1
|
Archer H, Soares RAN, Jafarikia M, Lillie BN, Schenkel F, Squires EJ. Effect of SNPs in the Promoter Region on the Expression of Cytochrome P450 2E1 (CYP2E1) in Pig Liver. Animals (Basel) 2024; 14:1163. [PMID: 38672311 PMCID: PMC11047675 DOI: 10.3390/ani14081163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Boar taint, an unfavorable odor in the meat of intact male pigs, is caused primarily by the accumulation of two compounds: androstenone and skatole. This multifactorial trait is regulated by numerous dietary, management and genetic factors. At the mechanistic level, there are many genes known to be involved in boar taint metabolism. Cytochrome P450 2E1 (CYP2E1) impacts boar taint through the phase I metabolism of skatole. The aim of this study was to identify single-nucleotide polymorphisms (SNPs) within the CYP2E1 gene promoter and explore their relationship with the expression of CYP2E1 mRNA and protein. Sequencing of the promoter region using pools of genomic DNA identified seven promoter region SNPs at -159, -586, -1693, -1806, -2322, -2369 and -2514 bp upstream of the ATG start site. Genomic DNA was obtained from 65 boars from the three major swine breeds: Duroc, Landrace and Yorkshire, and individual animals were genotyped for the identified SNPs. RNA was isolated from liver tissue and quantitative PCR was performed to measure CYP2E1 gene expression, while levels of CYP2E1 protein in liver were measured by Western blotting. Significant within-breed variation in CYP2E1 protein and mRNA expression was observed, indicating significant differences in gene expression among individuals. However, levels of CYP2E1 mRNA and protein were not significantly correlated. Two SNPs within the promoter were significantly associated with CYP2E1 mRNA expression, but not with protein expression. This study provides evidence of additional mutations affecting the gene expression of CYP2E1 and suggests that factors that affect the differences in translation of CYP2E1 mRNA may also be important in affecting skatole metabolism.
Collapse
Affiliation(s)
- Holly Archer
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada (M.J.); (F.S.)
| | - Riani A. N. Soares
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada (M.J.); (F.S.)
| | - Mohsen Jafarikia
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada (M.J.); (F.S.)
- Canadian Centre for Swine Improvement Inc., Ottawa, ON K1A 0C6, Canada
| | - Brandon N. Lillie
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Flavio Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada (M.J.); (F.S.)
| | - E. James Squires
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada (M.J.); (F.S.)
| |
Collapse
|
2
|
Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res 2024; 31:dsae008. [PMID: 38447059 PMCID: PMC11090087 DOI: 10.1093/dnares/dsae008] [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: 12/23/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.
Collapse
Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chenyu Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Li Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuping Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| |
Collapse
|
3
|
Jochems R, Gaustad AH, Styrishave B, Zak LJ, Oskam IC, Grindflek E, Myromslien FD, Kommisrud E, Krogenæs AK. Follicular fluid steroid hormones and in vitro embryo development in Duroc and Landrace pigs. Theriogenology 2022; 190:15-21. [PMID: 35863097 DOI: 10.1016/j.theriogenology.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/01/2022] [Accepted: 07/09/2022] [Indexed: 11/28/2022]
Abstract
The Duroc sire line has a smaller litter size compared to the Landrace dam line and we have previously observed fewer surface follicles on Duroc ovaries one day after weaning. In that same study, a broader cumulus expansion and faster nuclear maturation were observed for Duroc oocytes at 20 h of in vitro maturation (IVM), while Landrace oocytes showed more advanced stages of cortical granule distributions. However, no differences between breeds were observed after the final IVM period. The aim of this study was to assess subsequent in vitro embryo production (IVP) in Duroc and Landrace. Furthermore, follicle diameter and steroid hormone levels in follicular fluid (FF) were measured to study possible relation to oocyte developmental competence. Follicular phase sow ovaries were collected one day after weaning and follicle size of the 10 largest follicles were measured per ovary before aspiration. Cumulus-oocyte complexes (COCs) were matured in vitro, and cumulus expansion was analysed by assessing individual COC areas at 0 and 20 h. Fertilization of Duroc and Landrace oocytes was performed with sperm from both a Duroc and a Landrace boar. A larger follicle diameter was observed for Landrace animals (5.7 vs. 4.8 mm, P < 0.0001) and individual COC area was additionally larger at 0 h after aspiration (P < 0.0001) compared to Duroc. Contrary, cumulus expansion from 0 to 20 h of maturation was broader for Duroc oocytes than for Landrace (407 ± 67% vs. 319 ± 31%, P < 0.0001). After fertilization, cleavage rate was higher for Duroc oocytes, and the highest blastocyst yield was obtained for Duroc oocytes fertilized with the Landrace sperm. Steroid hormone analysis of the follicular fluid showed differences in the pathways between breeds with a higher total level of estrogens (P = 0.01) and aromatase products/substrates ratio (P < 0.01) in Landrace compared to Duroc. In conclusion, results suggest that Duroc oocytes have a better in vitro oocyte developmental competence when cultured under the same in vitro conditions and breed differences in steroidogenesis were found in the early follicular phase.
Collapse
Affiliation(s)
- Reina Jochems
- Norsvin SA, Hamar, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway.
| | | | - Bjarne Styrishave
- Toxicology and Drug Metabolism Group, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Louisa J Zak
- Topigs Norsvin Research Center, Beuningen, the Netherlands
| | - Irma C Oskam
- The Livestock Production Research Centre, Norwegian University of Life Sciences, Ås, Norway
| | | | - Frøydis D Myromslien
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Anette K Krogenæs
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| |
Collapse
|
4
|
Botelho ME, Lopes MS, Mathur PK, Knol EF, e Silva FF, Lopes PS, Gimarães SEF, Marques DB, Veroneze R. Weighted genome-wide association study reveals new candidate genes related to boar taint compounds 1. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
5
|
Endocrine Fertility Parameters-Genomic Background and their Genetic Relationship to Boar Taint in German Landrace and Large White. Animals (Basel) 2021; 11:ani11010231. [PMID: 33477702 PMCID: PMC7831948 DOI: 10.3390/ani11010231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h2) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h2 differed between the breeds except for follicle-stimulating hormone (FSH) (h2: 0.28-0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (rg) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on S
us
S
crofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, rg partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes.
Collapse
|
6
|
Botelho ME, Lopes MS, Mathur PK, Knol EF, Guimarães SEF, Marques DBD, Lopes PS, Silva FF, Veroneze R. Applying an association weight matrix in weighted genomic prediction of boar taint compounds. J Anim Breed Genet 2020; 138:442-453. [PMID: 33285013 DOI: 10.1111/jbg.12528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/13/2020] [Accepted: 11/14/2020] [Indexed: 12/14/2022]
Abstract
Biological information regarding markers and gene association may be used to attribute different weights for single nucleotide polymorphism (SNP) in genome-wide selection. Therefore, we aimed to evaluate the predictive ability and the bias of genomic prediction using models that allow SNP weighting in the genomic relationship matrix (G) building, with and without incorporating biological information to obtain the weights. Firstly, we performed a genome-wide association studies (GWAS) in data set containing single- (SL) or a multi-line (ML) pig population for androstenone, skatole and indole levels. Secondly, 1%, 2%, 5%, 10%, 30% and 50% of the markers explaining the highest proportions of the genetic variance for each trait were selected to build gene networks through the association weight matrix (AWM) approach. The number of edges in the network was computed and used to derive weights for G (AWM-WssGBLUP). The single-step GBLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used as standard scenarios. All scenarios presented predictive abilities different from zero; however, the great overlap in their confidences interval suggests no differences among scenarios. Most of scenarios of based on AWM provide overestimations for skatole in both SL and ML populations. On the other hand, the skatole and indole prediction were no biased in the ssGBLUP (S1) in both SL and ML populations. Most of scenarios based on AWM provide no biased predictions for indole in both SL and ML populations. In summary, using biological information through AWM matrix and gene networks to derive weights for genomic prediction resulted in no increase in predictive ability for boar taint compounds. In addition, this approach increased the number of analyses steps. Thus, we can conclude that ssGBLUP is most appropriate for the analysis of boar taint compounds in comparison with the weighted strategies used in the present work.
