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Amandykova M, Akhatayeva Z, Kozhakhmet A, Kapassuly T, Orazymbetova Z, Yergali K, Khamzin K, Iskakov K, Dossybayev K. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat-Wool Sheep Breed. Genes (Basel) 2023; 14:1988. [PMID: 38002931 PMCID: PMC10671688 DOI: 10.3390/genes14111988] [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: 09/09/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat-wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat-wool sheep using the Illumina iScan® system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat-wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH1-2 Mb were much higher than ROH2-4 Mb and ROH8-16 Mb in the three sheep populations. Most of individuals had small number of ROH>16 Mb. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated FROH presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (BMP2, BMPR2, BMPRIB, CLOCK, KDM2B, TIAM1, TASP1, MYBPC1, MYOM1, and CACNA2D1), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat-wool sheep breed.
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Affiliation(s)
- Makpal Amandykova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zhanerke Akhatayeva
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Altynay Kozhakhmet
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Tilek Kapassuly
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zarina Orazymbetova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
| | - Kanagat Yergali
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kadyrzhan Khamzin
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Iskakov
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Dossybayev
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
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Yue C, Wang J, Shen Y, Zhang J, Liu J, Xiao A, Liu Y, Eer H, Zhang QE. Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring. Front Vet Sci 2023; 10:1186040. [PMID: 37388464 PMCID: PMC10301830 DOI: 10.3389/fvets.2023.1186040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction The Tan sheep is a popular local breed in China because of its tenderness and flavor. The Hu sheep breed is also famous for its high litter size, and its muscle growth rate is faster than that of Tan sheep. However, the epigenetic mechanism behind these muscle-related phenotypes is unknown. Methods In this study, the longissimus dorsi tissue from 18 6 month-old Tan sheep, Hu sheep, and Tan-Hu F2 generation (6 sheep per population) were collected. After genomic DNA extraction, whole-genome bisulfite sequencing (WGBS) and bioinformatics analysis were performed to construct genome-wide DNA methylome maps for the Tan sheep, Hu sheep and their Tan-Hu F2 generation. Results Distinct genome-wide DNA methylation patterns were observed between Tan sheep and Hu sheep. Moreover, DNA methylated regions were significantly increased in the skeletal muscle from Tan sheep vs. the F2 generation compared to the Hu sheep vs. F2 generation and the Tan sheep vs. Hu sheep. Compared with Hu sheep, the methylation levels of actin alpha 1 (ACTA1), myosin heavy chain 11 (MYH11), Wiskott-Aldrich syndrome protein (WAS), vav guanine nucleotide exchange factor 1 (VAV1), fibronectin 1 (FN1) and Rho-associated protein kinase 2 (ROCK2) genes were markedly distinct in the Tan sheep. Furthermore, Gene Ontology analysis indicated that these genes were involved in myotube differentiation, myotube cell development, smooth muscle cell differentiation and striated muscle cell differentiation. Conclusion The findings from this study, in addition to data from previous research, demonstrated that the ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 genes may exert regulatory effects on muscle development.
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Affiliation(s)
- Caijuan Yue
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jiakang Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yifei Shen
- Institute of Marxism, China University of Geosciences, Wuhan, Hubei, China
| | - Junli Zhang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jian Liu
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Aiping Xiao
- Animal Husbandry Extension Station, Yinchuan, Ningxia, China
| | - Yisha Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
| | - Hehua Eer
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Qiao-e Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
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Zhang T, Li C, Deng J, Jia Y, Qu L, Ning Z. Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting. Animals (Basel) 2023; 13:ani13061012. [PMID: 36978553 PMCID: PMC10044502 DOI: 10.3390/ani13061012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic modifications play an important role in regulating animal adaptation to external stress. To explore how DNA methylation regulates the expression levels of related genes during forced molting (FM) of laying hens, the hypothalamus and ovary tissues were analyzed at five periods using Whole-Genome Bisulfite Sequencing. The results show that methylation levels fluctuated differently in the exon, intron, 5′UTR, 3′UTR, promoter, and intergenic regions of the genome during FM. In addition, 16 differentially methylated genes (DMGs) regulating cell aging, immunity, and development were identified in the two reversible processes of starvation and redevelopment during FM. Comparing DMGs with differentially expressed genes (DEGs) obtained in the same periods, five hypermethylated DMGs (DSTYK, NKTR, SMOC1, SCAMP3, and ATOH8) that inhibited the expression of DEGs were found. Therefore, DMGs epigenetically modify the DEGs during the FM process of chickens, leading to the rapid closure and restart of their reproductive function and a re-increase in the egg-laying rate. Therefore, this study further confirmed that epigenetic modifications could regulate gene expression during FM and provides theoretical support for the subsequent optimization of FM technology.
