1
|
Suárez-Vega A, Gutiérrez-Gil B, Fonseca PAS, Hervás G, Pelayo R, Toral PG, Marina H, de Frutos P, Arranz JJ. Milk transcriptome biomarker identification to enhance feed efficiency and reduce nutritional costs in dairy ewes. Animal 2024; 18:101250. [PMID: 39096599 DOI: 10.1016/j.animal.2024.101250] [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: 02/05/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 08/05/2024] Open
Abstract
In recent years, rising prices for high-quality protein-based feeds have significantly increased nutrition costs. Consequently, investigating strategies to reduce these expenses and improve feed efficiency (FE) have become increasingly important for the dairy sheep industry. This research investigates the impact of nutritional protein restriction (NPR) during prepuberty and FE on the milk transcriptome of dairy Assaf ewes (sampled during the first lactation). To this end, we first compared transcriptomic differences between NPR and control ewes. Subsequently, we evaluated gene expression differences between ewes with divergent FE, using feed conversion ratio (FCR), residual feed intake (RFI), and consensus classifications of high- and low-FE animals for both indices. Lastly, we assess milk gene expression as a predictor of FE phenotype using random forest. No effect was found for the prepubertal NPR on milk performance or FE. Moreover, at the milk transcriptome level, only one gene, HBB, was differentially expressed between the NPR (n = 14) and the control group (n = 14). Further, the transcriptomic analysis between divergent FE sheep revealed 114 differentially expressed genes (DEGs) for RFI index (high-FERFI = 10 vs low-FERFI = 10), 244 for FCR (high-FEFCR = 10 vs low-FEFCR = 10), and 1 016 DEGs between divergent consensus ewes for both indices (high-FEconsensus = 8 vs low-FEconsensus = 8). These results underscore the critical role of selected FE indices for RNA-Seq analyses, revealing that consensus divergent animals for both indices maximise differences in transcriptomic responses. Genes overexpressed in high-FEconsensus ewes were associated with milk production and mammary gland development, while low-FEconsensus genes were linked to higher metabolic expenditure for tissue organisation and repair. The best prediction accuracy for FE phenotype using random forest was obtained for a set of 44 genes consistently differentially expressed across lactations, with Spearman correlations of 0.37 and 0.22 for FCR and RFI, respectively. These findings provide insights into potential sustainability strategies for dairy sheep, highlighting the utility of transcriptomic markers as FE proxies.
Collapse
Affiliation(s)
- A Suárez-Vega
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 Leon, Spain
| | - B Gutiérrez-Gil
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 Leon, Spain
| | - P A S Fonseca
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 Leon, Spain
| | - G Hervás
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - R Pelayo
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 Leon, Spain
| | - P G Toral
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - H Marina
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 Leon, Spain
| | - P de Frutos
- Instituto de Ganadería de Montaña (CSIC-University of León), Finca Marzanas s/n, 24346 Grulleros, León, Spain
| | - J J Arranz
- Dpto. Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24007 Leon, Spain.
| |
Collapse
|
2
|
Liu R, Fang X, Lu X, Liu Y, Li Y, Bai X, Ding X, Yang R. Polymorphisms of the SCD1 Gene and Its Association Analysis with Carcass, Meat Quality, Adipogenic Traits, Fatty Acid Composition, and Milk Production Traits in Cattle. Animals (Basel) 2024; 14:1759. [PMID: 38929378 PMCID: PMC11200384 DOI: 10.3390/ani14121759] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Stearoyl-CoA desaturase-1 (SCD1) is a key enzyme in the biosynthesis of monounsaturated fatty acids and is considered a candidate gene for improving milk and meat quality traits. Sanger sequencing was employed to investigate the genetic polymorphism of the fifth exon and intron of bovine SCD1, revealing four SNPs, g.21272246 A>G, g.21272306 T>C, g.21272422 C>T, and g.21272529 A>G. Further variance analysis and multiple comparisons were conducted to examine the relationship between variation sites and economic traits in Chinese Simmental cattle, as well as milk production traits in Holstein cows. The findings revealed these four loci exhibited significant associations with carcass traits (carcass weight, carcass length, backfat thickness, and waist meat thickness), meat quality (pH value, rib eye area, and marbling score), adipogenic traits (fat score and carcass fat coverage rate), and fatty acid composition (linoleic acid and α-linolenic acid). Furthermore, these loci were additionally found to be significantly associated with average milk yield and milk fat content in cows. In addition, a haplotype analysis of combinations of SNPs showed that H2H3 has a significant association with adipogenic traits and H2H2 was associated with higher levels of linoleic acid and α-linolenic acid than the other combinations. These results suggest that the four SNPs are expected to be prospective genetic markers for the above economic traits. In addition, the function of SNPs in exon 5 of SCD1 on gene expression and protein structure needs to be explored in the future.