Collapse
Affiliation(s)
- Margareth E Botelho
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marcos S Lopes
- Topigs Norsvin, Curitiba, Brazil.,Topigs Norsvin Research Center, Beuningen, the Netherlands
| | | | - Egbert F Knol
- Topigs Norsvin Research Center, Beuningen, the Netherlands
| | | | - Daniele B D Marques
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Paulo S Lopes
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Fabyano F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Renata Veroneze
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| |
Collapse
|
7
|
Wang X, Kadarmideen HN. Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint. Vet Sci 2020; 7:E77. [PMID: 32545802 PMCID: PMC7356388 DOI: 10.3390/vetsci7020077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data from nine porcine testis samples in three BT groups (low, medium and high BT). The results showed that the methylation levels of the first exons and first introns were lower than those of the other exons and introns. The first exons/introns of CpG island regions had even lower levels of methylation. A total of 123 differentially methylated promoters (DMPs), 194 differentially methylated exons (DMEs) and 402 differentially methylated introns (DMIs) were identified, of which 80 DMPs (DMP-CpGis), 112 DMEs (DME-CpGis) and 166 DMIs (DMI-CpGis) were discovered in CpG islands. Importantly, GPX1 contained one each of DMP, DME, DMI, DMP-CpGi, DME-CpGi and DMI-CpGi. Gene-GO term relationships and pathways analysis showed DMP-CpGi-related genes are mainly involved in methylation-related biological functions. In addition, gene-gene interaction networks consisted of nodes that were hypo-methylated GPX1, hypo-methylated APP, hypo-methylated ATOX1, hyper-methylated ADRB2, hyper-methylated RPS6KA1 and hyper-methylated PNMT. They could be used as candidate biomarkers for reducing boar taint in pigs, after further validation in large cohorts.
Collapse
Affiliation(s)
| | - Haja N. Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| |
Collapse
|
8
|
Brinke I, Große-Brinkhaus C, Roth K, Pröll-Cornelissen MJ, Henne H, Schellander K, Tholen E. Genomic background and genetic relationships between boar taint and fertility traits in German Landrace and Large White. BMC Genet 2020; 21:61. [PMID: 32513168 PMCID: PMC7282179 DOI: 10.1186/s12863-020-00865-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/28/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Due to ethical reasons, surgical castration of young male piglets in their first week of life without anesthesia will be banned in Germany from 2021. Breeding against boar taint is already implemented in sire breeds of breeding organizations but in recent years a low demand made this trait economically less important. The objective of this study was to estimate heritabilities and genetic relationships between boar taint compounds androstenone and skatole and maternal/paternal reproduction traits in 4'924 Landrace (LR) and 4'299 Large White (LW) animals from nucleus populations. Additionally, genome wide association analysis (GWAS) was performed per trait and breed to detect SNP marker with possible pleiotropic effects that are associated with boar taint and fertility. RESULTS Estimated heritabilities (h2) were 0.48 (±0.08) for LR (0.39 ± 0.07 for LW) for androstenone and 0.52 (±0.08) for LR (0.32 ± 0.07 for LW) for skatole. Heritabilities for reproduction did not differ between breeds except age at first insemination (LR: h2 = 0.27 (±0.05), LW: h2 = 0.34 (±0.05)). Estimates of genetic correlation (rg) between boar taint and fertility were different in LR and LW breeds. In LR an unfavorable rg of 0.31 (±0.15) was observed between androstenone and number of piglets born alive, whereas this rg in LW (- 0.15 (±0.16)) had an opposite sign. A similar breed-specific difference is observed between skatole and sperm count. Within LR, the rg of 0.08 (±0.13) indicates no relationship between the traits, whereas the rg of - 0.37 (±0.14) in LW points to an unfavorable relationship. In LR GWAS identified QTL regions on SSC5 (21.1-22.3 Mb) for androstenone and on SSC6 (5.5-7.5 Mb) and SSC14 (141.1-141.6 Mb) for skatole. For LW, one marker was found on SSC17 at 48.1 Mb for androstenone and one QTL on SSC14 between 140.5 Mb and 141.6 Mb for skatole. CONCLUSION Knowledge about such genetic correlations could help to balance conventional breeding programs with boar taint in maternal breeds. QTL regions with unfavorable pleiotropic effects on boar taint and fertility could have deleterious consequences in genomic selection programs. Constraining the weighting of these QTL in the genomic selection formulae may be a useful strategy to avoid physiological imbalances.
Collapse
Affiliation(s)
- Ines Brinke
- Institute of Animal Science, University of Bonn, 53115, Bonn, Germany
| | | | - Katharina Roth
- Institute of Animal Science, University of Bonn, 53115, Bonn, Germany
| | - Maren J Pröll-Cornelissen
- Institute of Animal Science, University of Bonn, 53115, Bonn, Germany.,Association for Bioeconomy Research (FBF e.V.), Adenauerallee 174, 53113, Bonn, Germany
| | - Hubert Henne
- BHZP GmbH, An der Wassermühle 8, 21368 Dahlenburg-Ellringen, Germany
| | - Karl Schellander
- Institute of Animal Science, University of Bonn, 53115, Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, 53115, Bonn, Germany
| |
Collapse
|
9
|
Characterization of Porcine Hepatic and Intestinal Drug Metabolizing CYP450: Comparison with Human Orthologues from A Quantitative, Activity and Selectivity Perspective. Sci Rep 2019; 9:9233. [PMID: 31239454 PMCID: PMC6592956 DOI: 10.1038/s41598-019-45212-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/04/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, the pig has gained attention as a potential model for human drug metabolism. Cytochrome P450 enzymes (CYP450), a superfamily of biotransformation enzymes, are pivotal in drug metabolism. Porcine CYP450 has been demonstrated to convert typical substrates of human CYP450. Nevertheless, knowledge and insight into porcine CYP450 quantity and substrate selectivity is scant, especially regarding intestinal CYP450. The current study aimed to map the quantities of hepatic and intestinal CYP450 in the conventional pig by using a proteomic approach. Moreover, the selectivity of the six most common used probe substrates (phenacetin, coumarin, midazolam, tolbutamide, dextromethorphan, and chlorzoxazone) for drug metabolizing enzyme subfamilies (CYP1A, CYP2A, CYP3A, CYP2C, CYP2D and CYP2E respectively), was investigated. Hepatic relative quantities were 4% (CYP1A), 31% (CYP2A), 14% (CYP3A), 10% (CYP2C), 28% (CYP2D) and 13% (CYP2E), whereas for the intestine only duodenal CYP450 could be determined with 88% for CYP3A and 12% for CYP2C. Furthermore, the results indicate that coumarin (CYP2A), midazolam (CYP3A), tolbutamide (CYP2C), and dextromethorphan (CYP2D) are as selective for porcine as for human CYP450. However, phenacetin (CYP1A2) and chlorzoxazone (CYP2E1) are less selective for the specific enzyme, despite similarities in selectivity towards the different enzymes involved compared to humans.
