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Sarviaho K, Uimari P, Martikainen K. Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population. J Dairy Sci 2024; 107:4822-4832. [PMID: 38490540 DOI: 10.3168/jds.2024-24105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits (e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G) overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.
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Affiliation(s)
- Katri Sarviaho
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland.
| | - Pekka Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Katja Martikainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland
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Ji Q, Zhang F, Su Q, He T, Wu Z, Zhu K, Chen X, Wang Z, Hou S, Gui L. Effect of supplementing lysins and methionine to low-protein diets on growth performance, hepatic antioxidant capacity, immune status, and glycolytic activity of tibetan sheep. BMC Genomics 2024; 25:557. [PMID: 38834972 DOI: 10.1186/s12864-024-10480-2] [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: 10/31/2023] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Reducing the levels of dietary protein is an effective nutritional approach in lowering feed cost and nitrogen emissions in ruminants. The purpose of this study was to evaluate the effects of dietary Lys/Met ratio in a low protein diet (10%, dry matter basis) on the growth performance and hepatic function (antioxidant capacity, immune status, and glycolytic activity) in Tibetan lambs. Ninety two-month-old rams with an average weight of 15.37 ± 0.92 kg were randomly assigned to LP-L (dietary Lys/Met = 1:1), LP-M (dietary Lys/Met = 2:1) and LP-H (dietary Lys/Met = 3:1) treatments. The trial was conducted over 100 d, including 10 d of adaption to the diets. Hepatic phenotypes, antioxidant capacity, immune status, glycolytic activity and gene expression profiling was detected after the conclusion of the feeding trials. The results showed that the body weight was higher in the LP-L group when compared to those on the LP-M group (P < 0.05). In addition, the activities of the catalase (CAT) and glutathione peroxidase (GSH-Px) in the LP-L group were significantly increased compared with the LP-M group (P < 0.05), while the malondialdehyde (MDA) levels in LP-H group were significantly decreased (P < 0.05). Compared with LP-H group, both hepatic glycogen (P < 0.01) and lactate dehydrogenase (LDH) (P < 0.05) were significantly elevated in LP-L group. For the LP-L group, the hepatocytes were arranged radially with the central vein in the center, and hepatic plates exhibited tight arrangement. Transcriptome analysis identified 29, 179, and 129 differentially expressed genes (DEGs) between the LP-M vs. LP-L, LP-H vs. LP-M, and LP-H vs. LP-L groups, respectively (Q-values < 0.05 and |log2Fold Change| > 1). Gene Ontology (GO) and correlation analyses showed that in the LP-L group, core genes (C1QA and JUNB) enriched in oxidoreductase activity were positively correlated with antioxidant indicators, while the MYO9A core gene enriched in the immune response was positively associated with immune indicators, and core genes enriched in molecular function (PDK3 and PDP2) were positively correlated with glycolysis indicators. In summary, low-protein diet with a low Lys/Met ratio (1:1) could reduce the hepatic oxidative stress and improve the glycolytic activity by regulating the expression of related genes of Tibetan sheep.
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Affiliation(s)
- Qiurong Ji
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Fengshuo Zhang
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Quyangangmao Su
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Tingli He
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Zhenling Wu
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Kaina Zhu
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Xuan Chen
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Zhiyou Wang
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Shengzhen Hou
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China
| | - Linsheng Gui
- Qinghai University College of Agriculture and Animal Husbandry, Xining, 810016, China.