Collapse
Affiliation(s)
- Ruimin Liu
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China
| | - Xibi Fang
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
| | - Xin Lu
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
| | - Yue Liu
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
| | - Yue Li
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
| | - Xue Bai
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China
| | - Xiangbin Ding
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China
| | - Runjun Yang
- College of Animal Science, Jilin University, Changchun 130062, China (X.L.)
| |
Collapse
|
3
|
Suárez-Vega A, Frutos P, Gutiérrez-Gil B, Esteban-Blanco C, Toral PG, Arranz JJ, Hervás G. Feed efficiency in dairy sheep: An insight from the milk transcriptome. Front Vet Sci 2023; 10:1122953. [PMID: 37077950 PMCID: PMC10106586 DOI: 10.3389/fvets.2023.1122953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/16/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionAs higher feed efficiency in dairy ruminants means a higher capability to transform feed nutrients into milk and milk components, differences in feed efficiency are expected to be partly linked to changes in the physiology of the mammary glands. Therefore, this study aimed to determine the biological functions and key regulatory genes associated with feed efficiency in dairy sheep using the milk somatic cell transcriptome.Material and methodsRNA-Seq data from high (H-FE, n = 8) and low (L-FE, n = 8) feed efficiency ewes were compared through differential expression analysis (DEA) and sparse Partial Least Square-Discriminant analysis (sPLS-DA).ResultsIn the DEA, 79 genes were identified as differentially expressed between both conditions, while the sPLS-DA identified 261 predictive genes [variable importance in projection (VIP) > 2] that discriminated H-FE and L-FE sheep.DiscussionThe DEA between sheep with divergent feed efficiency allowed the identification of genes associated with the immune system and stress in L-FE animals. In addition, the sPLS-DA approach revealed the importance of genes involved in cell division (e.g., KIF4A and PRC1) and cellular lipid metabolic process (e.g., LPL, SCD, GPAM, and ACOX3) for the H-FE sheep in the lactating mammary gland transcriptome. A set of discriminant genes, commonly identified by the two statistical approaches, was also detected, including some involved in cell proliferation (e.g., SESN2, KIF20A, or TOP2A) or encoding heat-shock proteins (HSPB1). These results provide novel insights into the biological basis of feed efficiency in dairy sheep, highlighting the informative potential of the mammary gland transcriptome as a target tissue and revealing the usefulness of combining univariate and multivariate analysis approaches to elucidate the molecular mechanisms controlling complex traits.
Collapse
Affiliation(s)
- Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Pilar Frutos
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Pablo G. Toral
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
| | - Juan-José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
- *Correspondence: Juan-José Arranz
| | - Gonzalo Hervás
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
| |
Collapse
|
4
|
Xu Y, Xiong J, Gao W, Wang X, Shan S, Zhao L, Cheng G. Dietary Fat and Polyunsaturated Fatty Acid Intakes during Childhood Are Prospectively Associated with Puberty Timing Independent of Dietary Protein. Nutrients 2022; 14:nu14020275. [PMID: 35057456 PMCID: PMC8778261 DOI: 10.3390/nu14020275] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/29/2022] Open
Abstract
Dietary fat and fat quality have been inconsistently associated with puberty timing. The aim of this study was to investigate the prospective associations of dietary fat, saturated fatty acid (SFA), polyunsaturated fatty acid (PUFA), and monounsaturated fatty acid (MUFA) with puberty timing. Using longitudinal data from China Health and Nutrition Survey (CHNS) and Southwest China Childhood Nutrition and Growth (SCCNG) Study, we analyzed dietary data, anthropometric measurements, and potential confounders. Dietary intakes were assessed by 3-day 24-h recalls. Age at Tanner stage 2 for breast/genital development (B2/G2) and age at menarche/voice break (M/VB) were used as puberty development markers. Cox proportional hazard regression models were used to estimate the relevance of dietary intake of total fat, SFA, PUFA, and MUFA on puberty timing. Among 3425 girls and 2495 boys, children with higher intakes of total fat and PUFA were more likely to reach their B2/G2 or M/VB at an earlier age. Associations were not attenuated on additional adjustment for childhood dietary protein intake. However, higher intakes of SFA or MUFA were not independently associated with puberty development. A higher intake of dietary fat and PUFA in prepuberty was associated with earlier puberty timing, which was independent of dietary protein intake.
