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Lin C, Wang W, Zhang D, Huang K, Li X, Zhang Y, Zhao Y, Wang J, Zhou B, Cheng J, Xu D, Li W, Zhao L, Ma Z, Yang X, Huang Y, Cui P, Liu J, Zeng X, Zhai R, Sun L, Weng X, Wu W, Zhang X, Zheng W. Polymorphisms in SHISA3 and RFC3 genes and their association with feed conversion ratio in Hu sheep. Front Vet Sci 2023; 9:1010045. [PMID: 36686193 PMCID: PMC9850526 DOI: 10.3389/fvets.2022.1010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
In animal husbandry, feed efficiency is a crucial economic trait. In this study, the general linear model was used to perform association analysis for various genotypes and feed conversion ratio (FCR)-related traits. Reverse transcription-quantitative PCR (RT-qPCR) was used to detect the expression of SHISA3 and RFC3 mRNA levels in 10 tissues from 6 sheep. The results showed that SNPs in the NC_040257.1:c.625 T > C and NC_040261.1:g.9905 T > C were analyzed whether they were associated to feed efficiency parameters in Hu sheep (body weight, feed intake, average daily growth, and feed conversion ratio). NC_040257.1:c.625 T > C was shown to be significantly associated with body weight at 80, 100, and 120 days as well as feed conversion ratio (P < 0.05), whereas NC_040261.1:g.9905 T > C was found to be significantly associated with average daily weight gain from 80-140 days (ADG80-140) and FCR (P < 0.05). In Hu sheep, the CC genotypes of SHISA3 and RFC3 were the most common genotypes related to feed efficiency traits. Furthermore, the feed conversion ratio of the combined genotypes TT SHISA3-CC RFC3, TT SHISA3-CT RFC3, TT SHISA3-TT RFC3, CT SHISA3-CC RFC3 and CT SHISA3-CT RFC3 was significantly better than the FCR of CC SHISA3-TT RFC3. RT-qPCR results showed that the expression levels of SHISA3 were lower in the lung than in spleen, kidney, muscle and lymph (P < 0.05), and RFC3 was the lung had a highly significant higher expression level than the heart, liver, spleen, and muscle (P < 0.01). In conclusion, SHISA3 and RFC3 polymorphisms can be used as genetic markers for improving feed conversion efficiency in Hu sheep.
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Affiliation(s)
- Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, 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
| | - Kai Huang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun 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
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Landi Sun
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China,*Correspondence: Xiaoxue Zhang ✉
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China,Wenxin Zheng ✉
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Addo S, Jung L. An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs. Front Genet 2022; 13:909986. [DOI: 10.3389/fgene.2022.909986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
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Klees S, Heinrich F, Schmitt AO, Gültas M. agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species. Biology (Basel) 2021; 10:790. [PMID: 34440019 DOI: 10.3390/biology10080790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.
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Wang J, Sui J, Mao C, Li X, Chen X, Liang C, Wang X, Wang SH, Jia C. Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats. Genes (Basel) 2021; 12:genes12020180. [PMID: 33513983 PMCID: PMC7911279 DOI: 10.3390/genes12020180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The development of hair follicle in cashmere goats shows significant periodic change, as with mice and humans. However, for cashmere goat with double-coat, the periodic change may be due to other regulatory molecules and signal pathways. To understand the mechanism of periodic development of hair follicle, we performed a weighted gene coexpression network analysis (WGCNA) to mine key genes and establish an interaction network by utilizing the NCBI public dataset. Ten coexpression modules, including 7689 protein-coding genes, were constructed by WGCNA, six of which are considered to be significantly related to the development of the hair follicle cycle. A functional enrichment analysis for each model showed that they are closely related to ECM- receptor interaction, focal adhesion, PI3K-Akt signaling pathway, estrogen signaling pathway, and so on. Combined with the analysis of differential expressed genes, 12 hub genes from coexpression modules were selected as candidate markers, i.e., COL1A1, C1QTNF6, COL1A2, AQP3, KRTAP3-1, KRTAP11-1, FA2H, NDUFS5, DERL2, MRPL14, ANTKMT and XAB2, which might be applied to improve cashmere production.
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Pauletto M, Tolosi R, Dacasto M, Giantin M. Missense single nucleotide variants affecting CYP3A catalytic activity are present in Limousine cattle. Italian Journal of Animal Science 2020. [DOI: 10.1080/1828051x.2020.1808100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Marianna Pauletto
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
| | - Roberta Tolosi
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
| | - Mauro Dacasto
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
| | - Mery Giantin
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
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Xie R, Shi L, Liu J, Deng T, Wang L, Liu Y, Zhao F. Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds. Animals (Basel) 2019; 9:E518. [PMID: 31374971 DOI: 10.3390/ani9080518] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/17/2022] Open
Abstract
Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (FROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (FHOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The FROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between FROH and FHOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection.