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Zhou L, Raza SHA, Ma B, Shater AF, Mohammedsaleh ZM, Jahejo AR, Li J, Gui L. Mutations in FGFR1 were associated with growth traits in sheep ( Ovis aries). Anim Biotechnol 2023; 34:1-7. [PMID: 34097574 DOI: 10.1080/10495398.2021.1929271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
For its role in the mediation of myoblast proliferation, fibroblast growth factor receptor 1 (FGFR1) was considered a functional candidate gene for growth performance in Tibetan sheep. Via the polymerase chain reaction-restriction fragment length polymorphism (PCR-PFLP) approach, four single nucleotide polymorphisms (SNPs) including g.14752C > T (intron 1), g.45361A > G (intron 7), g.49400A > G (3'UTR region) and g.49587A > T (3'UTR region), were identified in 422 ewes. The association analysis demonstrated that individuals carrying the AA genotype of g.49400A > G had significantly greater withers height, length than those with GG genotype (p < 0.05). Individuals with genotype AA of g.49587A > T had significantly greater weight and chest circumference than those with genotype TT (p < 0.01). Additionally, the individuals with Hap1/1 diplotypes (CAAA-CAAA) were highly significantly associated with weight and chest circumference than Hap1/2 diplotypes (CAAA-CAAT) (p < 0.05). The quantitative real-time polymerase chain reaction (qPCR) analysis revealed that the FGFR1 was detectable expressed in muscle tissues within three different age stage. Remarkably higher mRNA expression was detected at fetal lamb stage as compared with adult ewes (p < 0.01). The outcome of this research confirmed that both g.49400A > G and g.49587A > T of FGFR1 were involved in growth-related traits, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep.
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Affiliation(s)
- Li Zhou
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, People's Republic of China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Boyan Ma
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, People's Republic of China
| | - Abdullah F Shater
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
| | - Zuhair M Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
| | - Ali Raza Jahejo
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jiangwei Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, People's Republic of China
| | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, People's Republic of China
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Shikida R, Kim M, Futohashi M, Nishihara K, Lee H, Suzuki Y, Baek Y, Masaki T, Ikuta K, Iwamoto E, Uemoto Y, Haga S, Terada F, Roh S. Physiological roles and regulation of hepatic angiopoietin-like protein 3 in Japanese Black cattle (Bos taurus) during the fattening period. J Anim Sci 2023; 101:skad198. [PMID: 37317898 PMCID: PMC10294557 DOI: 10.1093/jas/skad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/13/2023] [Indexed: 06/16/2023] Open
Abstract
Angiopoietin-like protein 3 (ANGPTL3) is expressed predominantly in the liver and plays a major role in regulating the circulating triglyceride and lipoprotein fraction concentrations by inhibiting lipoprotein lipase (LPL) activity. Given these physiological roles, ANGPTL3 may play an important role in metabolic changes related to fat accumulation during the fattening period in Japanese Black. This study aimed to reveal the physiological roles of hepatic ANGPTL3 in Japanese Black steers (Bos taurus) during the fattening period and investigate the regulatory effects of hepatic ANGPTL3. To investigate the gene expression and protein localization of ANGPTL3, 18 tissue samples were collected from tree male Holstein bull calves aged 7 wk. Biopsied liver tissues and blood samples were collected from 21 Japanese Black steers during the early (T1; 13 mo of age), middle (T2; 20 mo), and late fattening phases (T3; 28 mo). Relative mRNA expression, blood metabolite concentrations, hormone concentrations, growth, and carcass traits were analyzed. To identify the regulatory factors of hepatic ANGPTL3, primary bovine hepatocytes collected by two Holstein calves aged 7 wk were incubated with insulin, palmitate, oleate, propionate, acetate, or beta-hydroxybutyric acid (BHBA). The ANGPTL3 gene was most highly expressed in the liver, with minor expression in the renal cortex, lungs, reticulum, and jejunum in Holstein bull calves. In Japanese Black steers, relative ANGPTL3 mRNA expressions were less as fattening progressed, and blood triglyceride, total cholesterol, and nonesterified fatty acid (NEFA) concentrations increased. Relative ANGPTL8 and Liver X receptor alpha (LXRα) mRNA expressions decreased in late and middle fattening phases, respectively. Furthermore, relative ANGTPL3 mRNA expression was positively correlated with ANGPTL8 (r = 0.650; P < 0.01) and ANGPTL4 (r = 0.540; P < 0.05) in T3 and T1, respectively, and LXRα showed no correlation with ANGPTL3. Relative ANGTPL3 mRNA expression was negatively correlated with total cholesterol (r = -0.434; P < 0.05) and triglyceride (r = -0.645; P < 0.01) concentrations in T3 and T1, respectively; There was no significant correlation between ANGTPL3 and carcass traits. Relative ANGTPL3 mRNA expression in cultured bovine hepatocytes was downregulated in oleate treatment. Together, these findings suggest that ANGPTL3 downregulation in late fattening phases is associated with the changes in lipid metabolism.
