1
|
Teixeira SA, Marques DBD, Costa TC, Oliveira HC, Costa KA, Carrara ER, da Silva W, Guimarães JD, Neves MM, Ibelli AMG, Cantão ME, Ledur MC, Peixoto JO, Guimarães SEF. Transcription Landscape of the Early Developmental Biology in Pigs. Animals (Basel) 2021; 11:ani11051443. [PMID: 34069910 PMCID: PMC8157595 DOI: 10.3390/ani11051443] [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: 04/09/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Since pre- and postnatal development are programmed during early prenatal life, studies addressing the complete transcriptional landscape during organogenesis are needed. Therefore, we aimed to disentangle differentially expressed (DE) genes between fetuses (at 35 days old) and embryos (at 25 days old) through RNA-sequencing analysis using the pig as model. In total, 1705 genes were DE, including the top DE IBSP, COL6A6, HBE1, HBZ, HBB, and NEUROD6 genes, which are associated with developmental transition from embryos to fetuses, such as ossification, skeletal muscle development, extracellular matrix organization, cardiovascular system, erythrocyte differentiation, and neuronal system. In pathway analysis, embryonic development highlighted those mainly related to morphogenic signaling and cell interactions, which are crucial for transcriptional control during the establishment of the main organs in early prenatal development, while pathways related to myogenesis, neuronal development, and cardiac and striated muscle contraction were enriched for fetal development, according to the greater complexity of organs and body structures at this developmental stage. Our findings provide an exploratory and informative transcriptional landscape of pig organogenesis, which might contribute to further studies addressing specific developmental events in pigs and in other mammals.
Collapse
Affiliation(s)
- Susana A. Teixeira
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Daniele B. D. Marques
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Thaís C. Costa
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Haniel C. Oliveira
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Karine A. Costa
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Eula R. Carrara
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - Walmir da Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
| | - José D. Guimarães
- Department of Veterinary Medicine, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil;
| | - Mariana M. Neves
- Department of General Biology, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil;
| | - Adriana M. G. Ibelli
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Maurício E. Cantão
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Mônica C. Ledur
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Jane O. Peixoto
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil; (A.M.G.I.); (M.E.C.); (M.C.L.); (J.O.P.)
| | - Simone E. F. Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil; (S.A.T.); (D.B.D.M.); (T.C.C.); (H.C.O.); (K.A.C.); (E.R.C.); (W.d.S.)
- Correspondence: ; Tel.: +55-31-36124671
| |
Collapse
|
2
|
Sollero BP, Guimarães SEF, Rilington VD, Tempelman RJ, Raney NE, Steibel JP, Guimarães JD, Lopes PS, Lopes MS, Ernst CW. Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace cross-bred pigs. Anim Genet 2011; 42:600-12. [PMID: 22035001 DOI: 10.1111/j.1365-2052.2011.02186.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Skeletal muscle development is a complex process involving the coordinated expression of thousands of genes. The aim of this study was to identify differentially expressed genes in longissimus dorsi (LD) muscle of pigs at 40 and 70 days (d) of gestation (developmental stages encompassing primary and secondary fibre formation) in Yorkshire-Landrace (YL) cross-bred pigs and Piau pigs (a naturalized Brazilian breed), which are two breed types that differ in muscularity. Foetuses were obtained from gilts at each gestational age (n = 3 YL; n = 4 Piau), and transcriptional profiling was performed using the Pigoligoarray microarray containing 20 400 oligonucleotides. A total of 486 oligonucleotides were differentially expressed (fold change (FC) ≥ 1.5; false discovery rate (FDR) ≤ 0.05) between 40 and 70 d gestation in either YL or Piau pigs, and a total of 1300 oligonucleotides were differentially expressed (FC ≥ 1.5; FDR ≤ 0.05) between YL and Piau pigs at either age. Gene ontology annotation and pathway analyses determined functional classifications for differentially expressed genes and revealed breed type-specific developmental expression patterns. Thirteen genes were selected for confirmation by qRT-PCR analyses, and expression patterns for most of these genes were confirmed, providing further insight into the roles of these genes in pig muscle development. This study revealed both developmental and breed type-specific patterns of gene expression in foetal pig skeletal muscle, including genes not previously associated with myogenesis. This information will contribute to future pig genetic improvement efforts.