Collapse
|
10
|
Mastrangelo S, Ben Jemaa S, Sottile G, Casu S, Portolano B, Ciani E, Pilla F. Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations. J Anim Breed Genet 2019; 136:526-534. [PMID: 31206848 DOI: 10.1111/jbg.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022]
Abstract
Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case-control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST ) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and FST analyses. Moreover, one candidate marker identified by GWAS and FST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome-wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome-wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations.
Collapse
Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Gianluca Sottile
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, Sassari, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, Bari, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| |
Collapse
|
11
|
Kurtz S, Petersen B. Pre-determination of sex in pigs by application of CRISPR/Cas system for genome editing. Theriogenology 2019; 137:67-74. [PMID: 31208775 DOI: 10.1016/j.theriogenology.2019.05.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In livestock industries, one sex is usually preferred because of the impact on the production (e.g. milk from cows, eggs from laying hens). Furthermore, in pig production, the male-specific boar taint is a big hurdle for consumer acceptance. Consequently, a shift in the ratio towards the desired sex would be a great benefit. The most widely applied method for pre-determination of the sex is fluorescence-activated sperm sorting, which relies on the different DNA content of the X- and Y-chromosomal sperm. However, the successful practical adaption of this method depends on its ease of use. At present, sperm sexing via fluorescence-activated cell sorting (FACS) has only reached commercial application in cattle. Nevertheless, sperm sexing technology still needs to be improved with respect to efficiency and reliability, to obtain high numbers of sexed sperm and less invasive sperm treatment to avoid damage. New genome editing technologies such as Zinc finger nucleases (ZFN), Transcription-activator like endonucleases (TALENs) and the CRISPR/Cas system have emerged and offer great potential to affect determination of the sex at the genome level. The sex-determining region on the Y chromosome (SRY) serves as a main genetic switch of male gender development. It was previously shown that a knockout of the SRY gene in mice and rabbits displayed suppressed testis development in the fetal gonadal ridges resulting in a female phenotype. These new technologies hold great opportunities to pre-determine sex in pigs. However, further investigations are needed to exploit their full potential for practical application.
Collapse
Affiliation(s)
- Stefanie Kurtz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Mariensee, Neustadt am Rübenberge, Germany
| | - Björn Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Mariensee, Neustadt am Rübenberge, Germany.
| |
Collapse
|
12
|
Drag M, Hansen MB, Kadarmideen HN. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs. PLoS One 2018; 13:e0192673. [PMID: 29438444 PMCID: PMC5811030 DOI: 10.1371/journal.pone.0192673] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/29/2018] [Indexed: 01/14/2023] Open
Abstract
Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.
Collapse
Affiliation(s)
- Markus Drag
- Section of Anatomy, Biochemistry and Physiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mathias B. Hansen
- Section of Anatomy, Biochemistry and Physiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Haja N. Kadarmideen
- Section of Anatomy, Biochemistry and Physiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section of Systems Genomics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
- * E-mail:
| |
Collapse
|
13
|
van Son M, Agarwal R, Kent MP, Grove H, Grindflek E, Lien S. Exploiting whole genome sequence data to fine map and characterize candidate genes within a quantitative trait loci region affecting androstenone on porcine chromosome 5. Anim Genet 2017; 48:653-659. [PMID: 29034488 PMCID: PMC5698758 DOI: 10.1111/age.12615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2017] [Indexed: 11/30/2022]
Abstract
Male piglets are routinely castrated to eliminate boar taint. However, this treatment is undesirable, and alternative approaches, including genetic strategies to reduce boar taint, are demanded. Androstenone is one of the causative agents of boar taint, and a QTL region affecting this pheromone has previously been reported on SSC5: 22.6–24.8 Mb in Duroc. The QTL region is one of the few reported for androstenone that does not simultaneously affect levels of other sex steroids. The main objective of this study was to fine map this QTL. Whole genome sequence data from 23 Norwegian Duroc boars were analyzed to detect new polymorphisms within the QTL region. A subset of 161 SNPs was genotyped in 834 Duroc sires and analyzed for association with androstenone in adipose tissue and testosterone, estrone sulphate and 17β‐estradiol in blood plasma. Our results revealed 100 SNPs significantly associated with androstenone levels in fat (P < 0.001) with 94 of the SNPs being in strong linkage disequilibrium in the region 23.03–24.27 Mb. This haplotype block contains at least four positional candidate genes (HSD17B6,SDR9C7,RDH16 and STAT6) involved in androstenone biosynthesis. No significant associations were found between any of the SNPs and levels of testosterone and estrogens, confirming previous findings. The amount of phenotypic variance explained by single SNPs within the haplotype block was as high as 5.4%. As the SNPs in this region significantly affect levels of androstenone without affecting levels of other sex steroids, they are especially interesting as genetic markers for selection against boar taint.
Collapse
Affiliation(s)
- M van Son
- Topigs Norsvin, Storhamargata 44, 2317, Hamar, Norway
| | - R Agarwal
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432, Ås, Norway
| | - M P Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432, Ås, Norway
| | - H Grove
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432, Ås, Norway
| | - E Grindflek
- Topigs Norsvin, Storhamargata 44, 2317, Hamar, Norway
| | - S Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432, Ås, Norway
| |
Collapse
|
14
|
Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs. Sci Rep 2017; 7:12205. [PMID: 28939879 PMCID: PMC5610188 DOI: 10.1038/s41598-017-11928-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 09/01/2017] [Indexed: 11/08/2022] Open
Abstract
Boar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. Differential expression analysis revealed substantial changes with log-transformed fold changes of liver and testis from -3.39 to 2.96 and -7.51 to 3.53, respectively. Co-expression network analysis revealed one module with a correlation of -0.27 in liver and three modules with correlations of 0.31, -0.44 and -0.49 in testis. Differential expression and co-expression analysis revealed candidate biomarkers with varying biological functions: phase I (COQ3, COX6C, CYP2J2, CYP2B6, ACOX2) and phase II metabolism (GSTO1, GSR, FMO3) of skatole and androstenone in liver to steroidgenesis (HSD17B7, HSD17B8, CYP27A1), regulation of steroidgenesis (STARD10, CYB5R3) and GnRH signalling (MAPK3, MAP2K2, MAP3K2) in testis. Overrepresented pathways included "Ribosome", "Protein export" and "Oxidative phosphorylation" in liver and "Steroid hormone biosynthesis" and "Gap junction" in testis. Future work should evaluate the biomarkers in large populations to ensure their usefulness in genomic selection programs.