Collapse
Affiliation(s)
- Yujie Xu
- Department of Nutrition and Food Safety, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Y.X.); (W.G.)
| | - Jingyuan Xiong
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China;
| | - Wanke Gao
- Department of Nutrition and Food Safety, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Y.X.); (W.G.)
| | - Xiaoyu Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China; (X.W.); (S.S.)
| | - Shufang Shan
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China; (X.W.); (S.S.)
| | - Li Zhao
- Department of Health Policy and Management, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China;
| | - Guo Cheng
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China; (X.W.); (S.S.)
- Correspondence: ; Tel.: +86-28-85502220
| |
Collapse
|
5
|
Bioinformatics analysis and genetic polymorphisms in genomic region of the bovine SH2B2 gene and their associations with molecular breeding for body size traits in qinchuan beef cattle. Biosci Rep 2021; 40:222267. [PMID: 32110807 PMCID: PMC7069895 DOI: 10.1042/bsr20192113] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 11/17/2022] Open
Abstract
The Src homology 2 B 2 (SH2B2) gene regulate energy balance and body weight at least partially by enhancing Janus kinase-2 (JAK2)-mediated cytokine signaling, including leptin and/or GH signaling. Leptin is an adipose hormone that controls body weight. The objective of the present study is to evaluate the association between body measurement traits and SH2B2 gene polymorphisms as responsible mutations. For this purpose, we selected four single-nucleotide polymorphisms (SNPs) in SH2B2 gene, including two in intron 5 (g.20545A>G, and g.20570G>A, one synonymous SNP g.20693T>C, in exon 6 and one in intron 8 (g.24070C>A, and genotyped them in Qinchuan cattle. SNPs in sample populations were in medium polymorphism level (0.250<PIC<0.500). Association study indicated that the g.20570G>A, g.20693T>C, and g.24070C>A, significantly (P < 0.05) associated with body length (BL) and chest circumference (CC) in Qinchuan cattle. In addition, H4H3 and H5H5 diplotype had highly significantly (P < 0.01) greater body length (BL), rump length (RL), and chest circumference (CC) than H4H2. Our investigation will not only extend the spectrum of genetic variation of bovine SH2B2 gene, but also provide useful information for the marker assisted selection in beef cattle breeding program.
Collapse
|
6
|
Pećina M, Ivanković A. Candidate genes and fatty acids in beef meat, a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1991240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mateja Pećina
- Zavod za specijalno stočarstvo, Sveučilište u Zagrebu Agronomski fakultet, Zagreb, Hrvatska
| | - Ante Ivanković
- Zavod za specijalno stočarstvo, Sveučilište u Zagrebu Agronomski fakultet, Zagreb, Hrvatska
| |
Collapse
|
7
|
Olasege BS, Zhang S, Zhao Q, Liu D, Sun H, Wang Q, Ma P, Pan Y. Genetic parameter estimates for body conformation traits using composite index, principal component, and factor analysis. J Dairy Sci 2019; 102:5219-5229. [PMID: 31056333 DOI: 10.3168/jds.2018-15561] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 03/03/2019] [Indexed: 11/19/2022]
Abstract
Information about genetic parameters is population specific and it is crucial for designing animal breeding programs and predicting response to selection. This study was carried out to estimate the genetic parameters for 23 body conformation traits of 45,517 Chinese Holstein reared in Eastern China from 1995 to 2017 with the Bayesian inference method using a linear animal mixed model. The methods to integrate these traits included (1) using the composite index from the Dairy Association of China and (2) applying principal component analysis and factor analysis to explore the relationship between the conformation traits. Estimates of heritability using the composite index were low (0.04; feet and legs) to moderate (0.23; body capacity). Strong genetic correlations were observed between the individual body conformation traits. Both principal components (1 to 7; eigenvalues ≥ 1) and latent factors (1 to 7; eigenvalues ≥ 1) explained 60.37% of total variability. Principal component 1 and factor 1 accounted for the traits that are usually associated with milk production. Moderate to low heritability were estimated through multi-trait analysis for principal components (from 0.07 to 0.21) and latent factors (from 0.07 to 0.23). Genetic correlations among the 2 multivariate techniques are typically lower compared with the one existing among the measured traits. Results from these analyses suggest the possibility of using both principal component analysis and factor analysis in morphological evaluation, simplifying the information given by the body conformation traits into new variables that could be useful for the genetic improvement of the Chinese Holstein population. This information could also be used to avoid analyzing large number of correlated traits, thereby improving precision and reducing computation burdens to analyze large and complex data.