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Affiliation(s)
- Tongyu Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chengfeng Li
- Hubei Shendan Healthy Food Co., Ltd., Xiaogan 432600, China
| | - Jianwen Deng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100091, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
- Correspondence:
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Zequan X, Yonggang S, Heng X, Yaodong W, Xin M, Dan L, Li Z, Tingting D, Zirong W. Transcriptome-based analysis of early post-mortem formation of pale, soft, and exudative (PSE) pork. Meat Sci 2022; 194:108962. [PMID: 36126390 DOI: 10.1016/j.meatsci.2022.108962] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 07/02/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Pale, soft, and exudative (PSE) meat can cause consumer dissatisfaction and economic losses. This study determined meat quality, glycolytic enzyme activity, and differential gene expression in the longissimus lumborum (LL) and semimembranosus (SM) of normal and PSE pork carcasses. The SM did not result in PSE meat. Hexokinase, lactate dehydrogenase, and pyruvate kinase activities were lower in the SM of PSE carcasses than in the normal carcasses. Functional enrichment analysis revealed that immune, inflammatory, and muscle fibre genes were significantly enriched in PSE pork. More specifically, PPP1R3G and MSS51 may be key genes regulating pork quality in the SM. Meanwhile, the differential expression of PLVAB, ADIPOQ, LEP, MYH4, MYH7, MYL3, MYL6B, FOS, ATF3, and HSPA6 may induce PSE formation in the LL. These results may provide insights into PSE pork formation mechanisms and reveal candidate genes for improving meat quality after validation.
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Affiliation(s)
- Xu Zequan
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China; Tecon Biology Ltd., Urumqi, Xinjiang, China
| | - Shao Yonggang
- College of Animal Science, Xinjiang Agricultural University, Xinjiang, China
| | - Xu Heng
- Tecon Biology Ltd., Urumqi, Xinjiang, China
| | | | - Ma Xin
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Liu Dan
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Zhang Li
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Du Tingting
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Wang Zirong
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Cao Y, Yu Y, Zhang L, Liu Y, Zheng K, Wang S, Jin H, Liu L, Cao Y. Transcript variants of long-chain acyl-CoA synthase 1 have distinct roles in sheep lipid metabolism. Front Genet 2022; 13:1021103. [PMID: 36482895 PMCID: PMC9723241 DOI: 10.3389/fgene.2022.1021103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/16/2022] [Indexed: 07/30/2023] Open
Abstract
Mutton has recently been identified to be a consumer favorite, and intermuscular fat is the key factor in determining meat tenderness. Long-chain acyl-CoA synthetase 1 (ACSL1) is a vital subtype of the ACSL family that is involved in the synthesis of lipids from acyl-CoA and the oxidation of fatty acids. The amplification of the ACSL1 gene using rapid amplification of cDNA ends revealed that the alternative polyadenylation (APA) results in two transcripts of the ACSL1 gene. Exon 18 had premature termination, resulting in a shorter CDS region. In this study, the existence of two transcripts of varying lengths translated normally and designated ACSL1-a and ACSL1-b was confirmed. Overexpression of ACSL1-a can promote the synthesis of an intracellular diglyceride, while ACSL1-b can promote triglyceride synthesis. The transfection of ACSL1 shRNA knocks down both the transcripts, the triglyceride content was significantly reduced after differentiation and induction; and lipidome sequencing results exhibited a significant decrease in 14-22 carbon triglyceride metabolites. The results of the present study indicated that the ACSL1 gene played a crucial role in the synthesis of triglycerides. Furthermore, the two transcripts involved in various interactions in the triglyceride synthesis process may be the topic of interest for future research and provide a more theoretical basis for sheep breeding.