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Affiliation(s)
- Rika Shikida
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Minji Kim
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Makoto Futohashi
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Koki Nishihara
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Huseong Lee
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Yutaka Suzuki
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yeolchang Baek
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Tatsunori Masaki
- Hyogo Prefectural Technology Center of Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan
| | - Kentaro Ikuta
- Hyogo Prefectural Technology Center of Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center of Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Satoshi Haga
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Fuminori Terada
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Sanggun Roh
- Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
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Ning Y, Zhang L, Wang W, Wu S. Effect of genetic variants in the SMAD1 and SMAD5 genes promoter on growth and beef quality traits in cattle. Gene 2022; 819:146220. [PMID: 35093446 DOI: 10.1016/j.gene.2022.146220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/15/2021] [Accepted: 01/13/2022] [Indexed: 11/27/2022]
Abstract
The SMAD1 and SMAD5 genes belong to mothers against decapentaplegic proteins family, which participate in the BMP pathway to control skeletal myogenesis and growth. In the present study, we analyzed the associations between polymorphisms of SMAD1 and SMAD5 genes promoter and important economical traits in Qinchuan cattle. Four SNPs in the SMAD1 gene promoter and three SNPs in the SMAD5 promoter were identified by sequencing of 448 Qinchuan cattles. Allelic and frequency analyses of these SNPs resulted in eight haplotypes both in the promoters of the two genes promoter and identified potential cis-regulatory transcription factor (TF) components. In addition, correlation analysis showed that cattle SMAD1 promoter activity of individuals with Hap4 (P < 0.01) was stronger than that of individuals with Hap2. while the transcriptional activity of individuals with Hap3 within SMAD5 gene promoter was significantly (P < 0.01) higher followed by H2. Uniformly, diplotypes H4-H6 of SMAD1 gene and H1-H3 of SMAD5 gene performed significant (P < 0.01) associations with body measurement and improved carcass quality traits. All these results have indicated that polymorphisms in SMAD1 and SMAD5 genes promoter could impact the transcriptional regulation and then affect muscle content in beef cattle. Moreover, both the SMAD1 and SMAD5 genes were expressed ubiquitously in 10 tissues and had higher expression in the longissimus thoracis tissue from 6-month-old and 12-month-old cattle than in cattle of other ages. We can conclude that SMAD1 and SMAD5 genes may play an important role in muscle growth and development, and the variants mapped within SMAD1 and SMAD5 genes can be utilized in molecular marker-assisted selection for cattle carcass quality and body measurement traits in breed improvement programs of Qinchuan cattle.
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Affiliation(s)
- Yue Ning
- College of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi 712000, China
| | - Le Zhang
- Institute of Physical Education, Yan'an University, Yan'an 716000, Shaanxi, China.
| | - Wenbo Wang
- College of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi 712000, China
| | - Sen Wu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
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Molecular cloning and characterization of angiopoietin-like protein-8 gene in pigs and its tissue-specific expression in different animals. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00824-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gui LS, Raza SHA, Zhou L, Garcia M, Abd El-Aziz AH, Wei D, Hou S, Jia J, Wang Z. Association between Single Nucleotide Polymorphisms in SIRT1 and SIRT2 Loci and Growth in Tibetan Sheep. Animals (Basel) 2020; 10:ani10081362. [PMID: 32781630 PMCID: PMC7459998 DOI: 10.3390/ani10081362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/05/2020] [Indexed: 12/19/2022] Open
Abstract
Simple Summary In summary, three single nucleotide polymorphisms (SNPs) were observed including two SNPs (g.3148 C > T and g.3570 G > A) in SIRT1, and one SNP (g.8074 T > A) in SIRT2 through sequence analysis. Association analyses suggested that all three SNPs were associated growth-related traits in Tibetan sheep. These findings imply that both SIRT1 and SIRT2 may play an important role in growth traits and are potential biomarkers for Marker-assisted selection (MAS). Abstract Silent information regulator 1 and 2 (SIRT1, 2) were NAD+-dependent histone or non-histone deacetylase, which emerged as key metabolic sensors in several tissues of mammals. In the present study, the search for polymorphisms within the ovine SIRT1 and SIRT2 loci as well as association analyses between SNPs and growth-related traits were performed in Tibetan sheep. To determine the expression pattern of SIRT1 and SIRT2 genes in Tibetan sheep, the quantitative real-time polymerase chain reaction (qPCR) analysis revealed that those two genes were widely expressed in diverse tissues. Expression of SIRT1 was less in abomasum of lamb, whereas it was greater in duodenum within adult stage. In the case of SIRT2, the greatest expression was observed in reticulum (lamb) and in muscle (adult), whereas the least expression was in liver for lamb and in kidney for adult animals. The association analysis demonstrated that g.3148 C > T polymorphism of SIRT1 affected heart girth (p = 0.002). The g.8074 T > A SNP of SIRT2 had a significant correlation with body weight (p = 0.011) and body length (p = 0.008). These findings suggested that the SIRT1 and SIRT2 polymorphism was involved in growth-related traits in Tibetan sheep, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep.