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Fonseca LD, Eler JP, Pereira MA, Rosa AF, Alexandre PA, Moncau CT, Salvato F, Rosa-Fernandes L, Palmisano G, Ferraz JBS, Fukumasu H. Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle. Sci Rep 2019; 9:5364. [PMID: 30926873 PMCID: PMC6441086 DOI: 10.1038/s41598-019-41813-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Improving nutrient utilization efficiency is essential for livestock, given the current scenario of increasing demand for animal protein and sustainable resource use. In this context, understanding the biology of feed efficiency (FE) in beef cattle allows the development of markers for identification and selection of best animals for animal production. Thus, 98 young Nellore bulls were evaluated for FE and at the end of the experiment liver samples from six High Feed Efficient (HFE) and six Low Feed Efficient (LFE) animals were collected for protein extraction, digestion and analysis by HPLC-MS/MS. Data were analyzed for differential abundant proteins (DAPs), protein networks, and functional enrichment. Serum endotoxin was also quantified. We found 42 DAPs and 3 protein networks significantly related to FE. The main pathways associated with FE were: microbial metabolism; biosynthesis of fatty acids, amino acids and vitamins; glycolysis/gluconeogenesis; xenobiotic metabolism and; antigen processing and presentation. Serum endotoxins were significantly higher in LFE animals supporting the results. Therefore, the findings presented here confirmed the altered hepatic metabolism and pronounced hepatic inflammation in LFE animals supporting that the increased bacterial load is at least in part responsible for the hepatic lesions and inflammation in LFE animals.
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Affiliation(s)
- Leydiana D Fonseca
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Joanir P Eler
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Mikaele A Pereira
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Alessandra F Rosa
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Pâmela A Alexandre
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Cristina T Moncau
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Fernanda Salvato
- Institute of Biology, State University of Campinas, Campinas, 13083-862, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - José B S Ferraz
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil.
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Higgins MG, Fitzsimons C, McClure MC, McKenna C, Conroy S, Kenny DA, McGee M, Waters SM, Morris DW. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. Sci Rep 2018; 8:14301. [PMID: 30250203 PMCID: PMC6155370 DOI: 10.1038/s41598-018-32374-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
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Affiliation(s)
- Marc G Higgins
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland.,Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Claire Fitzsimons
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.,Department of Agriculture, Fisheries and the Marine, Celbridge, Co. Kildare, Ireland
| | - Matthew C McClure
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland.,ABS-Global, DeForest, WI, USA
| | - Clare McKenna
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Stephen Conroy
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
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Skinkyte-Juskiene R, Kogelman LJ, Kadarmideen HN. Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity. Curr Genomics 2018; 19:289-299. [PMID: 29755291 PMCID: PMC5930450 DOI: 10.2174/1389202918666171005095059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/28/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Transcription Factors (TFs) control actuation of genes in the genome and are key mediators of complex processes such as obesity. Master Regulators (MRs) are the genes at the top of a regulation hierarchy which regulate other genes. OBJECTIVE To elucidate clusters of highly co-expressed TFs (modules), involved pathways, highly inter-connected TFs (hub-TFs) and MRs leading to obesity and leanness, using porcine model for human obesity. METHODS We identified 817 expressed TFs in RNA-Sequencing dataset representing extreme degrees of obesity (DO; lean, obese). We built a single Weighted Transcription Factor Co-expression Network (WTFCN) and TF sub-networks (based on the DO). Hub-TFs and MRs (using iRegulon) were identi-fied in biologically relevant WTFCNs modules. RESULTS Single WTFCN detected the Red module significantly associated with DO (P < 0.03). This module was enriched for regulation processes in the immune system, e.g.: Immune system process (Padj = 2.50E-06) and metabolic lifestyle disorders, e.g. Circadian rhythm - mammal pathway (Padj = 2.33E-11). Detected MR, hub-TF SPI1 was involved in obesity, immunity and osteoporosis. Within the obese sub-network, the Red module suggested possible associations with immunity, e.g. TGF-beta signaling pathway (Padj = 1.73E-02) and osteoporosis, e.g. Osteoclast differentiation (Padj = 1.94E-02). Within the lean sub-network, the Magenta module displayed associations with type 2 diabetes, obesity and os-teoporosis e.g. Notch signaling pathway (Padj = 2.40E-03), osteoporosis e.g. hub-TF VDR (a prime candidate gene for osteoporosis). CONCLUSION Our results provide insights into the regulatory network of TFs and biologically relevant hub TFs in obesity.