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Affiliation(s)
- Yang Cao
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yongsheng Yu
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Lichun Zhang
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Yu Liu
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Kaizhi Zheng
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sutian Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Haiguo Jin
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Lixiang Liu
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Yang Cao
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Science, Gongzhuling, China
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Silva-Vignato B, Cesar ASM, Afonso J, Moreira GCM, Poleti MD, Petrini J, Garcia IS, Clemente LG, Mourão GB, Regitano LCDA, Coutinho LL. Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness. Front Genet 2022; 13:935238. [PMID: 35991540 PMCID: PMC9386181 DOI: 10.3389/fgene.2022.935238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.
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Affiliation(s)
- Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food, and Nutrition, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | | | - Mirele Daiana Poleti
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
- *Correspondence: Luiz Lehmann Coutinho,
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Peng H, Hu M, Liu Z, Lai W, Shi L, Zhao Z, Ma H, Li Y, Yan S. Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep. Front Genet 2022; 13:868717. [PMID: 35480317 PMCID: PMC9035493 DOI: 10.3389/fgene.2022.868717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
It is well known that Dorper (DP) is a full-bodied, fast-growing and high dressing percentage breed, while the production performance of Small-tailed Han sheep (STH) is not so excellent, in contrast to DP. Therefore, in this study, a comparative transcriptomic analysis of liver and muscle tissues from DP and STH breeds was carried out to find differentially expressed genes (DEGs) that affect their growth and meat quality traits. The results showed that the total number of DEGs was 2,188 in the two tissues. There were 950, 160 up-regulated and 1,007, 71 down-regulated genes in the liver and muscle, respectively. Several DEGs such as TGFB1, TGFB3, FABP3, LPL may be associated with growth and development in DP. Also, several GO terms were found to be associated with muscle growth and development, such as developmental growth (GO:0048589), and myofibril (GO:0030016). Further validation of eight genes (6 up-regulated, and 2 down-regulated) was performed using quantitative RT-PCR. These findings will provide valuable information for studying growth and development as well as meat quality traits in sheep.
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Affiliation(s)
- Hongyang Peng
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Zhongli Zhao
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Huihai Ma
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yumei Li
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Yumei Li, ; Shouqing Yan,
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Yumei Li, ; Shouqing Yan,
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Wang M, Bissonnette N, Dudemaine PL, Zhao X, Ibeagha-Awemu EM. Whole Genome DNA Methylation Variations in Mammary Gland Tissues from Holstein Cattle Producing Milk with Various Fat and Protein Contents. Genes (Basel) 2021; 12:1727. [PMID: 34828333 PMCID: PMC8618717 DOI: 10.3390/genes12111727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022] Open
Abstract
Milk fat and protein contents are among key elements of milk quality, and they are attracting more attention in response to consumers' demand for high-quality dairy products. To investigate the potential regulatory roles of DNA methylation underlying milk component yield, whole genome bisulfite sequencing was employed to profile the global DNA methylation patterns of mammary gland tissues from 17 Canada Holstein cows with various milk fat and protein contents. A total of 706, 2420 and 1645 differentially methylated CpG sites (DMCs) were found between high vs. low milk fat (HMF vs. LMF), high vs. low milk protein (HMP vs. LMP), and high vs. low milk fat and protein (HMFP vs. LMFP) groups, respectively (q value < 0.1). Twenty-seven, 56 and 67 genes harboring DMCs in gene regions (denoted DMC genes) were identified for HMF vs. LMF, HMP vs. LMP and HMFP vs. LMFP, respectively. DMC genes from HMP vs. LMP and HMFP vs. LMFP comparisons were significantly overrepresented in GO terms related to aerobic electron transport chain and/or mitochondrial ATP (adenosine triphosphate) synthesis coupled electron transport. A total of 83 (HMF vs. LMF), 708 (HMP vs. LMP) and 408 (HMFP vs. LMFP) DMCs were co-located with 87, 147 and 158 quantitative trait loci (QTL) for milk component and yield traits, respectively. In conclusion, the identified methylation changes are potentially involved in the regulation of milk fat and protein yields, as well as the variation in reported co-located QTLs.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC H9X 3V9, Canada;
| | - Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
