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Tenke J, Vida O, Nagy I, Tossenberger J. Classifying Genetic Lines in Pork Production by Ileal Crude Protein and Amino Acid Digestibility in Growing Pigs. Animals (Basel) 2023; 13:1898. [PMID: 37370409 DOI: 10.3390/ani13121898] [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: 04/24/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The first aim of the study was to evaluate the effect of different dietary lysine (LYS) to energy (DE) ratios on the apparent ileal digestibility (AID) of crude protein (CP) and selected amino acids (AA) in growing pigs (40-60 kg) of different genotypes. The second aim was to classify genotypes into groups based on the AID of CP and AAs. The trials were conducted on a total of 90 cross-bred barrows (30 animals/genotype) in two replicates. Before the trial series, the experimental animals (average initial body weight (BW) = 40.9 ± 8.5 kg) were surgically fitted with post valve T-cannula (PVTC). The diets were formulated with six different total LYS/DE ratios. Titanium dioxide (TiO2) was added to the diets (5 g/kg) as an indigestible marker. Based on our results, it can be concluded that the LYS/DE ratio of the diets affected the AID of the CP and AA in different ways by each genotype (p < 0.05). It can also be concluded that pigs of different genetic potential can be classified with a high accuracy (91.7%) in respect of their CP and AA digestive capacity. Our results indicate the development of genetic-profile-based swine nutrition technologies as a future direction.
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Affiliation(s)
- János Tenke
- Albert Kázmér Faculty of Mosonmagyaróvár, Széchenyi István University, Lucsony Str. 2, H-9200 Mosonmagyaróvár, Hungary
- Bonafarm Agriculture-Swine Department, Ady Endre Str. 21, H-7754 Bóly, Hungary
| | - Orsolya Vida
- DSM Nutritional Products Hungary Ltd., Japán Fasor 4, H-2367 Újhartyán, Hungary
| | - István Nagy
- Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor Str. 40, H-7400 Kaposvár, Hungary
| | - János Tossenberger
- Albert Kázmér Faculty of Mosonmagyaróvár, Széchenyi István University, Lucsony Str. 2, H-9200 Mosonmagyaróvár, Hungary
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Integrated Single-Trait and Multi-Trait GWASs Reveal the Genetic Architecture of Internal Organ Weight in Pigs. Animals (Basel) 2023; 13:ani13050808. [PMID: 36899665 PMCID: PMC10000129 DOI: 10.3390/ani13050808] [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: 01/07/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs.
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Fang F, Li J, Guo M, Mei Q, Yu M, Liu H, Legarra A, Xiang T. Genomic evaluation and genome-wide association studies for total number of teats in a combined American and Danish Yorkshire pig populations selected in China. J Anim Sci 2022; 100:6585233. [PMID: 35553682 PMCID: PMC9259599 DOI: 10.1093/jas/skac174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
Joint genomic evaluation by combining data recordings and genomic information from different pig herds and populations is of interest for pig breeding companies because the efficiency of genomic selection (GS) could be further improved. In this work, an efficient strategy of joint genomic evaluation combining data from multiple pig populations is investigated. Total Teat Number (TTN), a trait that is equally recorded on 13 060 American Yorkshire (AY) populations (~14.68 teats) and 10 060 Danish Yorkshire (DY) pigs (~14.29 teats), was used to explore the feasibility and accuracy of GS combining datasets from different populations. We first estimated the genetic correlation (rg) of TTN between AY and DY pig populations (rg=0.79, se=0.23). Then we employed the genome-wide association study (GWAS) to identify QTL regions that are significantly associated with TTN and investigate the genetic architecture of TTN in different populations. Our results suggested that the genomic regions controlling TTN are slight different in the two Yorkshire populations, where the candidate QTL regions were on SSC 7 and SSC 8 for AY population and on SSC 7 for DY population. Finally, we explored an optimal way of genomic prediction for TTN via three different Genomic Best Linear Unbiased Prediction (GBLUP) models and we concluded that when TTN across populations are regarded as different, but correlated, traits in a multi-trait model, predictive abilities for both Yorkshire populations improve. As a conclusion, joint genomic evaluation for target traits in multiple pig populations is feasible in practice and more accurate, provided a proper model is used.