Collapse
|
15
|
Zadinová K, Stupka R, Stratil A, Čítek J, Vehovský K, Lebedová N, Šprysl M, Okrouhlá M. Association analysis of SNPs in the porcine CYP2E1 gene with skatole, indole, and androstenone levels in backfat of a crossbred pig population. Meat Sci 2017; 131:68-73. [DOI: 10.1016/j.meatsci.2017.04.236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/08/2017] [Accepted: 04/28/2017] [Indexed: 11/29/2022]
|
16
|
Olfactory evaluation of boar taint: effect of factors measured at slaughter and link with boar taint compounds. Animal 2017; 11:2084-2093. [DOI: 10.1017/s1751731117000994] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
17
|
Świątkiewicz M, Oczkowicz M, Ropka-Molik K, Hanczakowska E. The effect of dietary fatty acid composition on adipose tissue quality and expression of genes related to lipid metabolism in porcine livers. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
18
|
Robic A, Feve K, Louveau I, Riquet J, Prunier A. Exploration of steroidogenesis-related genes in testes, ovaries, adrenals, liver and adipose tissue in pigs. Anim Sci J 2015; 87:1041-7. [PMID: 27436769 DOI: 10.1111/asj.12532] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/07/2015] [Accepted: 07/21/2015] [Indexed: 12/20/2022]
Abstract
To explore the metabolism of steroids in the pig species, a qualitative PCR analysis was performed for the main transcript of 27 genes involved in steroid metabolism. We compared samples of testes, adipose tissue and liver from immature and peripubertal males, adrenal cortex from peripubertal males, ovaries from cyclic females and adipose tissue from peripubertal females. Some genes were shown to have a tissue-specific expression. Two of them were expressed only in testes, ovaries and adrenals: CYP11A1 and CYP11B. The CYP21 and HSD17B3 genes, were expressed respectively only in adrenals and only in testes. Very few differences were observed between transcriptional patterns of peripubertal testes and adrenal glands as well as between male and female fat tissues. However, the expression of genes involved in the sulfonation of steroids was higher in testes than in adrenals from males. Main differences between ovaries and testes were observed for HSD17B1/2/3, AKR1C-pig6 and sulfotransferase genes (SULT2A1/SULT2B1). The present study shows that the SRD5A2 and CYP21 genes were not involved in the testicular biosynthesis of androstenone. It also shows that porcine adrenal glands produce essentially corticosteroids and that fat tissue is unable to produce de novo steroids.
Collapse
Affiliation(s)
- Annie Robic
- INRA, UMR1388-GenPhySE, Castanet Tolosan, France
| | - Katia Feve
- INRA, UMR1388-GenPhySE, Castanet Tolosan, France
| | - Isabelle Louveau
- INRA, UMR1348-PEGASE, Saint-Gilles, France.,Agrocampus Ouest, Rennes, France
| | | | - Armelle Prunier
- INRA, UMR1348-PEGASE, Saint-Gilles, France.,Agrocampus Ouest, Rennes, France
| |
Collapse
|
19
|
Lukić B, Pong-Wong R, Rowe SJ, de Koning DJ, Velander I, Haley CS, Archibald AL, Woolliams JA. Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs. Anim Genet 2015; 46:607-16. [PMID: 26449733 PMCID: PMC4949655 DOI: 10.1111/age.12369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2015] [Indexed: 02/01/2023]
Abstract
Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (≥0.3 μg/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62 153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross‐validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome‐wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h2, were 0.54–0.56 and 0.75–0.94 for androstenone and skatole respectively. The whole‐genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.
Collapse
Affiliation(s)
- B Lukić
- Faculty of Agriculture in Osijek, J.J. Strossmayer University of Osijek, Kralja Petra Svačića 1d, 31000, Osijek, Croatia.,The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - R Pong-Wong
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - S J Rowe
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - D J de Koning
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - I Velander
- Pig Research Centre, Danish Agriculture & Food Council, Axeltorv 3, København, V 1609, Denmark
| | - C S Haley
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - A L Archibald
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - J A Woolliams
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| |
Collapse
|
20
|
Bagheri M, Moradi-Sharhrbabak M, Miraie-Ashtiani R, Safdari-Shahroudi M, Abdollahi-Arpanahi R. Case–control approach application for finding a relationship between candidate genes and clinical mastitis in Holstein dairy cattle. J Appl Genet 2015; 57:107-12. [DOI: 10.1007/s13353-015-0299-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/01/2015] [Accepted: 06/09/2015] [Indexed: 11/30/2022]
|
21
|
Neuhoff C, Gunawan A, Farooq MO, Cinar MU, Große-Brinkhaus C, Sahadevan S, Frieden L, Tesfaye D, Tholen E, Looft C, Schellander K, Uddin MJ. Preliminary study of FMO1, FMO5, CYP21, ESR1, PLIN2 and SULT2A1 as candidate gene for compounds related to boar taint. Meat Sci 2015; 108:67-73. [PMID: 26047979 DOI: 10.1016/j.meatsci.2015.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 02/05/2023]
Abstract
An association study between polymorphisms of six genes and boar taint related compounds androstenone, skatole and indole was performed in a boar population (n=370). Significant association (P<0.05) was detected for SNP of FMO5 (g.494A>G) with all boar taint compounds, SNP of CYP21 (g.3911T>C) with skatole and indole, and SNP of ESR1 (g.672C>T) with androstenone and indole. mRNA expression of CYP21 and ESR1 was higher in CAB (castrated boar) compared to non-castrated boars; whereas, the expression of FMO5 and ESR1 was higher in LBT (low boar taint) compared to HBT (high boar taint) in liver tissue. FMO5, CYP21 and ESR1 proteins were less detectable in HBT compared with LBT and CAB in liver tissues. These findings suggest that FMO5, CYP21 and ESR1 gene variants might have effects on the boar taint compounds.
Collapse
Affiliation(s)
- Christiane Neuhoff
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Asep Gunawan
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany; Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, 16680 Bogor, Indonesia.
| | - Malik Omar Farooq
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Mehmet Ulas Cinar
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany; Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Turkey.
| | - Christine Große-Brinkhaus
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Sudeep Sahadevan
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Luc Frieden
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Dawit Tesfaye
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Christian Looft
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Karl Schellander
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Muhammad Jasim Uddin
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| |
Collapse
|
22
|
Schroyen M, Janssens S, Stinckens A, Brebels M, Bertolini F, Lamberigts C, Bekaert K, Vanhaecke L, Aluwé M, Tuyttens FAM, Millet S, Buys N. The MC4R c.893G>A mutation: a marker for growth and leanness associated with boar taint odour in Belgian pig breeds. Meat Sci 2014; 101:1-4. [PMID: 25462375 DOI: 10.1016/j.meatsci.2014.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 10/24/2022]
Abstract
Since surgical castration of male piglets without anaesthesia is under heavy societal pressure, finding a sustainable solution to reduce boar taint has become urgent. One way to circumvent this animal welfare violation is raising entire male pigs whilst selecting against the tainted phenotype through marker-assisted selection. Since slaughtering at a lower weight is often suggested to reduce boar taint, selection using a marker for that trait could be a promising strategy. Therefore, in this study a melanocortin 4 receptor (MC4R) mutation, frequently described in different pig breeds as marker for fat content, weight gain and feed intake, was examined in relation to boar taint in pig breeds used in Belgian pig farms. Although results suggest an association between this mutation and a boar taint odour score assigned by experts, no association was found between the mutation and the concentration of the individual chemical boar taint components androstenone, skatole and indole.