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Affiliation(s)
- Ruta Skinkyte-Juskiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg C, Denmark
| | - Lisette J.A. Kogelman
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg C, Denmark
- Danish Headache Center, Department of Neurology, Glostrup Research Institute, Rigshospitalet Glostrup, Nordre Ringvej 69, 2600 Glostrup, Denmark
| | - Haja N. Kadarmideen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg C, Denmark
- Section of Systems Genomics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kgs. Lyngby, Denmark
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Sharma VK, Kundu SS, Datt C, Prusty S, Kumar M, Sontakke UB. Buffalo heifers selected for lower residual feed intake have lower feed intake, better dietary nitrogen utilisation and reduced enteric methane production. J Anim Physiol Anim Nutr (Berl) 2017; 102:e607-e614. [PMID: 29027698 DOI: 10.1111/jpn.12802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 07/16/2017] [Indexed: 02/05/2023]
Abstract
This study was conducted to evaluate the utilisation of the residual feed intake (RFI) as a feed efficiency selection tool and its relationship with methane emissions. Eighteen Murrah buffalo (Bubalus bubalis) heifers were fed ad libitum with total mixed ration (TMR) for 120 days. Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid-test metabolic body size (MBW0.75 ), heifers were assigned into low and high RFI groups. The RFI varied from -0.09 to +0.12 kg DM/day with average RFI of -0.05 and 0.05 kg DM/day in low and high RFI heifers respectively. Low RFI heifers ate 11.6% less DM each day, yet average daily gain (ADG) and feed utilisation were comparable among low and high RFI groups. Low RFI heifers required significantly (p < .05) less metabolizable energy for maintenance (MEm) compared to high RFI heifers. Apparent nutrient digestibility showed non-significant difference (p > .05) among low and high RFI groups. Although the nitrogen balance was similar among heifers of low and high RFI groups, nitrogen metabolism was significantly higher (p > .05) in high RFI heifers. Comparison of data from heifers exhibiting the low (n = 9) and high (n = 9) RFI showed that the low RFI heifers have lower enteric methane production and methane losses than high RFI heifers. In conclusion, results of this study revealed that selection of more efficient buffalo heifers has multiple benefits, such as decreased feed intake and less emission of methane.
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Affiliation(s)
- V K Sharma
- Krishi Vigyan Kendra, Sher-e-Kashmir University of Agricultural Sciences and Technology-Jammu, Kathua, India
| | - S S Kundu
- Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, India
| | - C Datt
- Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, India
| | - S Prusty
- Department of Animal Nutrition, CGKV, Bilaspur, India
| | - M Kumar
- Department of Animal Nutrition, College of Veterinary Science and Animal Husbandry, DUVASU, Mathura, India
| | - U B Sontakke
- Panchayat Samiti Etapalli, Gadchiroli, Maharashtra, India
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Cohen-Zinder M, Asher A, Lipkin E, Feingersch R, Agmon R, Karasik D, Brosh A, Shabtay A. FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves. Physiol Genomics 2016; 48:367-76. [PMID: 26993365 DOI: 10.1152/physiolgenomics.00121.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/09/2016] [Indexed: 01/08/2023] Open
Abstract
Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1-3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 (FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; A<G substitution), in the promoter region of the gene, was significantly associated with all three RFIs. As the three RFI classes reflect changing diets and ages with concomitant RFI phenotypic consistency, the above polymorphisms and in particular FABP4_5, might be considered possible markers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation.
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Affiliation(s)
- Miri Cohen-Zinder
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel;
| | - Aviv Asher
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel; Israeli Center for Interdisciplinary Research in Chronobiology, University of Haifa, Haifa, Israel
| | - Ehud Lipkin
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel; and
| | - Roi Feingersch
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Rotem Agmon
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Arieh Brosh
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ariel Shabtay
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
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Santana M, Oliveira G, Gomes R, Silva S, Leme P, Stella T, Mattos E, Rossi P, Baldi F, Eler J, Ferraz J. Genetic parameter estimates for feed efficiency and dry matter intake and their association with growth and carcass traits in Nellore cattle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sharma VC, Mahesh MS, Mohini M, Datt C, Nampoothiri VM. Nutrient utilisation and methane emissions in Sahiwal calves differing in residual feed intake. Arch Anim Nutr 2014; 68:345-57. [PMID: 25156936 DOI: 10.1080/1745039x.2014.951193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The presented study aimed at investigating the residual feed intake (RFI) of Sahiwal calves, nutrient utilisation as affected by RFI and its relationship with methane (CH4) emissions and some blood metabolites. Eighteen male Sahiwal calves (10-18 months of age; mean body weight 133 kg) were fed ad libitum with a total mixed ration. After calculating RFI for individual calves (-0.40 to +0.34 kg DM/d), they were divided into three groups with low, medium and high RFI, respectively. Dry matter intake (DMI) was higher (p < 0.05) in Group High RFI, whereas digestibility of all nutrients except crude protein and ether extract was significantly higher in Group Low RFI. Nitrogen balance was also significantly higher in Group Low RFI (20.2 g/d) than in Group High RFI (17.0 g/d). Average daily gain and feed conversion ratio were similar among the groups. With exception of glucose, concentrations of all measured blood metabolites were higher in Group High RFI (p < 0.05). Compared with Group High RFI, the CH4 emission of Group Low RFI was significantly lower (on the basis g/d and g/kg DMI by 11% and 19%, respectively). Furthermore, the CH4 emission [g/d] was significantly correlated with RFI (r = 0.77). Because higher feed efficiency and less CH4 production were observed in Group Low RFI, it was concluded that RFI can be used as a measure of feed efficiency, which has a potential to select Sahiwal calves for lowered CH4 emissions.
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Affiliation(s)
- Vimlesh C Sharma
- a Environmental Laboratory, Dairy Cattle Nutrition Division , National Dairy Research Institute (Deemed University) , Karnal , Haryana , India
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