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Affiliation(s)
- Lin-sheng Gui
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Sayed Haidar Abbas Raza
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Li Zhou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Matthew Garcia
- School of Animal Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA;
| | - Ayman Hassan Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt;
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China;
| | - Shengzhen Hou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Jianlei Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Zhiyou Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
- Correspondence:
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Gao Y, Huang B, Bai F, Wu F, Zhou Z, Lai Z, Li S, Qu K, Jia Y, Lei C, Dang R. Two Novel SNPs in RET Gene Are Associated with Cattle Body Measurement Traits. Animals (Basel) 2019; 9:E836. [PMID: 31640119 PMCID: PMC6826558 DOI: 10.3390/ani9100836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022] Open
Abstract
The rearrangement of the transfection (RET) gene, which mediates the functions of the ganglion in the gastrointestinal tract, plays an important role in the development of the gastrointestinal nervous system. Therefore, the RET gene is a potential factor influencing animal body measurement. The aim of this study was to reveal the significant genetic variations in the bovine RET gene and investigate the relationship between genotypes and body measurement in two Chinese cattle breeds (Qinchuan and Nanyang cattle). In this study, two SNPs (c.1407A>G and c.1425C>G) were detected in the exon 7 of RET gene by sequencing. For the SNP1 and SNP2, the GG genotype was significantly associated with body height, hip height, and chest circumference in Qinchuan cattle (p < 0.05). Individuals with an AG-CC genotype showed the lowest value of all body measurement in both breeds. Our results demonstrate that the polymorphisms in the bovine RET gene were significantly associated with body measurement, which could be used as DNA marker on the marker-assisted selection (MAS) and improve the performance of beef cattle.
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Affiliation(s)
- Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China.
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Fei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Zihui Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Zhenyu Lai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China.
| | - Yutang Jia
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei 230001, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
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Gui LS, Raza SHA, Garcia M, Sun YG, Ullah I, Han YC. Genetic variants in the SIRT6 transcriptional regulatory region affect gene activity and carcass quality traits in indigenous Chinese beef cattle (Bos taurus). BMC Genomics 2018; 19:785. [PMID: 30382814 PMCID: PMC6211504 DOI: 10.1186/s12864-018-5149-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/08/2018] [Indexed: 01/21/2023] Open
Abstract
Background The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is predominately expressed in kidney, compared with other tissues. In 535 indigenous Chinese beef cattle, two novel single nucleotide polymorphisms (SNPs) were identified within the promoter region of the SIRT6 gene. Results Association analysis indicated that G allele of the c.-1100 A > G had a positive effect on fat deposition, and the Hap4/4 diplotype had more favourable results than other dipoltypes with respect to the evaluation of carcass quality traits. Furthermore, promoter activity associated with the Hap3 haplotype was measured at higher levels than the Hap1 haplotype, which would be in agreement with the previously described association analysis. Conclusion The SIRT6 promoter variants significantly affect transcriptional levels and subsequently significantly influence bovine intramscular fat content.
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Affiliation(s)
- Lin-Sheng Gui
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China.,College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Matthew Garcia
- Utah State University, School of Animal Dairy and Veterinary Sciences, Logan, UT, 84322, USA
| | - Yong-Gang Sun
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China
| | - Irfan Ullah
- College of Bio-medical engineering Chongqing University Chongqing, Shapingba 400044, People's Republic of China
| | - Yin-Cang Han
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China.