Collapse
Affiliation(s)
- M Schroyen
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - S Janssens
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - A Stinckens
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - M Brebels
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - F Bertolini
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - C Lamberigts
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - K Bekaert
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - L Vanhaecke
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - M Aluwé
- Animal Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Scheldeweg 68, B-9090 Melle, Belgium
| | - F A M Tuyttens
- Animal Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Scheldeweg 68, B-9090 Melle, Belgium
| | - S Millet
- Animal Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Scheldeweg 68, B-9090 Melle, Belgium
| | - N Buys
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium.
| |
Collapse
|
23
|
Gunawan A, Sahadevan S, Cinar MU, Neuhoff C, Große-Brinkhaus C, Frieden L, Tesfaye D, Tholen E, Looft C, Wondim DS, Hölker M, Schellander K, Uddin MJ. Identification of the novel candidate genes and variants in boar liver tissues with divergent skatole levels using RNA deep sequencing. PLoS One 2013; 8:e72298. [PMID: 23991084 PMCID: PMC3753299 DOI: 10.1371/journal.pone.0072298] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/09/2013] [Indexed: 02/02/2023] Open
Abstract
Boar taint is the unpleasant odour of meat derived from non-castrated male pigs, caused by the accumulation of androstenone and skatole in fat. Skatole is a tryptophan metabolite produced by intestinal bacteria in gut and catabolised in liver. Since boar taint affects consumer's preference, the aim of this study was to perform transcriptome profiling in liver of boars with divergent skatole levels in backfat by using RNA-Seq. The total number of reads produced for each liver sample ranged from 11.8 to 39.0 million. Approximately 448 genes were differentially regulated (p-adjusted <0.05). Among them, 383 genes were up-regulated in higher skatole group and 65 were down-regulated (p<0.01, FC>1.5). Differentially regulated genes in the high skatole liver samples were enriched in metabolic processes such as small molecule biochemistry, protein synthesis, lipid and amino acid metabolism. Pathway analysis identified the remodeling of epithelial adherens junction and TCA cycle as the most dominant pathways which may play important roles in skatole metabolism. Differential gene expression analysis identified candidate genes in ATP synthesis, cytochrome P450, keratin, phosphoglucomutase, isocitrate dehydrogenase and solute carrier family. Additionally, polymorphism and association analysis revealed that mutations in ATP5B, KRT8, PGM1, SLC22A7 and IDH1 genes could be potential markers for skatole levels in boars. Furthermore, expression analysis of exon usage of three genes (ATP5B, KRT8 and PGM1) revealed significant differential expression of exons of these genes in different skatole levels. These polymorphisms and exon expression differences may have impacts on the gene activity ultimately leading to skatole variation and could be used as genetic marker for boar taint related traits. However, further validation is required to confirm the effect of these genetic markers in other pig populations in order to be used in genomic selection against boar taint in pig breeding programs.
Collapse
Affiliation(s)
- Asep Gunawan
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor, Indonesia
| | - Sudeep Sahadevan
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany
| | - Mehmet Ulas Cinar
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Christiane Neuhoff
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | | | - Luc Frieden
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Dawit Tesfaye
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Christian Looft
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Dessie Salilew Wondim
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Michael Hölker
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Karl Schellander
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Muhammad Jasim Uddin
- Institute of Animal Science, Faculty of Agriculture, University of Bonn, Bonn, Germany
| |
Collapse
|
24
|
Mathur PK, ten Napel J, Crump RE, Mulder HA, Knol EF. Genetic relationship between boar taint compounds, human nose scores, and reproduction traits in pigs. J Anim Sci 2013; 91:4080-9. [PMID: 23825333 DOI: 10.2527/jas.2013-6478] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A reduction in boar taint, an unpleasant odor arising in pork from some intact males, is desirable if routine castration of piglets needs to be stopped. Commercial slaughter pigs are typically crosses between sire lines mainly selected for finishing traits and dam lines mainly selected for reproduction traits. Previous studies suggest the possibility of reducing boar taint in sire lines due to favorable genetic correlations between boar taint and finishing traits. However, there are indications of unfavorable genetic associations between boar taint and female reproduction traits, but a lack of genetic correlation estimates remain a major roadblock in reducing boar taint in dam lines. This study was conducted to estimate genetic correlations between boar taint traits and female reproduction traits, investigate differences in these genetic relationships among sire and dam lines, and evaluate possible consequences of selection against boar taint in dam lines. The data consisted of 32,549 reproduction records from a Landrace dam line, 23,874 records from a Yorkshire dam line, and 3,745 records from a Pietrain sire line. Androstenone, skatole, and indole were measured on 1,896 carcasses, and human nose scores were recorded on 7,742 carcass samples. In general, the level of boar taint was significantly greater (P < 0.05) in the two dam lines than in the sire line. A majority of genetic correlations of boar taint compounds with reproduction traits were either low or nonsignificant, except for those of skatole and indole, with age at first insemination in dam lines that were -0.32 and -0.46, respectively. Genetic correlations also differed (P < 0.05) between sire and dam lines. The consequences of selection against boar taint in dam lines were evaluated, using selection indexes based on reproduction traits only, boar taint traits only, and both boar taint and reproduction traits. Selection on an index of only reproduction traits increased the number of carcasses with boar taint from 4 to 7.3% in 5 generations. Selection on a combined index reduced carcasses with boar taint from 4 to <0.1% in 19 generations at the cost of a 10% less economic gain in reproduction traits. In markets for intact males, overall economic gain is 78% greater than with selection for reproduction only. Breeding programs for boar taint in commercial production should include boar taint in breeding goals of dam lines as the levels of boar taint and the risk of a further increase are greater.
Collapse
Affiliation(s)
- P K Mathur
- TOPIGS Research Center IPG, PO Box 43, 6640 AA Beuningen, The Netherlands.
| | | | | | | | | |
Collapse
|
25
|
Bagheri M, Miraie-Ashtiani R, Moradi-Shahrbabak M, Nejati-Javaremi A, Pakdel A, von Borstel U, Pimentel E, König S. Selective genotyping and logistic regression analyses to identify favorable SNP-genotypes for clinical mastitis and production traits in Holstein dairy cattle. Livest Sci 2013. [DOI: 10.1016/j.livsci.2012.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
26
|
Mörlein D, Lungershausen M, Steinke K, Sharifi AR, Knorr C. A single nucleotide polymorphism in the CYP2E1 gene promoter affects skatole content in backfat of boars of two commercial Duroc-sired crossbred populations. Meat Sci 2012; 92:739-44. [PMID: 22795630 DOI: 10.1016/j.meatsci.2012.06.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/15/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
Abstract
The prevention of unpleasant boar taint is the main reason for castration of male piglets. This study aimed to investigate how the malodorous compound skatole is affected by a single nucleotide polymorphism (g.2412 C>T at -586 ATG) in the porcine cytochrome p450 II E1 (CYP2E1) gene. 119 boars of two commercial Duroc-sired crossbred populations raised at different farms were investigated. Skatole and androstenone in backfat averaged 114±125 ng/g and 1206±895 ng/g melted fat, respectively. The frequency of the genotypes CC, CT, and TT was 25, 52, and 23%, respectively. CC boars had the highest average skatole levels (175 ng/g) compared to CT (92 ng/g) and TT (93 ng/g). Applying suggested sensory threshold levels for skatole (>150 ng/g) and androstenone (>2000 ng/g), 30% of the carcasses may be unacceptably tainted while the proportion of tainted carcasses is significantly higher within genotype CC (56.7%) compared to genotypes CT (24.3%) and TT (14.8%). Effective reduction of tainted carcasses appears feasible applying marker assisted selection.
