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Ma C, Sun Y, Wang J, Kang L, Jiang Y. Identification of a promoter polymorphism affecting GPAT3 gene expression that is likely related to intramuscular fat content in pigs. Anim Biotechnol 2020; 33:1378-1381. [PMID: 33345707 DOI: 10.1080/10495398.2020.1858847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The intramuscular fat content (IMF) is an economically important trait in pigs and the Laiwu pig is famous for its excessively extremely high level of IMF. Our previous transcriptome study revealed that the dynamic expression of glycerol-phosphate acyltransferase 3 (GPAT3) is consistent with changes in the IMF of Laiwu pigs. In this study, we further analyzed the expression and polymorphism of GPAT3 in its promoter region. The results indicated that the expression of GPAT3 increased dramatically from 120 to 240 days and is consistent with changes in IMF deposition, and at both mRNA and protein levels, GPAT3 expression was markedly higher in the LD muscle of Laiwu pigs than that of Duroc × Landrace × Yorkshire pigs. Deletion from -1695 to -1187 of porcine GPAT3 greatly increased its transcription. Of the two SNPs identified, the transition from C to T at -1526 site increased the transcription of porcine GPAT3 and allele T mainly distributed in Laiwu pig population. These results collectively suggest that the SNP at -1526 site of GPAT3 may contribute to IMF deposition by affecting its expression in pigs.
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Affiliation(s)
- Cai Ma
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, PR China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, PR China
| | - Jiying Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, PR China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, PR China
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Zhu S, Guo T, Zhao H, Qiao G, Han M, Liu J, Yuan C, Wang T, Li F, Yue Y, Yang B. Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep. Front Genet 2020; 11:848. [PMID: 32849829 PMCID: PMC7411260 DOI: 10.3389/fgene.2020.00848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
Adaptation to high-altitude hypoxia is essential for domestic animals, such as yak, Tibetan chicken, and Tibetan sheep, living on high plateaus, as it ensures efficient oxygen absorption and utilization. Red blood cells are the primary medium for transporting oxygen in the blood. However, little is known about the genetic mechanism of erythrocyte traits. Genome-wide association studies (GWASs) based on single markers or haplotypes have identified potential mechanisms for genetic variation and quantitative traits. To identify loci associated with erythrocyte traits, we performed a GWAS based on the method of the single marker and haplotype in 498 Alpine Merino sheep for six erythrocyte traits: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV). Forty-two significant single-nucleotide polymorphisms (SNPs) associated with the six erythrocyte traits were detected by means of a single-marker GWAS, and 34 significant haplotypes associated with five erythrocyte traits were detected by means of haplotype analysis. We identified six genes (DHCR24, SPATA9, FLI1, PLCB1, EFNB2, and SH2B3) as potential genes of interest via gene function annotations, location, and expression variation. In particular, FLI1 and PLCB1 were associated with hematopoiesis and erythropoiesis, respectively. These results provide a theoretical basis for analyzing erythrocyte traits and high-altitude hypoxia adaptation in Alpine Merino sheep and will be a useful reference for future studies of plateau-dwelling livestock.
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Affiliation(s)
- Shaohua Zhu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tingting Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongchang Zhao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guoyan Qiao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Han
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbin Liu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yuan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, China
| | - Yaojing Yue
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bohui Yang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Identification of lncRNAs and Genes Responsible for Fatness and Fatty Acid Composition Traits between the Tibetan and Yorkshire Pigs. Int J Genomics 2019; 2019:5070975. [PMID: 31281828 PMCID: PMC6589220 DOI: 10.1155/2019/5070975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/10/2019] [Accepted: 03/03/2019] [Indexed: 12/15/2022] Open
Abstract
Tibetan pigs from the Tibetan Plateau are characterized with a significant phenotypic difference relative to lowland pigs. In this study, a significant difference of the fatness and fatty acid composition traits was observed between the Tibetan and Yorkshire pigs. To uncover the involved mechanism, the expression profile of long noncoding RNAs (lncRNAs) and genes was compared between them. After serial filtered steps, 1,964 lncRNAs were obtained through our computational pipeline. In total, 63 and 715 lncRNAs and genes were identified to be differentially expressed. Evidence from cis- and trans-targeting analysis of lncRNAs demonstrated that some lncRNAs, such as MSTRG.14097 and MSTRG.8034, played important roles in the fatness and fatty acid composition traits. Bioinformatics analysis revealed that many candidate genes were responsible for the two traits. Of these, FASN, ACACA, SCD, ME3, PDHB, ACSS1, ACSS2, and ACLY were identified, which functioned in regulating the level of hexadecanoic acid, hexadecenoic acid, octadecenoic acid, and monounsaturated fatty acid. And LPGAT1, PDK4, ACAA1, and ADIPOQ were associated with the content of stearic acid, octadecadienoic acid, and polyunsaturated fatty acid. Candidate genes, which were responsible for fatness trait, consisted of FGF2, PLAG1, ADIPOQ, IRX3, MIF, IL-34, ADAM8, HMOX1, Vav1, and TLR8. In addition, association analysis also revealed that 34 and 57 genes significantly correlated to the fatness and fatty acid composition trait, respectively. Working out the mechanism caused by these lncRNAs and candidate genes is proven to be complicated but is invaluable to our understanding of fatness and fatty acid composition traits.
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Wu S, Wang Y, Ning Y, Guo H, Wang X, Zhang L, Khan R, Cheng G, Wang H, Zan L. Genetic Variants in STAT3 Promoter Regions and Their Application in Molecular Breeding for Body Size Traits in Qinchuan Cattle. Int J Mol Sci 2018; 19:ijms19041035. [PMID: 29596388 PMCID: PMC5979584 DOI: 10.3390/ijms19041035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 11/16/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation in STAT3, followed by measurements of its mRNA expression during fetal and adult stages of Qinchuan cattle. We then sequenced the STAT3 promoter region to determine genetic variants and evaluate their association with body size traits. From fetus to adult, STAT3 expression increased significantly in muscle, fat, heart, liver, and spleen tissues (p < 0.01), but decreased in the intestine, lung, and rumen (p < 0.01). We identified and named five single nucleotide polymorphisms (SNPs): SNP1-304A>C, SNP2-285G>A, SNP3-209A>C, SNP4-203A>G, and SNP5-188T>C. These five mutations fell significantly outside the Hardy-Weinberg equilibrium (HWE) (Chi-squared test, p < 0.05) and significantly associated with body size traits (p < 0.05). Individuals with haplotype H3H3 (CC-GG-CC-GG-CC) were larger in body size than other haplotypes. Therefore, variations in the STAT3 gene promoter regions, most notably haplotype H3H3, may benefit marker-assisted breeding of Qinchuan cattle.
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Affiliation(s)
- Sen Wu
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yaning Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yue Ning
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Xiaoyu Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Le Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
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