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Tian Y, Yang X, Du J, Zeng W, Wu W, Di J, Huang X, Tian K. Differential Methylation and Transcriptome Integration Analysis Identified Differential Methylation Annotation Genes and Functional Research Related to Hair Follicle Development in Sheep. Front Genet 2021; 12:735827. [PMID: 34659357 PMCID: PMC8515899 DOI: 10.3389/fgene.2021.735827] [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: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Hair follicle growth and development are a complex and long-term physiological process, which is regulated by a variety of physical factors and signal pathways. Increasing the understanding of the epigenetic regulation and function of candidate genes related to hair follicle development will help to better understand the molecular regulatory mechanisms of hair follicle development. In this study, the methylated DNA immunoprecipitation sequencing (MeDIP-seq) was used to obtain the genome-wide methylation map of the hair follicular development of Super Merino sheep in six stages (fetal skin tissue at 65d, 85d, 105d, 135d, 7d, and 30d after birth). Combined with the results of previous RNA-sequencing, 65 genes were screened out that were both differential methylation and differential expression, including EDN1, LAMC2, NR1D1, RORB, MyOZ3, and WNT2 gene. Differential methylation genes were enriched in Wnt, TNF, TGF-beta, and other signaling pathways related to hair follicle development. The bisulfite sequencing PCR results and MeDIP-seq were basically consistent, indicating that the sequencing results were accurate. As a key gene in the Wnt signaling pathway, both differential methylation and expression gene identified by MeDIP-seq and RNA-seq, further exploration of the function of WNT2 gene revealed that the DNA methylation of exon 5 (CpG11 site) promoted the expression of WNT2 gene. The overexpression vector of lentivirus pLEX-MCS-WNT2 was constructed, and WNT2 gene effectively promoted the proliferation of sheep skin fibroblasts. The results showed that WNT2 gene could promote the growth and development of skin and hair follicles. The results of this study will provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.
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Affiliation(s)
- Yuezhen Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuemei Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jianwen Du
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weidan Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weiwei Wu
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jiang Di
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Kechuan Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
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10
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Genome-wide DNA methylation profiles provide insight into epigenetic regulation of red and white muscle development in Chinese perch Siniperca chuatsi. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110647. [PMID: 34271193 DOI: 10.1016/j.cbpb.2021.110647] [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: 03/02/2021] [Revised: 06/04/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022]
Abstract
Fish skeletal muscles are composed of spatially well-separated fiber types, namely, red and white muscles with different physiological functions and metabolism. To compare the DNA methylation profiles of the two types of muscle tissues and identify potential candidate genes for the muscle growth and development under epigenetic regulation, genome-wide DNA methylation of the red and white muscle in Chinese perch Siniperca chuatsi were comparatively analyzed using bisulfate sequencing methods. An average of 0.9 billion 150-bp paired-end reads were obtained, of which 86% were uniquely mapped to the genome. Methylation mostly occurred at CG sites at a ratio of 94.43% in the red muscle and 93.16% in the white muscle. The mean methylation levels at C-sites were 5.95% in red muscle and 5.83% in white muscle, whereas the mean methylation levels of CG, CHG, and CHH were 73.23%, 0.62%, and 0.67% in red muscle, and 71.01%, 0.62%, and 0.67% in white muscle, respectively. A total of 4192 differentially methylated genes (DMGs) were identified significantly enriched in cell signaling pathways related to skeletal muscle differentiation and growth. Various muscle-related genes, including myosin gene isoforms and regulatory factors, are differentially methylated in the promoter region between the red and white muscles. Further analysis of the transcriptional expression of these genes showed that the muscle regulatory factors (myf5, myog, pax3, pax7, and twitst2) and myosin genes (myh10, myh16, myo18a, myo7a, myo9a, and myl3) were differentially expressed between the two kinds of muscles, consistent with the DNA methylation analysis results. ELISA assays confirmed that the level of 5mC in red muscle was significantly higher than in white muscle (P < 0.05). The RT-qPCR assays revealed that the expression levels of the three DNA methylation transferase (dnmt) subtypes, dnmt1, dnmt3ab, and dnmt3bb1, were significantly higher in red muscle than in white muscle. The higher DNA methylation levels in the red muscle may result from higher DNA methylation transferase expression in the red muscles. Thus, this study might provide a theoretical foundation to better understand epigenetic regulation in the growth and development of red and white muscles in animals, at least in Chinese perch fish.