Collapse
Affiliation(s)
- B P Sollero
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Davoli R, Braglia S, Russo V, Varona L, te Pas MFW. Expression profiling of functional genes in prenatal skeletal muscle tissue in Duroc and Pietrain pigs. J Anim Breed Genet 2010; 128:15-27. [PMID: 21214640 DOI: 10.1111/j.1439-0388.2010.00867.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In livestock, skeletal muscle is a tissue of major economic importance for meat production and muscle mass is largely determined during the prenatal period by the number and the size of muscle fibres. The understanding of gene expression changes during prenatal pig muscle development is still limited. In this study, genes identified as differentially expressed in a previous microarray research and chosen for the function of the coded protein as putative candidate involved in myogenesis were considered to analyse their expression profile during foetal growth of Duroc and Pietrain pigs. The eleven genes were considered by real-time PCR for a time-course evaluation of the transcription level at six stages of prenatal longissimus dorsi development. The results suggest that the most relevant variations in mRNA levels of the analysed genes seem to follow temporal waves of gene expression. Significant changes of transcription were observed at 21-35 and 63-91 days, the two main phases of skeletal muscle development. During the early phases of Pietrain embryos' development, 10 of the 11 genes showed an induction. In Duroc embryos, a second phase of gene up-regulation can be identified in the phase 63-77 days. These results provide new data on developmental changes of expression profile of 11 genes involved in different functional pathways related to prenatal myogenic processes in Duroc and Pietrain pigs.
Collapse
Affiliation(s)
- R Davoli
- DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Villa Levi-Coviolo, Reggio Emilia, Italy.
| | | | | | | | | |
Collapse
|
4
|
Reed KM, Mendoza KM, Juneja B, Fahrenkrug SC, Velleman S, Chiang W, Strasburg GM. Characterization of expressed sequence tags from turkey skeletal muscle. Anim Genet 2008; 39:635-44. [PMID: 18828862 DOI: 10.1111/j.1365-2052.2008.01787.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study was designed to identify important muscle gene homologues in the turkey. Three skeletal muscle cDNA libraries representing distinct muscle developmental stages were constructed. A total of 20,042 clones were sequenced resulting in 13,023 finished high-quality sequences (trimmed, quality scored and masked) for analysis. Sequence clustering produced 1113 contigs and 4144 singletons (5257 putative transcripts). Sequences were compared by blastn to the chicken whole-genome sequence and to the Ensembl and NCBI databases to identify homologous sequences. These surveys indicated that most of the important muscle genes are included in the sequence collection. Examination of contigs identified 1288 single nucleotide polymorphisms and in 320 of those the minor allele was observed to be present in more than one sequence. This resource provides sequence variants for numerous genes in the turkey, as demonstrated by the SNP haplotypes that were constructed for 10 genes. Sequences obtained in this study provide the basis for constructing a skeletal muscle-focused microarray, a tool that will facilitate the analysis of genes expressed during turkey muscle development, as well as the expression of genes underlying the genetic basis of muscle characteristics associated with meat quality.
Collapse
Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, MN 55108, USA.