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Affiliation(s)
- Fang Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieling Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Quanshun Mei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Huiming Liu
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele 8830, Denmark
| | - Andres Legarra
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Tao Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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Liu Z, Li H, Zhong Z, Jiang S. A Whole Genome Sequencing-Based Genome-Wide Association Study Reveals the Potential Associations of Teat Number in Qingping Pigs. Animals (Basel) 2022; 12:1057. [PMID: 35565484 PMCID: PMC9100799 DOI: 10.3390/ani12091057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Teat number plays an important role in the reproductive performance of sows and the growth of piglets. However, the quantitative trait loci (QTLs) and candidate genes for the teat number-related traits in Qingping pigs remain unknown. In this study, we performed GWAS based on whole-genome single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) for the total number of teats and five other related traits in 100 Qingping pigs. SNPs and Indels of all 100 pigs were genotyped using 10× whole genome resequencing. GWAS using General Linear Models (GLM) detected a total of 28 SNPs and 45 Indels as peak markers for these six traits. We also performed GWAS for the absolute difference between left and right teat number (ADIFF) using Fixed and random model Circulating Probability Unification (FarmCPU). The most strongly associated SNP and Indel with a distance of 562,788 bp were significantly associated with ADIFF in both GLM and FarmCPU models. In the 1-Mb regions of the most strongly associated SNP and Indel, there were five annotated genes, including TRIML1, TRIML2, ZFP42, FAT1 and MTNR1A. We also highlighted TBX3 as an interesting candidate gene for SSC14. Enrichment analysis of candidate genes suggested the Wnt signaling pathway may contribute to teat number-related traits. This study expanded significant marker-trait associations for teat number and provided useful molecular markers and candidate genes for teat number improvement in the breeding of sows.
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Affiliation(s)
- Zezhang Liu
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100083, China;
| | - Zhuxia Zhong
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
| | - Siwen Jiang
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
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Li Y, Liu X, Bai X, Wang Y, Leng L, Zhang H, Li Y, Cao Z, Luan P, Xiao F, Gao H, Sun Y, Wang N, Li H, Wang S. Genetic parameters estimation and genome‐wide association studies for internal organ traits in an F
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chicken population. J Anim Breed Genet 2022; 139:434-446. [DOI: 10.1111/jbg.12674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Yudong Li
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Xin Liu
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Xue Bai
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Fan Xiao
- Fujian Sunnzer Biotechnology Development Co., Ltd Guangze P.R. China
| | - Haihe Gao
- Fujian Sunnzer Biotechnology Development Co., Ltd Guangze P.R. China
| | - Yuhang Sun
- Fujian Sunnzer Biotechnology Development Co., Ltd Guangze P.R. China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding Ministry of Agriculture and Rural Affairs Harbin P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction Education Department of Heilongjiang Province Harbin P.R. China
- College of Animal Science and Technology Northeast Agricultural University Harbin P.R. China
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Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population. Animals (Basel) 2020; 10:ani10112186. [PMID: 33266466 PMCID: PMC7700692 DOI: 10.3390/ani10112186] [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: 10/09/2020] [Revised: 10/29/2020] [Accepted: 11/06/2020] [Indexed: 01/28/2023] Open
Abstract
Simple Summary The number of thoracic vertebrae (NTV) and number of vertebrae (NV) varies among pig breeds with a high correlation of about 0.8. It is important to discover variants associated with the NTV by considering the effect of the NV in pig. The results suggest that regulation variants on SSC7 might play crucial roles in the NTV and the FOS on SSC7 should be further studied as a critical candidate gene. In addition, BMPR1A was identified as a novel candidate gene affecting the NTV in pigs. Abstract The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.
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Amaral AJ, Bressan MC, Almeida J, Bettencourt C, Moreira O, Sá J, Gama-Carvalho M, Bessa R, Gama LT. Combining genome-wide association analyses and gene interaction networks to reveal new genes associated with carcass traits, meat quality and fatty acid profiles in pigs. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.12.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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An B, Xia J, Chang T, Wang X, Miao J, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle. Physiol Genomics 2018; 50:523-531. [DOI: 10.1152/physiolgenomics.00022.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.
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Affiliation(s)
- Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xiaoqiao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jian Miao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
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Chalkias H, Jonas E, Andersson LS, Jacobson M, de Koning DJ, Lundeheim N, Lindgren G. Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel. J Appl Genet 2017; 58:249-259. [PMID: 28050760 PMCID: PMC5391382 DOI: 10.1007/s13353-016-0382-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/24/2016] [Indexed: 11/29/2022]
Abstract
The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.
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Affiliation(s)
- Helena Chalkias
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Elisabeth Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden.