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11
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Lin W, Ren T, Li W, Liu M, He D, Liang S, Luo W, Zhang X. Novel 61-bp Indel of RIN2 Is Associated With Fat and Hatching Weight Traits in Chickens. Front Genet 2021; 12:672888. [PMID: 34276778 PMCID: PMC8280519 DOI: 10.3389/fgene.2021.672888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
The Ras and Rab interactor 2 (RIN2) gene, which encodes RAS and Rab interacting protein 2, can interact with GTP-bound Rab5 and participate in early endocytosis. This study found a 61-bp insertion/deletion (indel) in the RIN2 intron region, and 3 genotypes II, ID, and DD were observed. Genotype analysis of mutation sites was performed on 665 individuals from F2 population and 8 chicken breeds. It was found that the indel existed in each breed and that yellow feathered chickens were mainly of the DD genotype. Correlation analysis of growth and carcass traits in the F2 population of Xinghua and White Recessive Rock chickens showed that the 61-bp indel was significantly correlated with abdominal fat weight, abdominal fat rate, fat width, and hatching weight (P < 0.05). RIN2 mRNA was expressed in all the tested tissues, and its expression in abdominal fat was higher than that in other tissues. In addition, the expression of the RIN2 mRNA in the abdominal fat of the DD genotype was significantly higher than that of the II genotype (P < 0.05). The transcriptional activity results showed that the luciferase activity of the pGL3-DD vector was significantly higher than that of the pGL3-II vector (P < 0.01). Moreover, the results indicate that the polymorphisms in transcription factor binding sites (TFBSs) of 61-bp indel may affect the transcriptional activity of RIN2, and thus alter fat traits in chicken. The results of this study showed that the 61-bp indel was closely related to abdominal fat-related and hatching weight traits of chickens, which may have reference value for molecular marker-assisted selection of chickens.
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Affiliation(s)
- Wujian Lin
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Manqing Liu
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danlin He
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Shaodong Liang
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wen Luo
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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12
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An X, Zhang S, Li T, Chen N, Wang X, Zhang B, Ma Y. Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb. PeerJ 2021; 9:e11295. [PMID: 33987003 PMCID: PMC8086582 DOI: 10.7717/peerj.11295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/27/2021] [Indexed: 11/20/2022] Open
Abstract
To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude fat, and low crude fiber, which is widely distributed in China. In this study, 12 Dorper ♂×Hu ♀ crossbred weaned male lambs were seleted into four groups based on the feed that ratio of the B. papyrifera fermented feed in the total mixed diet (0%, 6%, 18%, and 100%), to character the lambs' longissimus dorsi (LD) fatty acids, morphology and transcriptome. Results showed that the muscle fiber's diameter and area were the smallest in the 100% group. The highest content of beneficial fatty acids and the lowest content of harmful fatty acids in group 18%. RNA-seq identified 443 differentially expressed genes (DEGs) in the LD of lambs from 4 groups. Among these genes, 169 (38.1%) were up-regulated and 274 (61.9%) were down-regulated. The DEGs were mostly enriched in in fatty acid metabolism, arginine and proline metabolism, and PPAR signaling pathways. Our results provide knowledge to understand effect of different ratios of B. papyrifera fermented feed on sheep meat quality traits, also a basis for understanding of the molecular regulation mechanism of B. papyrifera fermented feed affecting on sheep meat quality.
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Affiliation(s)
- Xuejiao An
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shengwei Zhang
- Gansu Provincial Farmer Education and Training Station, Lanzhou, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Nana Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xia Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Baojun Zhang
- Gansu Provincial Farmer Education and Training Station, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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13
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Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals. Animals (Basel) 2021; 11:ani11030835. [PMID: 33809500 PMCID: PMC7999090 DOI: 10.3390/ani11030835] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Skeletal muscle mass is an important economic trait, and muscle development and growth is a crucial factor to supply enough meat for human consumption. Thus, understanding (candidate) genes regulating skeletal muscle development is crucial for understanding molecular genetic regulation of muscle growth and can be benefit the meat industry toward the goal of increasing meat yields. During the past years, significant progress has been made for understanding these mechanisms, and thus, we decided to write a comprehensive review covering regulators and (candidate) genes crucial for muscle development and growth in farm animals. Detection of these genes and factors increases our understanding of muscle growth and development and is a great help for breeders to satisfy demands for meat production on a global scale. Abstract Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.
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14
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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15
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Guo L, Sun H, Zhao Q, Xu Z, Zhang Z, Liu D, Qadri QR, Ma P, Wang Q, Pan Y. Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data. Anim Genet 2021; 52:143-154. [PMID: 33458851 DOI: 10.1111/age.13034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 12/26/2022]
Abstract
Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.