Collapse
Affiliation(s)
- Daniel Mörlein
- Department of Animal Science, University of Göttingen, Göttingen, Germany
| | | | | | | | | |
Collapse
|
27
|
Zhang W, Fang M, Li Y, Nie Q, Zhang X. Identification of TDRP1 Gene and Its Association with Pig Reproduction Traits. DNA Cell Biol 2012; 31:371-7. [DOI: 10.1089/dna.2011.1328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Wei Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Meixia Fang
- Department of Laboratory Animal Science, Medical College of Jinan University, Guangzhou, China
| | - Ying Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| |
Collapse
|
28
|
Gregersen VR, Conley LN, Sørensen KK, Guldbrandtsen B, Velander IH, Bendixen C. Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds. BMC Genomics 2012; 13:22. [PMID: 22244367 PMCID: PMC3315726 DOI: 10.1186/1471-2164-13-22] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 01/13/2012] [Indexed: 11/29/2022] Open
Abstract
Background Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. Results Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL), 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 μg/g). In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. Conclusions Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.
Collapse
Affiliation(s)
- Vivi R Gregersen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, P,O, Box 50, DK-8830 Tjele, Denmark
| | | | | | | | | | | |
Collapse
|
29
|
Windig JJ, Mulder HA, Ten Napel J, Knol EF, Mathur PK, Crump RE. Genetic parameters for androstenone, skatole, indole, and human nose scores as measures of boar taint and their relationship with finishing traits. J Anim Sci 2012; 90:2120-9. [PMID: 22247111 DOI: 10.2527/jas.2011-4700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The purpose of this study was to evaluate measures of boar (Sus scrofa) taint as potential selection criteria to reduce boar taint so that castration of piglets will become unnecessary. Therefore, genetic parameters of boar taint measures and their genetic correlations with finishing traits were estimated. In particular, the usefulness of a human panel assessing boar taint (human nose score) was compared with chemical assessment of boar taint compounds, androstenone, skatole, and indole. Heritability estimates for androstenone, skatole, and indole were 0.54, 0.41, and 0.33, respectively. The heritability for the human nose score using multiple panelists was 0.12, and ranged from 0.12 to 0.19 for individual panelists. Genetic correlations between scores of panelists were generally high up to unity. The genetic correlations between human nose scores and the boar taint compounds ranged from 0.64 to 0.999. The boar taint compounds and human nose scores had low or favorable genetic correlations with finishing traits. Selection index estimates indicated that the effectiveness of a breeding program based on human nose scores can be comparable to a breeding program based on the boar taint compounds themselves. Human nose scores can thus be used as a cheap and fast alternative for the costly determination of boar taint compounds, needed in breeding pigs without boar taint.
Collapse
Affiliation(s)
- J J Windig
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands.
| | | | | | | | | | | |
Collapse
|
30
|
Lervik S, von Krogh K, Karlsson C, Olsaker I, Andresen Ø, Dahl E, Verhaegen S, Ropstad E. Steroidogenesis in primary cultures of neonatal porcine Leydig cells from Duroc and Norwegian Landrace breeds. Theriogenology 2011; 76:1058-69. [DOI: 10.1016/j.theriogenology.2011.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 10/17/2022]
|
31
|
Role of the cytochrome P450 enzyme system in veterinary pharmacokinetics: where are we now? Where are we going? Future Med Chem 2011; 3:855-79. [PMID: 21644832 DOI: 10.4155/fmc.11.37] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Drug metabolism is a core determinant of the dose-effectiveness-toxicity relationship of many compounds. It is also critical to the human food safety assessment of drug residues in the edible tissues of food-producing animals. This article describes the current state of knowledge regarding the role of the cytochrome P450 superfamily of enzymes in determining the metabolic profile of compounds administered to companion animals (e.g., dog and cat) and to food-producing animal species (e.g., cattle, swine, chickens). In turn, this knowledge reflects the collection of insights derived from the recognized population variability observed in human drug metabolism, our general understanding of the kinetics of various drug-metabolism pathways, emerging tools that enable the role of pharmacogenetics to be studied and the characterization of drug metabolism in individual veterinary species. Ultimately, by increasing our insights with regard to factors that can influence drug metabolism, our knowledge of metabolic pathways, sources of within- and between-species variability in pharmacokinetics and the development of in silico models that can be used to predict pharmacokinetic profiles from these diverse sources of information. We will improve our ability to generate the population inferences needed to insure the target animal safety, product effectiveness and the human food safety of veterinary pharmaceuticals.
Collapse
|
32
|
Grindflek E, Lien S, Hamland H, Hansen MHS, Kent M, van Son M, Meuwissen THE. Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids. BMC Genomics 2011; 12:362. [PMID: 21752240 PMCID: PMC3149590 DOI: 10.1186/1471-2164-12-362] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 07/13/2011] [Indexed: 01/19/2023] Open
Abstract
Background Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like testosterone and estrogens. This represents a challenge when performing selection against androstenone in breeding programs, without simultaneously decreasing levels of other steroids. The aim of this study was to use high-density genome wide association (GWA) in combination with linkage disequilibrium-linkage analysis (LDLA) to identify quantitative trait loci (QTL) associated with boar taint compounds and related sex steroids in commercial Landrace (n = 1,251) and Duroc (n = 918) breeds. Results Altogether, 14 genome wide significant (GWS) QTL regions for androstenone in subcutaneous fat were obtained from the LDLA study in Landrace and 14 GWS QTL regions in Duroc. LDLA analysis revealed that 7 of these QTL regions, located on SSC 1, 2, 3, 7 and 15, were obtained in both breeds. All 14 GWS androstenone QTLs in Landrace are also affecting the estrogens at chromosome wise significance (CWS) or GWS levels, while in Duroc, 3 of the 14 QTLs affect androstenone without affecting any of the estrogens. For skatole, 10 and 4 QTLs were GWS in the LDLA analysis for Landrace and Duroc respectively, with 4 of these detected in both breeds. The GWS QTLs for skatole obtained by LDLA are located at SSC 1, 5, 6, 7, 10, 11, 13 and 14. Conclusion This is the first report applying the Porcine 60 K SNP array for simultaneous analysis of boar taint compounds and related sex hormones, using both GWA and LDLA approaches. Several QTLs are involved in regulation of androstenone and skatole, and most of the QTLs for androstenone are also affecting the levels of estrogens. Seven QTLs for androstenone were detected in one breed and confirmed in the other, i.e. in an independent sample, although the majority of QTLs are breed specific. Most QTLs for skatole do not negatively affect other sex hormones and should be easier to implement into the breeding scheme.
Collapse
Affiliation(s)
- Eli Grindflek
- NORSVIN (The Norwegian Pig Breeders Association), 2304 Hamar, Norway.
