRKAG2, PHKA1, PHKA2, PHKG1, PHKG2, ITPR3, IGF1R, FGFR4, FGF1, and FGF18. The results of this study thus provide a theoretical basis for the mechanisms and candidate genes underlying skeletal muscle development in pigs.
Collapse
Affiliation(s)
- Xiaohong Guo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Wanfeng Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Meng Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Pengfei Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Wei Hei
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Zhiqiang He
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Yiqi Wu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Juan Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Chunbo Cai
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Bugao Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Guoqing Cao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| |
Collapse
|
38
|
Wood kraft pulp supplementation alters the rumen fermentation characteristics and epithelial transcriptomes in Holstein cattle during the high-grain diet challenge. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2019.114292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
39
|
Transcriptome Profile Analysis of Mammary Gland Tissue from Two Breeds of Lactating Sheep. Genes (Basel) 2019; 10:genes10100781. [PMID: 31597369 PMCID: PMC6826511 DOI: 10.3390/genes10100781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 12/16/2022] Open
Abstract
The mammary gland is a crucial tissue for milk synthesis and plays a critical role in the feeding and growth of mammalian offspring. The aim of this study was to use RNA-sequencing (RNA-Seq) technology to provide a transcriptome profile of the ovine mammary gland at the peak of lactation. Small-Tailed Han (STH) sheep (n = 9) and Gansu Alpine Merino (GAM) sheep (n = 9), breeds with phenotypic differences in milk production traits, were selected for the RNA-Seq analysis. This revealed 74 genes that were more highly expressed in the STHs than in the GAMs. Similarly, 143 genes that were expressed at lower levels in the STHs than in the GAMs, were identified. Gene ontogeny (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these differentially expressed genes (DEGs) were associated with binding and catalytic activities, hematopoietic cell lineages, oxytocin signaling pathway and neuroactive ligand–receptor interaction. This is the first study of the transcriptome profile of the ovine mammary gland in these Chinese breeds at peak lactation. The results provide for a better understanding of the genetic mechanisms involved in ovine lactation.
Collapse
|
40
|
Xu L, Shi L, Liu L, Liang R, Li Q, Li J, Han B, Sun D. Analysis of Liver Proteome and Identification of Critical Proteins Affecting Milk Fat, Protein, and Lactose Metabolism in Dariy Cattle with iTRAQ. Proteomics 2019; 19:e1800387. [DOI: 10.1002/pmic.201800387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/12/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Lingna Xu
- Department of Animal GeneticsBreeding 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 University Beijing 100193 China
| | - Lijun Shi
- Department of Animal GeneticsBreeding 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 University Beijing 100193 China
| | - Lin Liu
- Beijing Dairy Cattle Center Beijing 100192 China
| | - Ruobing Liang
- Department of Animal GeneticsBreeding 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 University Beijing 100193 China
| | - Qian Li
- Department of Animal Production and Environmental ControlCollege of Animal Science and TechnologyHebei Agricultural University Baoding 071001 China
| | - Jianguo Li
- Department of Animal Production and Environmental ControlCollege of Animal Science and TechnologyHebei Agricultural University Baoding 071001 China
| | - Bo Han
- Department of Animal GeneticsBreeding 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 University Beijing 100193 China
| | - Dongxiao Sun
- Department of Animal GeneticsBreeding 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 University Beijing 100193 China
| |
Collapse
|
41
|
Sun HZ, Plastow G, Guan LL. Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health. J Dairy Sci 2019; 102:5853-5870. [PMID: 31030919 DOI: 10.3168/jds.2018-16126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.
Collapse
Affiliation(s)
- H Z Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - G Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5.