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Affiliation(s)
- L Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - H Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - D Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q R Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - P Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
| | - Y Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
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16
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Pértille F, Ibelli AMG, Sharif ME, Poleti MD, Fröhlich AS, Rezaei S, Ledur MC, Jensen P, Guerrero-Bosagna C, Coutinho LL. Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes. Front Genet 2020; 11:508809. [PMID: 33240310 PMCID: PMC7667380 DOI: 10.3389/fgene.2020.508809] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environment. Here we compared a reduced fraction of the RBC methylome of chickens exposed to social isolation to non-exposed. These experiments were performed in two different locations: Brazil and Sweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposed in each facility and their different lineages. Birds were increasingly exposed to a social isolation treatment, combined with food and water deprivation, at random periods of the day from weeks 1-4 after hatching. We then collected the RBC DNA from individuals and compared a reduced fraction of their methylome between the experimental groups using two bioinformatic approaches to identify differentially methylated regions (DMRs): one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P ≤ 0.05, P ≤ 0.005, and P ≤ 0.0005) to identify DMRs between experimental groups, which were then used for different analyses. With both of the approaches more DMRs reached the defined significance thresholds in BR individuals compared to SW. However, more DMRs had higher fold change values in SW compared to BR individuals. Interestingly, ChrZ was enriched above expectancy for the presence of DMRs. Additionally, when analyzing the locations of these DMRs in relation to the transcription starting site (TSS), we found three peaks with high DMR presence: 10 kb upstream, the TSS itself, and 20-40 kb downstream. Interestingly, these peaks had DMRs with a high presence (>50%) of specific transcription factor binding sites. Three overlapping DMRs were found between the BR and SW population using the most relaxed p-value (P ≤ 0.05). With the most stringent p-value (P ≤ 0.0005), we found 7 and 4 DMRs between treatments in the BR and SW populations, respectively. This study is the first approximation to identify epigenetic biomarkers of long-term exposure to stress in different lineages of production animals.
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Affiliation(s)
- Fábio Pértille
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/"Luiz de Queiroz" College of Agriculture (ESALQ), Piracicaba, Brazil.,Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | | | - Maj El Sharif
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Mirele Daiana Poleti
- Animal Science Program, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Anna Sophie Fröhlich
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Shiva Rezaei
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | | | - Per Jensen
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden.,Evolutionary Biology Centre, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/"Luiz de Queiroz" College of Agriculture (ESALQ), Piracicaba, Brazil
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17
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Fan R, Gu Z, Guang X, Marín JC, Varas V, González BA, Wheeler JC, Hu Y, Li E, Sun X, Yang X, Zhang C, Gao W, He J, Munch K, Corbett-Detig R, Barbato M, Pan S, Zhan X, Bruford MW, Dong C. Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. Genome Biol 2020; 21:159. [PMID: 32616020 PMCID: PMC7331169 DOI: 10.1186/s13059-020-02080-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/21/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca. RESULTS Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α. CONCLUSIONS The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Zhongru Gu
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Juan Carlos Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bio Bio, Chillán, Chile
| | - Valeria Varas
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias., Universidad Austral de Chile, Valdivia, Chile
| | - Benito A. González
- Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Jane C. Wheeler
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Pachacamac, Lima, Peru
| | - Yafei Hu
- BGI Genomics, BGI, Shenzhen, China
| | - Erli Li
- BGI Genomics, BGI, Shenzhen, China
| | | | | | | | - Wenjun Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Junping He
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Russel Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, Santa Cruz, CA USA
| | - Mario Barbato
- Department of Animal Science, Food and Technology – DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Xiangjiang Zhan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Michael W. Bruford
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, Wales UK
| | - Changsheng Dong
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
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18
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Cheng S, Wang X, Wang Q, Yang L, Shi J, Zhang Q. Comparative analysis of Longissimus dorsi tissue from two sheep groups identifies differentially expressed genes related to growth, development and meat quality. Genomics 2020; 112:3322-3330. [PMID: 32534014 DOI: 10.1016/j.ygeno.2020.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/23/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022]
Abstract
From a genetic perspective, the advantages of crossbreeding in sheep are unclear. In the present study, a comparative transcriptomic analysis was performed using Longissimus dorsi tissues from two sheep groups in order to identify differentially expressed genes (DEGs) related to growth, development and meat quality. Compared to Small Tail Han sheep, a total of 874 DEGs were identified in the crossbred sheep. Among these DEGs, 30, 116 and 32 DEGs were related to growth, development and meat quality, respectively. Seven DEGs highlighted by functional analysis as playing crucial roles in growth, development and meat quality were validated by the gene-act-network and co-expression-network. The expression levels of DEG mRNAs and proteins were further confirmed using RT-qPCR and western blot analyses. The results were consistent with the comparative transcriptome data. The data from this transcriptomic analysis will help to understand genetic heterosis and molecular-assisted breeding in sheep.
