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An L, Pan Y, Yuan M, Wen Z, Qiao L, Wang W, Liu J, Li B, Liu W. Full-Length Transcriptome and Gene Expression Analysis of Different Ovis aries Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis. Animals (Basel) 2023; 14:7. [PMID: 38200738 PMCID: PMC10777924 DOI: 10.3390/ani14010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Sheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and third-generation sequencing were constructed using extracted total RNA. Functional annotation of differentially expressed genes and isoforms facilitated the identification of key regulatory genes and isoforms associated with sheep fat metabolism. SMRT-seq generated 919,259 high-accuracy cDNA sequences after filtering. Full-length sequences were corrected using RNA-seq sequences, and 699,680 high-quality full-length non-chimeric (FLNC) reads were obtained. Upon evaluating the ratio of total lengths based on FLNC sequencing, it was determined that 36,909 out of 56,316 multiple-exon isoforms met the criteria for full-length status. This indicates the identification of 330,375 full-length FLNC transcripts among the 370,114 multiple-exon FLNC transcripts. By comparing the reference genomes, 60,276 loci and 111,302 isoforms were identified. In addition, 43,423 new genes and 44,563 new isoforms were identified. The results identified 185 (3198), 394 (3592), and 83 (3286) differentially expressed genes (transcripts) between tail and subcutaneous, tail and visceral, and subcutaneous and visceral adipose tissues, respectively. Functional annotation and pathway analysis revealed the following observations. (1) Among the differentially expressed genes (DEGs) of TF and SF tissues, the downregulation of ACADL, ACSL6, and NC_056060.1.2536 was observed in SF, while FFAR4 exhibited upregulation. (2) Among the DEGs of TF and VF tissues, expressions of ACADL, ACSL6, COL1A1, COL1A2, and SCD were downregulated in VF, with upregulation of FFAR4. (3) Among SF and VF expressions of COL1A1, COL1A2, and NC_056060.1.2536 were downregulated in VF. Specific differentially expressed genes (ACADL, ACSL6, COL1A1, COL1A2, FFAR4, NC_056060.1.2536, and SCD) and transcripts (NC_056066.1.1866.16 and NC_056066.1.1866.22) were identified as relevant to fat metabolism. These results provide a dataset for further verification of the regulatory pathway associated with fat metabolism in sheep.
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Affiliation(s)
- Lixia An
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
- School of Food & Environment, Jinzhong College of Information, Jinzhong 030801, China
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Mengjiao Yuan
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Zhonghao Wen
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Liying Qiao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Weiwei Wang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Jianhua Liu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Baojun Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
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Hodge MJ, de las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia. Genes (Basel) 2021; 12:genes12020203. [PMID: 33573244 PMCID: PMC7912062 DOI: 10.3390/genes12020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 01/27/2023] Open
Abstract
Reduced reproductive efficiency results in economic losses to the Australian sheep industry. Reproductive success, particularly after artificial insemination, is dependent on a number of contributing factors on both ewe and ram sides. Despite considerable emphasis placed on characterising ewe side contributions, little emphasis has been placed on characterising ram side contributions to conception success. Over 14,000 transcripts are in spermatozoa of other species, which are transferred to the ova on fertilisation. These transcripts conceivably influence early embryonic development and whether conception is successful. Semen was collected (n = 45) across three breeds; Merino, Dohne, and Poll Dorset. Following collection, each ejaculate was split in two; an aliquot was assessed utilising Computer Assisted Semen Analysis (CASA) and the remaining was utilised for RNA extraction and subsequent next-generation sequencing. Overall, 754 differentially expressed genes were identified in breed contrasts and contrast between ejaculates of different quality. Downstream analysis indicated that these genes could play significant roles in a broad range of physiological functions, including maintenance of spermatogenesis, fertilisation, conception, embryonic development, and offspring production performance. Overall results provide evidence that the spermatozoal transcriptome could be a crucial contributing factor in improving reproductive performance as well as in the overall productivity and profitability of sheep industries.
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Affiliation(s)
- Marnie J. Hodge
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia;
| | - Sara de las Heras-Saldana
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia;
| | | | - Cyril P. Stephen
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
| | - Sameer D. Pant
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Correspondence:
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Herault F, Vincent A, Dameron O, Le Roy P, Cherel P, Damon M. The Longissimus and Semimembranosus muscles display marked differences in their gene expression profiles in pig. PLoS One 2014; 9:e96491. [PMID: 24809746 PMCID: PMC4014511 DOI: 10.1371/journal.pone.0096491] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/09/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Meat quality depends on skeletal muscle structure and metabolic properties. While most studies carried on pigs focus on the Longissimus muscle (LM) for fresh meat consumption, Semimembranosus (SM) is also of interest because of its importance for cooked ham production. Even if both muscles are classified as glycolytic muscles, they exhibit dissimilar myofiber composition and metabolic characteristics. The comparison of LM and SM transcriptome profiles undertaken in this study may thus clarify the biological events underlying their phenotypic differences which might influence several meat quality traits. METHODOLOGY/PRINCIPAL FINDINGS Muscular transcriptome analyses were performed using a custom pig muscle microarray: the 15 K Genmascqchip. A total of 3823 genes were differentially expressed between the two muscles (Benjamini-Hochberg adjusted P value ≤0.05), out of which 1690 and 2133 were overrepresented in LM and SM respectively. The microarray data were validated using the expression level of seven differentially expressed genes quantified by real-time RT-PCR. A set of 1047 differentially expressed genes with a muscle fold change ratio above 1.5 was used for functional characterization. Functional annotation emphasized five main clusters associated to transcriptome muscle differences. These five clusters were related to energy metabolism, cell cycle, gene expression, anatomical structure development and signal transduction/immune response. CONCLUSIONS/SIGNIFICANCE This study revealed strong transcriptome differences between LM and SM. These results suggest that skeletal muscle discrepancies might arise essentially from different post-natal myogenic activities.
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Affiliation(s)
- Frederic Herault
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
| | - Annie Vincent
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
| | - Olivier Dameron
- Université de Rennes1, F-35000 Rennes, France
- IRISA team Dyliss, F-35000 Rennes, France
| | - Pascale Le Roy
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
| | - Pierre Cherel
- iBV-institut de Biologie Valrose, Université Nice-Sophia Antipolis UMR CNRS 7277 Inserm U1091, Parc Valrose, F-06108 Nice, France
| | - Marie Damon
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
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Shen X, Zeng H, Xie L, He J, Li J, Xie X, Luo C, Xu H, Zhou M, Nie Q, Zhang X. The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits. PLoS One 2012; 7:e33851. [PMID: 22496769 PMCID: PMC3322132 DOI: 10.1371/journal.pone.0033851] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 02/19/2012] [Indexed: 11/28/2022] Open
Abstract
Background Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits. Methodology/Principal Finding Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner. Conclusions/Significance Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.
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Affiliation(s)
- Xu Shen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Hua Zeng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang Xie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Institute of Animal Science and Veterinary, Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Jun He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Jian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiujuan Xie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Chenglong Luo
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Min Zhou
- Biotechnology Institute, Jiang Xi Education College, Nanchang, Jiangxi, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- * E-mail:
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