| |
Collapse
|
42
|
Protective Effect of Ginsenoside Rg1 on Oxidative Damage Induced by Hydrogen Peroxide in Chicken Splenic Lymphocytes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8465030. [PMID: 31178974 PMCID: PMC6501224 DOI: 10.1155/2019/8465030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
Previous investigation showed that ginsenoside Rg1 (Rg1) extracted from Panax ginseng C.A. Mey has antioxidative effect on oxidative stress in chickens. The present study was designed to investigate the protective effects of Rg1 on chicken lymphocytes against hydrogen peroxide-induced oxidative stress and the potential mechanisms. Cell viability, apoptotic cells, malondialdehyde, activity of superoxide dismutase, mitochondrial membrane potential, and [Ca2+]i concentration were measured, and transcriptome analysis and quantitative real-time polymerase chain reaction were used to investigate the effect of Rg1 on gene expression of the cells. The results showed that treatment of lymphocytes with H2O2 induced oxidative stress and apoptosis. However, pretreatment of the cells with Rg1 dramatically enhanced cell viability, reduced apoptotic cells, and decreased oxidative stress induced by H2O2. In addition, Rg1 reduced these H2O2-dependent decreases in mitochondrial membrane potential and reversed [Ca2+]i overload. Transcriptome analysis showed that 323 genes were downregulated and 105 genes were upregulated in Rg1-treated cells. The differentially expressed genes were involved in Toll-like receptors, peroxisome proliferator-activated receptor signaling pathway, and cytokine-cytokine receptor interaction. The present study indicated that Rg1 may act as an antioxidative agent to protect cell damage caused by oxidative stress via regulating expression of genes such as RELT, EDA2R, and TLR4.
Collapse
|
43
|
Pokharel K, Weldenegodguad M, Popov R, Honkatukia M, Huuki H, Lindeberg H, Peippo J, Reilas T, Zarovnyaev S, Kantanen J. Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions. Anim Genet 2019; 50:217-227. [PMID: 30957254 PMCID: PMC6593690 DOI: 10.1111/age.12783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 12/17/2022]
Abstract
Indigenous cattle breeds in northern Eurasia have adapted to harsh climate conditions. The local breeds are important genetic resources with cultural and historical heritages, and therefore, their preservation and genetic characterization are important. In this study, we profiled the whole‐blood transcriptome of two native breeds (Northern Finncattle and Yakutian cattle) and one commercial breed (Holstein) using high‐throughput RNA sequencing. More than 15 000 genes were identified, of which two, 89 and 162 genes were significantly upregulated exclusively in Northern Finncattle, Yakutian cattle and Holstein cattle respectively. The functional classification of these significantly differentially expressed genes identified several biological processes and pathways related to signalling mechanisms, cell differentiation and host–pathogen interactions that, in general, point towards immunity and disease resistance mechanisms. The gene expression pattern observed in Northern Finncattle was more similar to that of Yakutian cattle, despite sharing similar living conditions with the Holstein cattle included in our study. In conclusion, our study identified unique biological processes in these breeds that may have helped them to adapt and survive in northern and sub‐arctic environments.
Collapse
Affiliation(s)
- K Pokharel
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - M Weldenegodguad
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, Kuopio, FI-70311, Finland
| | - R Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), ul. Bestyzhevo-Marlinskogo 23/1, Yakutsk, 67001, The Sakha Republic (Yakutia), Russia
| | - M Honkatukia
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland.,The Nordic Genetic Resources Center (Nordgen), P.O. Box 115, Ås, NO-1431, Norway
| | - H Huuki
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - H Lindeberg
- Production Systems, Natural Resources Institute Finland (Luke), Halolantie 31A, Maaninka, FI-71750, Finland
| | - J Peippo
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - T Reilas
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - S Zarovnyaev
- GBU Saha Agroplem, ul. Ordzhonkidze 20/204, Yakutsk, 67700, The Sakha Republic (Yakutia), Russia
| | - J Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| |
Collapse
|
44
|
Pareek CS, Sachajko M, Jaskowski JM, Herudzinska M, Skowronski M, Domagalski K, Szczepanek J, Czarnik U, Sobiech P, Wysocka D, Pierzchala M, Polawska E, Stepanow K, Ogłuszka M, Juszczuk-Kubiak E, Feng Y, Kumar D. Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq. Vet Sci 2019; 6:vetsci6020036. [PMID: 30934933 PMCID: PMC6631511 DOI: 10.3390/vetsci6020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/16/2019] [Accepted: 03/26/2019] [Indexed: 12/26/2022] Open
Abstract
Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.
Collapse
Affiliation(s)
- Chandra Shekhar Pareek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Mateusz Sachajko
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Jedrzej M Jaskowski
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Magdalena Herudzinska
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Mariusz Skowronski
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Krzysztof Domagalski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Urszula Czarnik
- Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
| | - Przymeslaw Sobiech
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland.
| | - Dominika Wysocka
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland.
| | - Mariusz Pierzchala
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Ewa Polawska
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Kamila Stepanow
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Magdalena Ogłuszka
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Edyta Juszczuk-Kubiak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland.
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08 854, USA.