| | - Lisa S Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07, Uppsala, Sweden
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Nils Lundeheim
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden.,Capilet Genetics AB, SE-725 93, Västerås, Sweden
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He Y, Li X, Zhang F, Su Y, Hou L, Chen H, Zhang Z, Huang L. Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs. Genet Sel Evol 2015; 47:87. [PMID: 26576866 PMCID: PMC4647478 DOI: 10.1186/s12711-015-0168-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 10/30/2015] [Indexed: 12/01/2022] Open
Abstract
Background Recently, many genome-wide association studies (GWAS) have been conducted to understand the genetic architecture of economic important traits in farm animals. Pig is widely used as a biomedical animal model for its similarity with humans in terms of organ formation and disease mechanisms. Moreover, understanding the mechanisms that underlie the development of internal organs will impact the productive potential of pigs. Our aim was to uncover new single nucleotide polymorphisms (SNPs) associated with the weight of internal organs and carcass and also potential candidate genes. Methods We performed GWAS for the weight of heart, liver, spleen, kidney and carcass on five pig populations (White Duroc × Erhualian F2 intercross, Sutai population, Laiwu population, Erhualian population and commercial population, for a total of 2650 individuals). Genotype data was produced using the PorcineSNP60 Beadchip array. After quality control, the data was used for association tests under a general linear mixed model. Population stratification was adjusted by including a random polygenic effect based on a matrix of genotypic relationships. A meta-analysis of our GWAS datasets was conducted by summing up the Chi square values across breeds, with the degrees of freedom of the Chi square distribution equal to the effective number of breeds. Results Thirty-nine quantitative trait loci (QTL) located on 15 chromosomes were identified by the single-population GWAS at the suggestive level. Among these, nine QTL surpassed the 5 % genome-wide significance threshold, including four for heart weight on SSC (Sus scrofa chromosome) 2, 4, 7 and 10, two for liver weight on SSC7, two for spleen weight on SSC5 and SSC7 and one for carcass weight on SSC11. The QTL on SSC7 showed pleiotropic effects for heart, liver and spleen weights in the F2 population. In addition, two QTL were detected in several populations, including one on SSC2 for heart weight in the F2 and Sutai populations and one on SSC7 for liver weight in the F2 and Laiwu populations. The meta-analysis detected four novel QTL on SSC1, 3, 8 and 16 for carcass weight. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0168-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuna He
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xinjian Li
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Feng Zhang
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Ying Su
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lijuan Hou
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hao Chen
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhiyan Zhang
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Zhu J, Chen C, Yang B, Guo Y, Ai H, Ren J, Peng Z, Tu Z, Yang X, Meng Q, Friend S, Huang L. A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits. BMC Genomics 2015; 16:88. [PMID: 25765547 PMCID: PMC4336704 DOI: 10.1186/s12864-015-1240-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 01/13/2015] [Indexed: 12/20/2022] Open
Abstract
Background The pig, which shares greater similarities with human than with mouse, is important for agriculture and for studying human diseases. However, similarities in the genetic architecture and molecular regulations underlying phenotypic variations in humans and swine have not been systematically assessed. Results We systematically surveyed ~500 F2 pigs genetically and phenotypically. By comparing candidates for anemia traits identified in swine genome-wide SNP association and human genome-wide association studies (GWAS), we showed that both sets of candidates are related to the biological process “cellular lipid metabolism” in liver. Human height is a complex heritable trait; by integrating genome-wide SNP data and human adipose Bayesian causal network, which closely represents bone transcriptional regulations, we identified PLAG1 as a causal gene for limb bone length. This finding is consistent with GWAS findings for human height and supports the common genetic architecture between swine and humans. By leveraging a human protein-protein interaction network, we identified two putative candidate causal genes TGFB3 and DAB2IP and the known regulators MESP1 and MESP2 as responsible for the variation in rib number and identified the potential underlying molecular mechanisms. In mice, knockout of Tgfb3 and Tgfb2 together decreases rib number. Conclusion Our findings show that integrative network analyses reveal causal regulators underlying the genetic association of complex traits in swine and that these causal regulators have similar effects in humans. Thus, swine are a potentially good animal model for studying some complex human traits that are not under intense selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1240-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Zhu
- Jiangxi Agricultural University, Nanchang, Jiangxi, China. .,Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Congying Chen
- Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Bin Yang
- Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Yuanmei Guo
- Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Huashui Ai
- Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Jun Ren
- Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | | | - Zhidong Tu
- Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA, USA.
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA, USA.
| | | | - Lusheng Huang
- Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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12
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Hidalgo AM, Bastiaansen JWM, Harlizius B, Knol EF, Lopes MS, de Koning DJ, Groenen MAM. Asian low-androstenone haplotype on pig chromosome 6 does not unfavorably affect production and reproduction traits. Anim Genet 2014; 45:874-7. [PMID: 25262849 DOI: 10.1111/age.12226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2014] [Indexed: 11/28/2022]
Abstract
European pigs that carry Asian haplotypes of a 1.94-Mbp region on pig chromosome 6 have lower levels of androstenone, one of the two main compounds causing boar taint. The objective of our study was to examine potential pleiotropic effects of the Asian low-androstenone haplotypes. A single nucleotide polymorphism marker, rs81308021, distinguishes the Asian from European haplotypes and was used to investigate possible associations of androstenone with production and reproduction traits. Eight traits were available from three European commercial breeds. For the two sow lines studied, a favorable effect on number of teats was detected for the low-androstenone haplotype. In one of these sow lines, a favorable effect on number of spermatozoa per ejaculation was detected for the low-androstenone haplotype. No unfavorable pleiotropic effects were found, which suggests that selection for low-androstenone haplotypes within the 1.94 Mbp would not unfavorably affect the other eight relevant traits.