| | | | | | | | | | | | | |
Collapse
|
33
|
Grindflek E, Meuwissen THE, Aasmundstad T, Hamland H, Hansen MHS, Nome T, Kent M, Torjesen P, Lien S. Revealing genetic relationships between compounds affecting boar taint and reproduction in pigs. J Anim Sci 2011; 89:680-92. [PMID: 21346135 DOI: 10.2527/jas.2010-3290] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Boar taint is characterized by an unpleasant taste or odor in intact male pigs and is primarily attributed to increased concentrations of androstenone and skatole and to a lesser extent by increased indole. The boar taint compounds skatole and indole are produced by gut bacteria, metabolized in the liver, and stored in the fat tissue. Androstenone, on the other hand, is synthesized in the testis along with testosterone and estrogens, which are known to be important factors affecting fertility. The main goal of this study was to investigate the relationship between genetic factors involved in the primary boar taint compounds in an attempt to discover ways to reduce boar taint without decreasing fertility-related compounds. Heritabilities and genetic correlations between traits were estimated for compounds related to boar taint (androstenone, skatole, indole) and reproduction (testosterone, 17β-estradiol, and estrone sulfate). Heritabilities in the range of 0.47 to 0.67 were detected for androstenone concentrations in both fat and plasma, whereas those for skatole and indole were slightly less (0.27 to 0.41). The genetic correlations between androstenone in plasma and fat were extremely high (0.91 to 0.98) in Duroc and Landrace. In addition, genetic correlations between androstenone (both plasma and fat) and the other sex steroids (estrone sulfate, 17β-estradiol, and testosterone) were very high, in the range of 0.80 to 0.95. Furthermore, a genome-wide association study (GWA) and a combined linkage disequilibrium and linkage analysis (LDLA) were conducted on 1,533 purebred Landrace and 1,027 purebred Duroc to find genome regions involved in genetic control of the boar taint compounds androstenone, skatole, and indole, and sex hormones related to fertility traits. Up to 3,297 informative SNP markers were included for both breeds, including SNP from several boar taint candidate genes. From the GWA study, we found that altogether 27 regions were significant at a genome-wide level (P < 0.05) and an additional 7 regions were significant at a chromosomal level. From the LDLA study, 7 regions were significant on a genome-wide level and an additional 7 regions were significant at a chromosomal level. The most convincing associations were obtained in 6 regions affecting skatole and indole in fat on chromosomes 1, 2, 3, 7, 13, and 14, 1 region on chromosome 6 affecting androstenone in plasma only, and 5 regions on chromosomes 3, 4, 13, and 15 affecting androstenone, testosterone, and estrogens.
Collapse
Affiliation(s)
- E Grindflek
- NORSVIN (The Norwegian Pig Breeders Association), PO Box 504, 2304 Hamar, Norway.
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Rempel LA, Freking BA, Miles JR, Nonneman DJ, Rohrer GA, Schneider JF, Vallet JL. Association of porcine heparanase and hyaluronidase 1 and 2 with reproductive and production traits in a landrace-duroc-yorkshire population. Front Genet 2011; 2:20. [PMID: 22303316 PMCID: PMC3268575 DOI: 10.3389/fgene.2011.00020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 04/22/2011] [Indexed: 01/26/2023] Open
Abstract
The ovary and placenta are dynamic structures requiring constant modification both structurally and through cell-cell communication capabilities. The extracellular matrix and basement membranes are primarily composed of a milieu of glycosaminoglycans, including heparan sulfate and hyaluronan. Heparanase (HPSE) and hyaluronidases (HYAL) are responsible for degrading heparan sulfate and hyaluronan, respectively. Therefore, the objective of this study was to evaluate the relationship of SNPs distinct to HPSE, HYAL1, and HYAL2 with measurements of reproduction and production traits in swine. Single trait associations were performed on a Landrace-Duroc-Yorkshire population using SNPs discovered and identified in HPSE, HYAL1, and HYAL2. Analyses were conducted on an extended pedigree and SNPs were found to be associated with reproductive and production traits. Prior to multiple-testing corrections, SNPs within HPSE were weakly associated (P < 0.03) having additive effects with age at puberty (-2.5 ± 1.08 days), ovulation rate (0.5 ± 0.24 corpora lutea), and number of piglets born alive (0.9 ± 0.44 piglets). A HYAL1 and two HYAL2 SNP were nominally associated (P ≤ 0.0063) with number of piglets born alive after multiple-testing corrections (effects between 1.02 and 1.44 piglets), while one of the same HYAL2 markers maintained a modest association (P = 0.0043) having a dominant effect with number of piglets weaned (1.2 ± 0.41 piglets) after multiple-testing correction. Functionally, HPSE and HYAL1 and 2 have been shown to participate in events related to ovarian and placental activity. SNPs from these studies could potentially assist with understanding genetic components underlying sow lifetime productivity as measured by piglet survivability based on number born alive and number weaned, thereby contributing to a greater number of pigs/sow/year.
Collapse
Affiliation(s)
- Lea A Rempel
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture Clay Center, NE, USA
| | | | | | | | | | | | | |
Collapse
|
35
|
Ramos AM, Duijvesteijn N, Knol EF, Merks JWM, Bovenhuis H, Crooijmans RPMA, Groenen MAM, Harlizius B. The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars. BMC Genet 2011; 12:35. [PMID: 21507230 PMCID: PMC3111395 DOI: 10.1186/1471-2156-12-35] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 04/20/2011] [Indexed: 11/20/2022] Open
Abstract
Background Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the economic and animal welfare concerns there is interest in developing genetic markers that could be used in selection schemes to decrease the incidence of boar taint. The Porcine 60 K SNP Beadchip was used to genotype 891 pigs from a composite Duroc sire line, for which skatole levels in fat had been collected. Results The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels. These SNPs are grouped in three separate clusters located in the initial 6 Mb region of chromosome 6. The differences observed between the homozygote genotypes for SNPs in the three clusters were substantial, including a difference of 102.8 ng/g skatole in melted fat between the homozygotes for the ALGA0107039 marker. Single SNPs explain up to 22% of the phenotypic variance. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome. Conclusions This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p. These markers defined three independent clusters in the region, which contain a low number of protein-coding genes. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigs
Collapse
Affiliation(s)
- António M Ramos
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Lourenço VM, Pires AM, Kirst M. Robust linear regression methods in association studies. ACTA ACUST UNITED AC 2011; 27:815-21. [PMID: 21217123 DOI: 10.1093/bioinformatics/btr006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
MOTIVATION It is well known that data deficiencies, such as coding/rounding errors, outliers or missing values, may lead to misleading results for many statistical methods. Robust statistical methods are designed to accommodate certain types of those deficiencies, allowing for reliable results under various conditions. We analyze the case of statistical tests to detect associations between genomic individual variations (SNP) and quantitative traits when deviations from the normality assumption are observed. We consider the classical analysis of variance tests for the parameters of the appropriate linear model and a robust version of those tests based on M-regression. We then compare their empirical power and level using simulated data with several degrees of contamination. RESULTS Data normality is nothing but a mathematical convenience. In practice, experiments usually yield data with non-conforming observations. In the presence of this type of data, classical least squares statistical methods perform poorly, giving biased estimates, raising the number of spurious associations and often failing to detect true ones. We show through a simulation study and a real data example, that the robust methodology can be more powerful and thus more adequate for association studies than the classical approach. AVAILABILITY The code of the robustified version of function lmekin() from the R package kinship is provided as Supplementary Material.