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08 854, USA.
| |
Collapse
|
45
|
Morenikeji OB, Akinyemi MO, Wheto M, Ogunshola OJ, Badejo AA, Chineke CA. Transcriptome profiling of four candidate milk genes in milk and tissue samples of temperate and tropical cattle. J Genet 2019. [DOI: 10.1007/s12041-019-1060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
46
|
Das PP, Krishnan G, Doley J, Bhattacharya D, Deb SM, Chakravarty P, Das PJ. Establishing gene Amelogenin as sex-specific marker in yak by genomic approach. J Genet 2019; 98:7. [PMID: 30945688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker. Thus, an attempt was made to use the gene as an advanced molecular marker of sexing of the yak to improve breeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. The test is further refined with qPCR validation by quantifying the DNA copy number of the Amelogenin gene in male and female. We observed a high level of sequence polymorphisms of AMELX and AMELY in yak considered as novel identification. These tests can be further extended into several other specialized fields including forensics, meat production and processing, and quality control.
Collapse
Affiliation(s)
- P P Das
- Indian Council of Agricultural Research-National Research Centre on Yak, Dirang 790 101, India. ,
| | | | | | | | | | | | | |
Collapse
|
47
|
Li Y, Han B, Liu L, Zhao F, Liang W, Jiang J, Yang Y, Ma Z, Sun D. Genetic association of DDIT3, RPL23A, SESN2 and NR4A1 genes with milk yield and composition in dairy cattle. Anim Genet 2019; 50:123-135. [PMID: 30815908 DOI: 10.1111/age.12750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2018] [Indexed: 01/15/2023]
Abstract
Previously, we identified by RNA sequencing that DDIT3, RPL23A, SESN2 and NR4A1 genes were significantly differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentages; thus, these four genes are considered as promising candidates potentially affecting milk yield and composition traits in dairy cattle. In the present study, we further verified whether these genes have genetic effects on milk traits in a Chinese Holstein population. By re-sequencing part of the non-coding and the entire coding regions of the DDIT3, RPL23A, SESN2 and NR4A1 genes, a total of 35 SNPs and three insertions/deletions were identified, of which three were found in DDIT3, 12 in RPL23A, 16 in SESN2 and seven in NR4A1. Moreover, two of the insertions/deletions-g.125714860_125714872del and g.125714806delinsCCCC in SESN2-were novel and have not been reported previously. Subsequent single SNP analyses revealed multiple significant association with all 35 SNPs and three indels regressed against the dairy production traits (P-value = <0.0001-0.0493). In addition, with a linkage disequilibrium analysis, we found one, one, three, and one haplotype blocks in the DDIT3, RPL23A, SESN2 and NR4A1 genes respectively. Haplotype-based association analyses revealed that some haplotypes were also significantly associated with milk production traits (P-value = <0.0001-0.0461). We also found that 12 SNPs and two indels (two in DDIT3, two in RPL23A, nine in SESN2 and one in NR4A1) altered the specific transcription factor binding sites in the promoter, thereby regulating promoter activity, suggesting that they might be promising potential functional variants for milk traits. In summary, our findings first determined the genetic associations of DDIT3, RPL23A, SESN2 and NR4A1 with milk yield and composition traits in dairy cattle and also suggested potentially causal variants, which require in-depth validation.