Collapse
Affiliation(s)
- B S Olasege
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - S Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Q Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - D Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - H Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Q Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, PR China
| | - P Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Y Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, PR China.
| |
Collapse
|
8
|
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: 3.6] [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]
|
9
|
The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed. Mol Biol Rep 2018; 45:1445-1456. [PMID: 30006771 DOI: 10.1007/s11033-018-4211-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/09/2018] [Indexed: 12/25/2022]
Abstract
In the past few decades, enhancement of animal productivity has been gaining increasing attention among decisions-makers, politicians, mangers, and breeders, because of the increasing of world population and shortage of natural resources. The selection of high productivity animals is the main goal, through the application of genetic improvement programs. The use of molecular genetics has conferred significant breeding advantages over conventional breeding techniques. In this regard, many economic characteristics are controlled by a small number of multiple gene loci, each of which is responsible for trait diversity and hence they are referred to as quantitative trait loci (QTL). Single-nucleotide polymorphisms (SNPs), which have recently been discovered through DNA sequencing, are considered one of the most useful types of genetic marker. SNPs are found where different nucleotides occur at the same position in the DNA sequence. They are found in both coding and noncoding regions of the genome and are present at one SNP in every 1000 b. Strategies for the identification and application of markers are based on reference to examples of loci that can control various traits. Furthermore, markers for growth, body measurements, and meat quality traits are preferred, because they can be used to predict the performance of animals, via blood samples, in the first few days of animal life. Marker-assisted selection using SNPs, such asSIRT1, SIRT2, LPL, CRTC2, SIX4, UCPs, and ZBTB38as selection criteria of body measurements and meat traits in beef cattle, will be beneficial in selection and breeding programs. The proteomic is a novel marker and a new approache of biotechnology which increases the understanding of the biological processes, besides being a remarkable biomarker that interrelated to growth and meat quality traits. Proteomics is a vigorous tool as usage for deduces molecular processes between quality traits and muscle proteins, which are helpful in analyzing the mechanisms of biochemistry that influence quality. So they could be potential biomarker for some meat quality traits. Among them, Actin, Myosin, Heat shock proteins are used a novel approaches in the field of biotechnology to understand the proteomics changes. This review article highlights the novel findings on the potential use of MAS and proteomics as biomarker for the selection for meat quality and carcass traits in Qinchuan cattle breed.
Collapse
|
10
|
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: 25] [Impact Index Per Article: 3.6] [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.
Collapse
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.