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Affiliation(s)
- Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xueyin Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Qi Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Lei Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
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Cao Y, Wang S, Liu S, Wang Y, Jin H, Ma H, Luo X, Cao Y, Lian Z. Effects of Long-Chain Fatty Acyl-CoA Synthetase 1 on Diglyceride Synthesis and Arachidonic Acid Metabolism in Sheep Adipocytes. Int J Mol Sci 2020; 21:E2044. [PMID: 32192050 PMCID: PMC7139739 DOI: 10.3390/ijms21062044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 12/25/2022] Open
Abstract
Long-chain fatty acyl-CoA synthetase (ACSLs) is an essential enzyme for the synthesis of fatty acyl-CoA. ACSL1 plays a key role in the synthesis of triglycerides, phospholipids, and cholesterol esters. BACKGROUND In the current study, triglyceride content did not increase after overexpression of the ACSL1 gene. METHODS RNA-seq and lipid metabolome profiling were performed to determine why triglyceride levels did not change with ACSL1 overexpression. RESULTS Fatty acyl-CoA produced by ACSL1 was determined to be involved in the diglyceride synthesis pathway, and diglyceride content significantly increased when ACSL1 was overexpressed. Moreover, the arachidonic acid (AA) content in sheep adipocytes significantly increased, and the level of cyclooxygenase 2 (COX2) expression, the downstream metabolic gene, was significantly downregulated. Knocking down the ACSL1 gene was associated with an increase in COX2 mRNA expression, as well as an increase in prostaglandin content, which is the downstream metabolite of AA. CONCLUSIONS The overexpression of the ACSL1 gene promotes the production of AA via downregulation of COX2 gene expression.
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Affiliation(s)
- Yang Cao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.C.); (S.L.)
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling 136100, China; (Y.W.); (H.J.); (H.M.); (X.L.)
| | - Sutian Wang
- State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Shunqi Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.C.); (S.L.)
| | - Yanli Wang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling 136100, China; (Y.W.); (H.J.); (H.M.); (X.L.)
| | - Haiguo Jin
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling 136100, China; (Y.W.); (H.J.); (H.M.); (X.L.)
| | - Huihai Ma
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling 136100, China; (Y.W.); (H.J.); (H.M.); (X.L.)
| | - Xiaotong Luo
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling 136100, China; (Y.W.); (H.J.); (H.M.); (X.L.)
| | - Yang Cao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling 136100, China; (Y.W.); (H.J.); (H.M.); (X.L.)
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.C.); (S.L.)
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20
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Cheng S, Wang X, Zhang Q, He Y, Zhang X, Yang L, Shi J. Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep. Genes (Basel) 2020; 11:E183. [PMID: 32050672 PMCID: PMC7074365 DOI: 10.3390/genes11020183] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/24/2022] Open
Abstract
Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimusdorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5 and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection.
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Affiliation(s)
- Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
| | - Xueying Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Yuqin He
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Xia Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Lei Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
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21
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Ma X, Jia C, Chu M, Fu D, Lei Q, Ding X, Wu X, Guo X, Pei J, Bao P, Yan P, Liang C. Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes (Basel) 2019; 10:genes10120970. [PMID: 31779203 PMCID: PMC6947547 DOI: 10.3390/genes10120970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 02/04/2023] Open
Abstract
DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Congjun Jia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Qinhui Lei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
| | - Chunnian Liang
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
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Mastrangelo S, Ben Jemaa S, Sottile G, Casu S, Portolano B, Ciani E, Pilla F. Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations. J Anim Breed Genet 2019; 136:526-534. [PMID: 31206848 DOI: 10.1111/jbg.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022]
Abstract
Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case-control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST ) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and FST analyses. Moreover, one candidate marker identified by GWAS and FST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome-wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome-wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Gianluca Sottile
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, Sassari, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, Bari, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
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