Collapse
Affiliation(s)
- Y Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China.,Beijing Dairy Cattle Center, Beijing, 100192, China
| | - B Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| | - L Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - F Zhao
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - W Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| | - J Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| | - Y Yang
- Beijing Municipal Bureau of Agriculture, Beijing, 100101, China
| | - Z Ma
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - D Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| |
Collapse
|
48
|
Bhat SA, Ahmad SM, Ibeagha-Awemu EM, Bhat BA, Dar MA, Mumtaz PT, Shah RA, Ganai NA. Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle. PLoS One 2019; 14:e0211773. [PMID: 30721247 PMCID: PMC6363229 DOI: 10.1371/journal.pone.0211773] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
Jersey and Kashmiri cattle are important dairy breeds that contribute significantly to the total milk production of the Indian northern state of Jammu and Kashmir. The Kashmiri cattle germplasm has been extensively diluted through crossbreeding with Jersey cattle with the goal of enhancing its milk production ability. However, crossbred animals are prone to diseases resulting to unsustainable milk production. This study aimed to provide a comprehensive transcriptome profile of mammary gland epithelial cells at different stages of lactation and to find key differences in genes and pathways regulating milk traits between Jersey and Kashmiri cattle. Mammary epithelial cells (MEC) isolated from milk obtained from six lactating cows (three Jersey and three Kashmiri cattle) on day 15 (D15), D90 and D250 in milk, representing early, mid and late lactation, respectively were used. RNA isolated from MEC was subjected to next-generation RNA sequencing and bioinformatics processing. Casein and whey protein genes were found to be highly expressed throughout the lactation stages in both breeds. Largest differences in differentially expressed genes (DEG) were between D15 vs D90 (1,805 genes) in Kashmiri cattle and, D15 vs D250 (3,392 genes) in Jersey cattle. A total of 1,103, 1,356 and 1,397 genes were differentially expressed between Kashmiri and Jersey cattle on D15, D90 and D250, respectively. Antioxidant genes like RPLPO and RPS28 were highly expressed in Kashmiri cattle. Differentially expressed genes in both Kashmiri and Jersey were enriched for multicellular organismal process, receptor activity, catalytic activity, signal transducer activity, macromolecular complex and developmental process gene ontology terms. Whereas, biological regulation, endopeptidase activity and response to stimulus were enriched in Kashmiri cattle and, reproduction and immune system process were enriched in Jersey cattle. Most of the pathways responsible for regulation of milk production like JAK-STAT, p38 MAPK pathway, PI3 kinase pathway were enriched by DEG in Jersey cattle only. Although Kashmiri has poor milk production efficiency, the present study suggests possible physicochemical and antioxidant properties of Kashmiri cattle milk that needs to be further explored.
Collapse
Affiliation(s)
- Shakil Ahmad Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, India
- * E-mail:
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Basharat A. Bhat
- Department of Life Science, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, India
| | - Peerzada Tajamul Mumtaz
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, India
| | - Riaz A. Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, India
| | - Nazir A. Ganai
- Division of Animal Genetics and Breeding, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, India
| |
Collapse
|
49
|
Deng T, Liang A, Liang S, Ma X, Lu X, Duan A, Pang C, Hua G, Liu S, Campanile G, Salzano A, Gasparrini B, Neglia G, Liang X, Yang L. Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo. Front Genet 2019; 10:36. [PMID: 30804981 PMCID: PMC6371051 DOI: 10.3389/fgene.2019.00036] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/18/2019] [Indexed: 01/05/2023] Open
Abstract
The mammary gland is the production organ in mammals that is of great importance for milk production and quality. However, characterization of the buffalo mammary gland transcriptome and identification of the valuable candidate genes that affect milk production is limited. Here, we performed the differential expressed genes (DEGs) analysis of mammary gland tissue on day 7, 50, 140, and 280 after calving and conducted gene-based genome-wide association studies (GWAS) of milk yield in 935 Mediterranean buffaloes. We then employed weighted gene co-expression network analysis (WGCNA) to identify specific modules and hub genes related to milk yield based on gene expression profiles and GWAS data. The results of the DEGs analysis showed that a total of 1,420 DEGs were detected across different lactation points. In the gene-based analysis, 976 genes were found to have genome-wide association (P ≤ 0.05) that could be defined as the nominally significant GWAS geneset (NSGG), 9 of which were suggestively associated with milk yield (P < 10−4). Using the WGCNA analysis, 544 and 225 genes associated with milk yield in the turquoise module were identified from DEGs and NSGG datasets, respectively. Several genes (including BNIPL, TUBA1C, C2CD4B, DCP1B, MAP3K5, PDCD11, SRGAP1, GDPD5, BARX2, SCARA3, CTU2, and RPL27A) were identified and considered as the hub genes because they were involved in multiple pathways related to milk production. Our findings provide an insight into the dynamic characterization of the buffalo mammary gland transcriptome, and these potential candidate genes may be valuable for future functional characterization of the buffalo mammary gland.
Collapse
Affiliation(s)
- Tingxian Deng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Aixin Liang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shasha Liang
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Xiaoya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Xingrong Lu
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Anqin Duan
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chunying Pang
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shenhe Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Angela Salzano
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Bianca Gasparrini
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Gianluca Neglia
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Xianwei Liang
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
50
|
Ji Z, Chao T, Zhang C, Liu Z, Hou L, Wang J, Wang A, Wang Y, Zhou J, Xuan R, Wang G, Wang J. Transcriptome Analysis of Dairy Goat Mammary Gland Tissues from Different Lactation Stages. DNA Cell Biol 2019; 38:129-143. [DOI: 10.1089/dna.2018.4349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Chunlan Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Zhaohua Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Aili Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Yong Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jie Zhou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| |
Collapse
|