| |
Collapse
|
11
|
Raza SHA, Gui L, Khan R, Schreurs NM, Xiaoyu W, Wu S, Mei C, Wang L, Ma X, Wei D, Guo H, Zhang S, Wang X, Kaleri HA, Zan L. Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle. Gene 2017; 645:55-59. [PMID: 29273553 DOI: 10.1016/j.gene.2017.12.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/18/2017] [Indexed: 11/18/2022]
Abstract
Fatty acid synthase (FASN) is an enzyme involved with fat deposition and fatty acid composition in cattle. This study was conducted to detect single nucleotide polymorphisms (SNPs) of the FASN gene and explore their relationships with ultrasound carcass traits in order to assess the potential use of the FASN gene for the breeding selection of Qinchuan cattle for desirable carcass traits. The frequencies of SNP g.12740C>T, g.13192T>C and g.13232C>T were identified in 525 individual Qinchuan cattle which were also assessed for backfat depth, eye muscle area and intramuscular fat by ultrasound. According to the PIC values, g.13192T>C possessed an intermediate polymorphism (0.25<PIC<0.5). The SNPs of g.13232C>T, g.12740C>T possessed low polymorphism (PIC<0.25). Chi-square tests showed that g.13192T>C were in Hardy-Weinberg disequilibrium (c2<c0.052). Two SNPs were found to be associated with variation in ultrasound carcass traits. The H2H2 diplotypes had a greater back fat depth than H1H1, H1H4 and H1H2 (P<0.01). The TT genotype at g.13192T>C was associated with a greater eye muscle area and the TT genotype at g.13232C>T was associated with greater intramuscular fat. When these genotypes were combined there was no difference in eye muscle area and intramuscular fat between the diplotypes. The H2H2 diplotype was associated with carcass traits that are likely to provide economic advantage in Qinchuan cattle. Variations in the FASN genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
Collapse
Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China
| | - Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Nicola M Schreurs
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Wang Xiaoyu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Sen Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xueyao Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dawei Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xingping Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hubdar Ali Kaleri
- Department of Animal Science and Aquaculture, Dalhousie University, Canada
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China.
| |
Collapse
|
12
|
Yao D, Luo J, He Q, Shi H, Li J, Wang H, Xu H, Chen Z, Yi Y, Loor JJ. SCD1 Alters Long-Chain Fatty Acid (LCFA) Composition and Its Expression Is Directly Regulated by SREBP-1 and PPARγ 1 in Dairy Goat Mammary Cells. J Cell Physiol 2016; 232:635-649. [DOI: 10.1002/jcp.25469] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Dawei Yao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Qiuya He
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Hengbo Shi
- College of Life Sciences; Zhejiang Sci-Tech University; Hangzhou P. R. China
| | - Jun Li
- College of Animal Science and Technology; Henan University of Animal Husbandry and Economy; Zhengzhou Henan P. R. China
| | - Hui Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Huifen Xu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Zhi Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Yongqing Yi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi P. R. China
| | - Juan J. Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences; University of IIlinois; Urbana Illinois
| |
Collapse
|
13
|
A novel selection signature in stearoyl-coenzyme A desaturase (SCD) gene for enhanced milk fat content in Bubalus bubalis. Trop Anim Health Prod 2016; 48:1343-9. [DOI: 10.1007/s11250-016-1092-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022]
|
14
|
Pegolo S, Cecchinato A, Mele M, Conte G, Schiavon S, Bittante G. Effects of candidate gene polymorphisms on the detailed fatty acids profile determined by gas chromatography in bovine milk. J Dairy Sci 2016; 99:4558-4573. [DOI: 10.3168/jds.2015-10420] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/10/2016] [Indexed: 11/19/2022]
|
15
|
Aali M, Moradi-Shahrbabak H, Moradi-Shahrbabak M, Sadeghi M, Kohram H. Polymorphism in the SCD gene is associated with meat quality and fatty acid composition in Iranian fat- and thin-tailed sheep breeds. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
16
|
Li C, Sun D, Zhang S, Liu L, Alim MA, Zhang Q. A post-GWAS confirming the SCD gene associated with milk medium- and long-chain unsaturated fatty acids in Chinese Holstein population. Anim Genet 2016; 47:483-90. [PMID: 26970560 DOI: 10.1111/age.12432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2016] [Indexed: 12/12/2022]
Abstract