| | | | | | | | | | | | | |
Collapse
|
5
|
Martínez-Montemayor MM, Hill GM, Raney NE, Rilington VD, Tempelman RJ, Link JE, Wilkinson CP, Ramos AM, Ernst CW. Gene expression profiling in hepatic tissue of newly weaned pigs fed pharmacological zinc and phytase supplemented diets. BMC Genomics 2008; 9:421. [PMID: 18799003 PMCID: PMC2566318 DOI: 10.1186/1471-2164-9-421] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Accepted: 09/17/2008] [Indexed: 12/17/2022] Open
Abstract
Background Zinc (Zn) is an essential trace element. However, Zn bioavailability from commonly consumed plants may be reduced due to phytic acid. Zn supplementation has been used to treat diarrheal disease in children, and in the U.S. swine industry at pharmacological levels to promote growth and fecal consistency, but underlying mechanisms explaining these beneficial effects remain unknown. Moreover, adding supplemental phytase improves Zn bioavailability. Thus, we hypothesized that benefits of pharmacological Zn supplementation result from changes in gene expression that could be further affected by supplemental phytase. The goal of this study was to investigate the effects of feeding newly weaned pigs dietary Zn (150, 1,000, or 2,000 mg Zn/kg) as Zn oxide with or without phytase [500 phytase units (FTU)/kg] for 14 d on hepatic gene expression. Liver RNA from pigs fed 150, 1,000, or 2,000 mg Zn/kg, or 1,000 mg Zn/kg with phytase (n = 4 per treatment) was reverse transcribed and examined using the differential display reverse transcription polymerase chain reaction technique. Liver RNA from pigs fed 150 or 2,000 mg Zn/kg (n = 4 per treatment) was also evaluated using a 70-mer oligonucleotide microarray. Results Expressed sequence tags for 61 putatively differentially expressed transcripts were cloned and sequenced. In addition, interrogation of a 13,297 element oligonucleotide microarray revealed 650 annotated transcripts (FDR ≤ 0.05) affected by pharmacological Zn supplementation. Seven transcripts exhibiting differential expression in pigs fed pharmacological Zn with sequence similarities to genes encoding GLO1, PRDX4, ACY1, ORM1, CPB2, GSTM4, and HSP70.2 were selected for confirmation. Relative hepatic GLO1 (P < 0.0007), PRDX4 (P < 0.009) and ACY1 (P < 0.01) mRNA abundances were confirmed to be greater in pigs fed 1,000 (n = 8) and 2,000 (n = 8) mg Zn/kg than in pigs fed 150 (n = 7) mg Zn/kg. Relative hepatic HSP70.2 (P < 0.002) mRNA abundance was confirmed to be lower in pigs fed 2,000 mg Zn/kg than in pigs fed 150 or 1,000 mg Zn/kg. Conclusion Results suggest that feeding pharmacological Zn (1,000 or 2,000 mg Zn/kg) affects genes involved in reducing oxidative stress and in amino acid metabolism, which are essential for cell detoxification and proper cell function.
Collapse
|
6
|
Ponsuksili S, Murani E, Walz C, Schwerin M, Wimmers K. Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation. Physiol Genomics 2007; 29:267-79. [PMID: 17264241 DOI: 10.1152/physiolgenomics.00178.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The liver plays a central role in the regulation of the metabolic status, partitioning of nutrients, and expenditure of energy. To gain insight into hepatic metabolic pathways and key transcripts affecting traits related to body composition, liver expression profiles were compared of pigs of two breeds, the obese German Landrace (DL) and the lean Pietrain (Pi). Porcine oligonucleotide microarray were hybridized with liver cRNAs obtained at peripubertal age (180 days of age) and prenatal stages (35, 63, and 91 days postconception) that represent three developmental stages of liver, i.e., period of differentiation, period of metabolic activity, and period of glycogen accumulation. In terms of the number of genes regulated between DL and Pi, the most striking distinctions were found at peripubertal age with upregulation of key genes of lipid metabolism pathways (FASN, ACSS2, ACACA) in obese DL pigs and upregulation of genes of cell growth and/or maintenance, and protein syntheses, as well as cell proliferation pathways (PPARD, POU1F1, IGF2R), in lean Pi pigs. Moreover, time course analysis of breed-dependent expression profiles revealed breed-typical temporal regulation from prenatal stages to peripubertal age of genes assigned to biological processes involving lipid pathways and cell activity, i.e., breed differences are already initiated during early prenatal development. Information about mRNA expression levels of the two breeds differing in body composition, partitioning and utilization of nutrients and energy reveals functional candidate genes for traits related to obesity and leanness.
Collapse
Affiliation(s)
- Siriluck Ponsuksili
- Research Group Functional Genomics, Research Institute for the Biology of Farm Animals, FBN, Dummerstorf, Germany
| | | | | | | | | |
Collapse
|
7
|
LOMBARDI VRM, FERNANDEZ-NOVOA L, ETCHEVERRIA I, SEOANE S, CACABELOS R. Studies on immunological, biochemical, hematological and growth regulation by Scomber scombrus fish protein extract supplementation in young pigs. Anim Sci J 2005. [DOI: 10.1111/j.1740-0929.2005.00252.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
8
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447433 DOI: 10.1002/cfg.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|