Collapse
Affiliation(s)
- V M Lourenço
- Department of Mathematics, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | | | | |
Collapse
|
37
|
Martins da Silva A, Rios A, Ramos E, Lôbo R, Oliveira H, de Freitas M. Association between IGF2 and CYP21 gene polymorphisms and characteristics of economic interest in Nellore cattle. GENETICS AND MOLECULAR RESEARCH 2011; 10:2140-7. [DOI: 10.4238/vol10-3gmr1184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
38
|
Pimentel ECG, Bauersachs S, Tietze M, Simianer H, Tetens J, Thaller G, Reinhardt F, Wolf E, König S. Exploration of relationships between production and fertility traits in dairy cattle via association studies of SNPs within candidate genes derived by expression profiling. Anim Genet 2010; 42:251-62. [DOI: 10.1111/j.1365-2052.2010.02148.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
39
|
Oskam IC, Lervik S, Tajet H, Dahl E, Ropstad E, Andresen Ø. Differences in testosterone, androstenone, and skatole levels in plasma and fat between pubertal purebred Duroc and Landrace boars in response to human chorionic gonadotrophin stimulation. Theriogenology 2010; 74:1088-98. [PMID: 20580070 DOI: 10.1016/j.theriogenology.2010.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 04/26/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
Abstract
The concentrations of the boar taint compounds androstenone and skatole in plasma and fat, together with those of testosterone in plasma, were investigated in pubertal purebred Duroc and Landrace boars following stimulation with human chorionic gonadotrophin (hCG). Higher initial levels of androstenone and testosterone were found in Duroc than Landrace boars. Duroc boars, which were approximately ten days older than the Landrace boars, also showed a more advanced stage of spermatogenesis than Landrace boars. While Landrace boars had the highest skatole levels. Following stimulation with hCG the relative increases in testosterone, androstenone, and skatole concentrations were highest in Landrace boars. The level of androstenone in fat three days after hCG stimulation exceeded 1 microg/g fat in all stimulated boars. The decreases in plasma levels of androstenone and testosterone on Days 2 and 3 after hCG stimulation were more pronounced in Landrace than Duroc boars. However, unlike the plasma androstenone and testosterone levels, the plasma concentrations of skatole did not decrease on Days 2 and 3 following stimulation, but remained elevated on Day 3. These results indicate that the lower levels of testicular steroids in Landrace boars compared with Duroc boars was not due to a lower production capacity, but more likely to a faster disappearance of steroids in Landrace boars. In the present study, age, live weight, and testicular development did not significantly contribute to the variation in fat androstenone. The present data and previous reports on candidate genes related to androstenone biosynthesis and metabolism suggests that future selection against factors associated with boar taint remains a possible solution for the problem of boar taint in the swine industry.
Collapse
Affiliation(s)
- I C Oskam
- The Norwegian School of Veterinary Science, Department of Production Animal Clinical Sciences. P.B. 8146, NO-0033 Oslo, Norway.
| | | | | | | | | | | |
Collapse
|
40
|
Duijvesteijn N, Knol EF, Merks JWM, Crooijmans RPMA, Groenen MAM, Bovenhuis H, Harlizius B. A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6. BMC Genet 2010; 11:42. [PMID: 20487517 PMCID: PMC2889844 DOI: 10.1186/1471-2156-11-42] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 05/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In many countries, male piglets are castrated shortly after birth because a proportion of un-castrated male pigs produce meat with an unpleasant flavour and odour. Main compounds of boar taint are androstenone and skatole. The aim of this high-density genome-wide association study was to identify single nucleotide polymorphisms (SNPs) associated with androstenone levels in a commercial sire line of pigs. The identification of major genetic effects causing boar taint would accelerate the reduction of boar taint through breeding to finally eliminate the need for castration. RESULTS The Illumina Porcine 60K+SNP Beadchip was genotyped on 987 pigs divergent for androstenone concentration from a commercial Duroc-based sire line. The association analysis with 47,897 SNPs revealed that androstenone levels in fat tissue were significantly affected by 37 SNPs on pig chromosomes SSC1 and SSC6. Among them, the 5 most significant SNPs explained together 13.7% of the genetic variance in androstenone. On SSC6, a larger region of 10 Mb was shown to be associated with androstenone covering several candidate genes potentially involved in the synthesis and metabolism of androgens. Besides known candidate genes, such as cytochrome P450 A19 (CYP2A19), sulfotransferases SULT2A1, and SULT2B1, also new members of the cytochrome P450 CYP2 gene subfamilies and of the hydroxysteroid-dehydrogenases (HSD17B14) were found. In addition, the gene encoding the ss-chain of the luteinizing hormone (LHB) which induces steroid synthesis in the Leydig cells of the testis at onset of puberty maps to this area on SSC6. Interestingly, the gene encoding the alpha-chain of LH is also located in one of the highly significant areas on SSC1. CONCLUSIONS This study reveals several areas of the genome at high resolution responsible for variation of androstenone levels in intact boars. Major genetic factors on SSC1 and SSC6 showing moderate to large effects on androstenone concentration were identified in this commercial breeding line of pigs. Known and new candidate genes cluster especially on SSC6. For one of the most significant SNP variants, the difference in the proportion of animals surpassing the threshold of consumer acceptance between the two homozygous genotypes was as much as 15.6%.
Collapse
Affiliation(s)
- Naomi Duijvesteijn
- IPG, Institute for Pig Genetics B.V., PO Box 43, 6640AA, Beuningen, the Netherlands.
| | | | | | | | | | | | | |
Collapse
|
41
|
Grindflek E, Berget I, Moe M, Oeth P, Lien S. Transcript profiling of candidate genes in testis of pigs exhibiting large differences in androstenone levels. BMC Genet 2010; 11:4. [PMID: 20100319 PMCID: PMC2823645 DOI: 10.1186/1471-2156-11-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 01/25/2010] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Boar taint is an unpleasant odor and flavor of the meat and occurs in a high proportion of uncastrated male pigs. Androstenone, a steroid produced in testis and acting as a sex pheromone regulating reproductive function in female pigs, is one of the main compounds responsible for boar taint. The primary goal of the present investigation was to determine the differential gene expression of selected candidate genes related to levels of androstenone in pigs. RESULTS Altogether 2560 boars from the Norwegian Landrace and Duroc populations were included in this study. Testicle samples from the 192 boars with most extreme high or low levels of androstenone in fat were used for RNA extraction, and 15 candidate genes were selected and analyzed by real-competitive PCR analysis. The genes Cytochrome P450 c17 (CYP17A1), Steroidogenic acute regulatory protein (STAR), Aldo-keto reductase family 1 member C4 (AKR1C4), Short-chain dehydrogenase/reductase family member 4 (DHRS4), Ferritin light polypeptide (FTL), Sulfotransferase family 2A, dehydroepiandrosterone-preferring member 1 (SULT2A1), Cytochrome P450 subfamily XIA polypeptide 1 (CYP11A1), Cytochrome b5 (CYB5A), and 17-beta-Hydroxysteroid dehydrogenase IV (HSD17B4) were all found to be significantly (P < 0.05) up-regulated in high androstenone boars in both Duroc and Landrace. Furthermore, Cytochrome P450 c19A2 (CYP19A2) was down-regulated and progesterone receptor membrane component 1 (PGRMC1) was up-regulated in high-androstenone Duroc boars only, while CYP21 was significantly down-regulated (2.5) in high-androstenone Landrace only. The genes Nuclear Receptor co-activator 4 (NCOA4), Sphingomyrlin phosphodiesterase 1 (SMPD1) and 3beta-hydroxysteroid dehydrogenase (HSD3B) were not significantly differentially expressed in any breeds. Additionally, association studies were performed for the genes with one or more detected SNPs. Association between SNP and androstenone level was observed in CYB5A only, suggesting cis-regulation of the differential transcription in this gene. CONCLUSION A large pig material of highly extreme androstenone levels is investigated. The current study contributes to the knowledge about which genes that is differentially expressed regard to the levels of androstenone in pigs. Results in this paper suggest that several genes are important in the regulation of androstenone level in boars and warrant further evaluation of the above mentioned candidate genes, including analyses in different breeds, identification of causal mutations and possible gene interactions.
Collapse
Affiliation(s)
- Eli Grindflek
- NORSVIN, The Norwegian Pig Breeders Association, Hamar, Norway.
| | | | | | | | | |
Collapse
|