The stearoyl-CoA desaturase (delta-9-desaturase) gene encodes a key enzyme in the cellular biosynthesis of monounsaturated fatty acids. In our initial genome-wide association study (GWAS) of Chinese Holstein cows, 19 SNPs fell in a 1.8-Mb region (20.3-22.1 Mb) on chromosome 26 underlying the SCD gene and were highly significantly associated with C14:1 or C14 index. The aims of this study were to verify whether the SCD gene has significant genetic effects on milk fatty acid composition in dairy cattle. By resequencing the entire coding region of the bovine SCD gene, a total of six variations were identified, including three coding variations (g.10153G>A, g.10213T>C and g.10329C>T) and three intronic variations (g.6926A>G, g.8646G>A and g.16158G>C). The SNP in exon 3, g.10329C>T, was predicted to result in an amino acid replacement from alanine (GCG) to valine (GTG) in the SCD protein. An association study for 16 milk fatty acids using 346 Chinese Holstein cows with accurate phenotypes and genotypes was performed using the mixed animal model with the proc mixed procedure in sas 9.2. All six detected SNPs were revealed to be associated with six medium- and long-chain unsaturated fatty acids (P = 0.0457 to P < 0.0001), specifically for C14:1 and C14 index (P = 0.0005 to P < 0.0001). Subsequently, strong linkage disequilibrium (D' = 0.88-1.00) was observed among all six SNPs in SCD and the five SNPs (rs41623887, rs109923480, rs42090224, rs42092174 and rs42091426) within the 1.8-Mb region identified in our previous GWAS, indicating that the significant association of the SCD gene with milk fatty acid content traits reduced the observed significant 1.8-Mb chromosome region in GWAS. Haplotype-based analysis revealed significant associations of the haplotypes encompassing the six SCD SNPs and one SNP (rs109923480) in a GWAS with C14:1, C14 index, C16:1 and C16 index (P = 0.0011 to P < 0.0001). In summary, our findings provide replicate evidence for our previous GWAS and demonstrate that variants in the SCD gene are significantly associated with milk fatty acid composition in dairy cattle, which provides clear evidence for an increased understanding of milk fatty acid synthesis and enhances opportunities to improve milk-fat composition in dairy cattle.
Collapse
Affiliation(s)
- C Li
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - D Sun
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - S Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - L Liu
- Beijing Dairy Cattle Center, Beijing, 100085, China
| | - M A Alim
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Q Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
17
|
Polymorphic effects of FABP4 and SCD genes on intramuscular fatty acid profiles in longissimus muscle from two cattle breeds. ACTA VET BRNO 2015. [DOI: 10.2754/avb201584040327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of this study was to evaluate the polymorphic effects of two single nucleotide polymorphisms (SNPs) of fatty acid binding protein (FABP4) and stearoyl-CoA desaturase (SCD) genes on intramuscular fatty acid profiles in the longissimus muscle in two cattle breeds. Two previously reported SNPs of bovine FABP4 (7516G>C) and SCD (878C>T) were in turn assessed for their associations with intramuscular fatty acid profiles from the upper sirloin cuts of Aberdeen Angus and Blonde d’Aquitaine cattle. In total, 33 animals were genotyped using PCR-RFLP. Intramuscular fatty acid composition was evaluated using two complementary statistical approaches: a classical univariate regression model and a multivariate approach using a combination of Principal Component Analysis and Random Forests. Significant effect of FABP4 SNP genotypes was found for several fatty acids including C15:0, C17:0, C18:0, C14:1, C17:1, C18:2n6, C20:4n6, C20:5n3, C22:5n3, total n-3, n-6 and total SFA (P < 0.05). These results suggest that FABP4 is a potential candidate gene affecting fatty acid composition in beef cattle.
Collapse
|
18
|
Gui LS, Zhang YR, Liu GY, Zan LS. Expression of the SIRT2 gene and its relationship with body size traits in Qinchuan cattle (Bos taurus). Int J Mol Sci 2015; 16:2458-71. [PMID: 25622258 PMCID: PMC4346846 DOI: 10.3390/ijms16022458] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/06/2015] [Accepted: 01/13/2015] [Indexed: 11/30/2022] Open
Abstract
Silent information regulator 2 (SIRT2) is a member of the sirtuin family of class III NAD (nicotinamide adenine dinucleotide)-dependent protein deacetylases and may regulate senescence, metabolism and apoptosis. The aims of this study were to investigate whether the SIRT2 gene could be used as a candidate gene in the breeding of Qinchuan cattle. Real-time polymerase chain reaction (RT-PCR) results showed that among all types of tissue that were analyzed, the highest mRNA expression levels of the gene were found in subcutaneous fat. DNA sequencing of 468 individual Qinchuan cattle identified two novel, single nucleotide polymorphisms (g.19501 C > T and g.19518 C > T) in the 3' untranslated region (3'UTR) of the SIRT2 gene. The frequencies of SNP g.19501 C > T and g.19518 C > T were in Hardy-Weinberg disequilibrium in all the samples (chi-square test, χ2 < χ0.052). An association analysis showed that the two loci were significantly correlated with some body size traits and the H2H2 (-CT-CT-) diplotypes performed better than other combinations. These results indicated that the variations in the SIRT2 gene and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
Collapse
Affiliation(s)
- Lin-Sheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Ya-Ran Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Gui-Yao Liu
- Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resource, Yangling 712100, China.