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Guo H, Raza SHA, Schreurs NM, Khan R, Wei D, Wang L, Zhang S, Zhang L, Wu S, Ullah I, Hosseini SM, Zan L. Genetic variants in the promoter region of the KLF3 gene associated with fat deposition in Qinchuan cattle. Gene 2018; 672:50-55. [DOI: 10.1016/j.gene.2018.06.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/16/2018] [Accepted: 06/07/2018] [Indexed: 12/12/2022]
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Fu W, Chen N, Han S, Huang J, Li F, Hao R, Chen H, Lei C, Ma Y. Tissue expression and variation analysis of three bovine adipokine genes revealed their effect on growth traits in native Chinese cattle. Reprod Domest Anim 2018; 53:1227-1234. [PMID: 30011090 DOI: 10.1111/rda.13244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/12/2018] [Accepted: 05/17/2018] [Indexed: 11/28/2022]
Abstract
Adipokines play a crucial role in the regulation of energy homeostasis; however, little is known about genetic alterations in this family that may contribute to economic traits in cattle. Therefore, this study conducts transcript profiles, variations and association studies of three major adipokines, leptin (LEP), tumour necrosis factor (TNF) and angiopoietin-like protein 8 (ANGPTL8), to evaluate their effects on native Chinese cattle. Using quantitative real-time PCR, the study revealed that the bovine LEP was expressed primarily in the back and visceral fat, while TNF was predominantly expressed in spleen and ANGPTL8 was mainly expressed in back fat and liver. Five single nucleotide polymorphisms (SNPs) including two missense SNPs (SNP1: g.12254T>C and SNP2: g.14177C>T) in LEP, a synonymous SNP (SNP3: g.2130A>G) in TNF and two SNPs (SNP4: g.629G>A and SNP5: g.884T>C) in the 5'UTR of ANGPTL8 were identified and genotyped in 537 individuals from six Chinese cattle breeds. Bioinformatics analysis revealed that SNP1 might disrupt the efficient binding of LEP to its receptor, SNP3 might affect translation efficiency of TNF, and SNP4 and SNP5 were likely to affect stability, splicing and nuclear export of ANGPTL8 mRNA. Consistently, association studies indicated that three SNPs (SNP1, SNP3 and SNP5) were significantly associated with body weight, heart girth, average daily gain, hip width and body length in 100 Nanyang cattle (p < 0.05). Overall, our results support the view that LEP, TNF and ANGPTL8 could be used as biomarkers to improve the growth performance in Chinese cattle selection programmes.
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Affiliation(s)
- Weiwei Fu
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuang Han
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Ruijie Hao
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China.,Agricultural College, Ningxia University, Yinchuan, Ningxia, China
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Chen N, Wang F, Yu N, Gao Y, Huang J, Dang R, Huang Y, Lan X, Lei C, Chen H. Polymorphisms in MX2 Gene Are Related with SCS in Chinese Dairy Cows. Anim Biotechnol 2017; 29:81-89. [PMID: 28471716 DOI: 10.1080/10495398.2017.1307217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Viral infections can play direct or indirect roles in the etiology of the bovine mastitis. Mx dynamin-like GTPase 2 (MX2) gene is a main effector of the antiviral innate immune defense mediated by type I interferon (IFN I), which was demonstrated to confer positive antiviral responses to many viruses. Given the importance of the MX2 in modulating the host immune response, MX2 gene may be a suitable candidate gene for studying disease resistance in dairy cattle. Here, we scanned the sequence variation of the MX2 gene in Chinese indigenous cattle breeds. Twenty-three previously reported SNPs were identified. To further analyze the effects of SNPs detected on mastitis disease, analysis of two SNPs (g.787527 C > T and g.787610 T > C) from 297 Chinese Holstein cows revealed a significant association with somatic cell score (SCS). Although functional studies are necessary to ascertain whether these two SNPs are causal polymorphisms or merely in linkage with the true causal SNPs, implementation of these two SNPs as genetic markers in the dairy industry may be beneficial in selecting individuals with lower SCS.
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Affiliation(s)
- Ningbo Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - FengQiao Wang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Nongqi Yu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Yuan Gao
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Jieping Huang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Ruihua Dang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Yongzhen Huang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Xianyong Lan
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Chuzhao Lei
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Hong Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
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