| | - Lin-Sen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
19
|
Asadollahpour Nanaei H, Ansari Mahyari S, Edriss MA. Effect of LEPR, ABCG2 and SCD1 Gene Polymorphisms on Reproductive Traits in the Iranian Holstein Cattle. Reprod Domest Anim 2014; 49:769-74. [DOI: 10.1111/rda.12365] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 05/28/2014] [Indexed: 01/16/2023]
Affiliation(s)
- H Asadollahpour Nanaei
- Department of Animal Science; College of Agriculture; Isfahan University of Technology; Isfahan Iran
| | - S Ansari Mahyari
- Department of Animal Science; College of Agriculture; Isfahan University of Technology; Isfahan Iran
| | - M-A Edriss
- Department of Animal Science; College of Agriculture; Isfahan University of Technology; Isfahan Iran
| |
Collapse
|
20
|
Gui L, Wang H, Wei S, Zhang Y, Zan L. Molecular characterization, expression profiles, and analysis of Qinchuan cattle SIRT1 gene association with meat quality and body measurement traits (Bos taurus). Mol Biol Rep 2014; 41:5237-46. [PMID: 24828021 DOI: 10.1007/s11033-014-3393-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/02/2014] [Indexed: 10/25/2022]
Abstract
Silent information regulator (SIRT1), was closely associated with senescence, metabolism, and apoptosis. The objective of this study was to investigate whether SIRT1 gene could be used as a candidate gene in the breeding process of Qinchuan cattle. Via sequencing technology conducted in 453 individuals of Qinchuan cattle, single nucleotide polymorphisms (G25764A, A25846G, and T25868C) with 5 haplotypes and 6 combined genotypes in 3' untranslated region of SIRT1 gene were identified. In addition, three loci were significantly associated with some of the body measurements and meat quality traits in Qinchuan cattle (P < 0.05), and the H2H2 (GG-AA-CC) diplotypes had better performance than other combinations in Qinchuan cattle. These results suggest that the SIRT1 gene could be used in marker assisted selection to improve the production traits of Qinchuan cattle.
Collapse
Affiliation(s)
- Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | | | | | | | | |
Collapse
|
21
|
Gutiérrez-Gil B, Arranz JJ, Pong-Wong R, García-Gámez E, Kijas J, Wiener P. Application of selection mapping to identify genomic regions associated with dairy production in sheep. PLoS One 2014; 9:e94623. [PMID: 24788864 PMCID: PMC4006912 DOI: 10.1371/journal.pone.0094623] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/19/2014] [Indexed: 11/18/2022] Open
Abstract
In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of "dairy breeds." This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.
Collapse
Affiliation(s)
| | | | - Ricardo Pong-Wong
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, United Kingdom
| | | | - James Kijas
- Animal, Food and Health Sciences, CSIRO, Brisbane, Australia
| | - Pamela Wiener
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, United Kingdom
| |
Collapse
|
22
|
Saatchi M, Garrick DJ, Tait RG, Mayes MS, Drewnoski M, Schoonmaker J, Diaz C, Beitz DC, Reecy JM. Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle. BMC Genomics 2013; 14:730. [PMID: 24156620 PMCID: PMC3819509 DOI: 10.1186/1471-2164-14-730] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/21/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this study was to determine the extent to which molecular markers could account for variation in fatty acid composition of skeletal muscle and identify genomic regions that harbor genetic variation. RESULTS Subsets of markers on the Illumina 54K bovine SNPchip were able to account for up to 57% of the variance observed in fatty acid composition. In addition, these markers could be used to calculate a direct genomic breeding values (DGV) for a given fatty acids with an accuracy (measured as simple correlations between DGV and phenotype) ranging from -0.06 to 0.57. Furthermore, 57 1-Mb regions were identified that were associated with at least one fatty acid with a posterior probability of inclusion greater than 0.90. 1-Mb regions on BTA19, BTA26 and BTA29, which harbored fatty acid synthase, Sterol-CoA desaturase and thyroid hormone responsive candidate genes, respectively, explained a high percentage of genetic variance in more than one fatty acid. It was also observed that the correlation between DGV for different fatty acids at a given 1-Mb window ranged from almost 1 to -1. CONCLUSIONS Further investigations are needed to identify the causal variants harbored within the identified 1-Mb windows. For the first time, Angus breeders have a tool whereby they could select for altered fatty acid composition. Furthermore, these reported results could improve our understanding of the biology of fatty acid metabolism and deposition.
Collapse
Affiliation(s)
- Mahdi Saatchi
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Dorian J Garrick
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Richard G Tait
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
- Present address: USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mary S Mayes
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Mary Drewnoski
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID 83844, USA
| | - Jon Schoonmaker
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA
| | - Clara Diaz
- INIA, Depto. de Mejora Genética Animal, Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Don C Beitz
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - James M Reecy
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| |
Collapse
|
23
|
Zetouni L, de Camargo GMF, da Silva Fonseca PD, Gil FMM, Lugo NAH, Aspilcueta-Borquis RR, Cervini M, Tonhati H. Effects of a single nucleotide polymorphism in the leptin gene on the productive traits of dairy buffaloes (Bubalus bubalis). Mol Biol Rep 2013; 40:5159-63. [PMID: 23661024 DOI: 10.1007/s11033-013-2618-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 04/30/2013] [Indexed: 12/31/2022]
Abstract
The gene responsible for coding the leptin hormone has been associated with productive and reproductive traits in cattle. In dairy cattle, different polymorphisms found in the leptin gene have been associated with several traits of economic interest, such as energy balance, milk yield and composition, live weight, fertility and dry matter consumption. The aim of this study was to detect genetic variability in the leptin gene of buffaloes and to test possible associations with milk yield, fat and protein percentages, age at first calving and first calving interval. Three genotypes (AA, AG and GG) were identified by polymerase chain reaction-restriction fragment length polymorphism, which presented genotypic frequencies of 0.30, 0.54 and 0.16, respectively. The allele frequencies were 0.57 for the A allele and 0.43 for the G allele. No significant effects were found in the present study, but there is an indicative that leptin gene affects lipid metabolism.
Collapse
Affiliation(s)
- Larissa Zetouni
- Animal Sciences Departament, São Paulo State University, Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, s/n-CEP, Jaboticabal, SP, 14884-900, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Liu M, Ling X, Xiong Y, Xu D. Molecular characterization of differentially expressed TXNIP gene and its association with porcine carcass traits. Mol Biol Rep 2012; 39:10439-46. [PMID: 23053948 DOI: 10.1007/s11033-012-1923-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 10/01/2012] [Indexed: 12/16/2022]
Abstract
Thioredoxin interacting protein (TXNIP), which plays a regulatory role in lipid metabolism and immune regulation, is down-regulated expressed in F(1) hybrids Landrace × Yorkshire skeletal muscle. Here we described the molecular characterization of porcine TXNIP gene. The full-length cDNA contains a coding sequence of 1,176 bp nucleotides with untranslated regions of 263 bp at 5'-end and 441 bp at 3'-end, respectively. The predicted molecular mass and isoelectric point of porcine TXNIP is 43.81 kDa and 7.385, respectively. The deduced 391 amino acids exhibit high identity with other mammalian TXNIP. The TXNIP gene contains eight coding exons and seven non coding introns, spans approximately 3,348 bp. The expression of porcine TXNIP mRNA is almost absent in Landrace × Yorkshire and lower level in 6-month-old pigs during skeletal muscle development. Other stages and breeds were high level expressed. Statistical analysis showed the TXNIP gene polymorphism (c.575-4T>C) was different between F(1) hybrids and their parents, was highly associated with dressing percentage (DP) and thorax-waist fat thickness (TFT) in the Yorkshire × Meishan F(2) population. The possible role of TXNIP was discussed.
Collapse
Affiliation(s)
- Min Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | | |
Collapse
|