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Affiliation(s)
- A M Hidalgo
- Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, Wageningen, 6700 AH, The Netherlands; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, Uppsala, 750 07, Sweden
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13
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Lopes MS, Bastiaansen JWM, Harlizius B, Knol EF, Bovenhuis H. A genome-wide association study reveals dominance effects on number of teats in pigs. PLoS One 2014; 9:e105867. [PMID: 25158056 PMCID: PMC4144910 DOI: 10.1371/journal.pone.0105867] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 07/29/2014] [Indexed: 12/31/2022] Open
Abstract
Dominance has been suggested as one of the genetic mechanisms explaining heterosis. However, using traditional quantitative genetic methods it is difficult to obtain accurate estimates of dominance effects. With the availability of dense SNP (Single Nucleotide Polymorphism) panels, we now have new opportunities for the detection and use of dominance at individual loci. Thus, the aim of this study was to detect additive and dominance effects on number of teats (NT), specifically to investigate the importance of dominance in a Landrace-based population of pigs. In total, 1,550 animals, genotyped for 32,911 SNPs, were used in single SNP analysis. SNPs with a significant genetic effect were tested for their mode of gene action being additive, dominant or a combination. In total, 21 SNPs were associated with NT, located in three regions with additive (SSC6, 7 and 12) and one region with dominant effects (SSC4). Estimates of additive effects ranged from 0.24 to 0.29 teats. The dominance effect of the QTL located on SSC4 was negative (−0.26 teats). The additive variance of the four QTLs together explained 7.37% of the total phenotypic variance. The dominance variance of the four QTLs together explained 1.82% of the total phenotypic variance, which corresponds to one-fourth of the variance explained by additive effects. The results suggest that dominance effects play a relevant role in the genetic architecture of NT. The QTL region on SSC7 contains the most promising candidate gene: VRTN. This gene has been suggested to be related to the number of vertebrae, a trait correlated with NT.
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Affiliation(s)
- Marcos S. Lopes
- TOPIGS Research Center IPG B.V., Beuningen, the Netherlands
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, the Netherlands
- * E-mail:
| | | | | | - Egbert F. Knol
- TOPIGS Research Center IPG B.V., Beuningen, the Netherlands
| | - Henk Bovenhuis
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, the Netherlands
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14
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Duijvesteijn N, Veltmaat JM, Knol EF, Harlizius B. High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development. BMC Genomics 2014; 15:542. [PMID: 24981054 PMCID: PMC4092218 DOI: 10.1186/1471-2164-15-542] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/25/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Selection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. Although many QTL were reported, they cover large chromosomal regions and the functional mutations and their underlying biological mechanisms have not yet been identified. To gain a better insight in the genetic architecture of the trait number of teats, we performed a genome-wide association study by genotyping 936 Large White pigs using the Illumina PorcineSNP60 Beadchip. The analysis is based on deregressed breeding values to account for the dense family structure and a Bayesian approach for estimation of the SNP effects. RESULTS The genome-wide association study resulted in 212 significant SNPs. In total, 39 QTL regions were defined including 170 SNPs on 13 Sus scrofa chromosomes (SSC) of which 5 regions on SSC7, 9, 10, 12 and 14 were highly significant. All significantly associated regions together explain 9.5% of the genetic variance where a QTL on SSC7 explains the most genetic variance (2.5%). For the five highly significant QTL regions, a search for candidate genes was performed. The most convincing candidate genes were VRTN and Prox2 on SSC7, MPP7, ARMC4, and MKX on SSC10, and vertebrae δ-EF1 on SSC12. All three QTL contain candidate genes which are known to be associated with vertebral development. In the new QTL regions on SSC9 and SSC14, no obvious candidate genes were identified. CONCLUSIONS Five major QTL were found at high resolution on SSC7, 9, 10, 12, and 14 of which the QTL on SSC9 and SSC14 are the first ones to be reported on these chromosomes. The significant SNPs found in this study could be used in selection to increase number of teats in pigs, so that the increasing number of live-born piglets can be nursed by the sow. This study points to common genetic mechanisms regulating number of vertebrae and number of teats.
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Affiliation(s)
- Naomi Duijvesteijn
- />TOPIGS Research Center IPG, PO Box 43, 6640AA Beuningen, The Netherlands
| | - Jacqueline M Veltmaat
- />Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61, Biopolis Drive, Singapore, Singapore 138673
| | - Egbert F Knol
- />TOPIGS Research Center IPG, PO Box 43, 6640AA Beuningen, The Netherlands
| | - Barbara Harlizius
- />TOPIGS Research Center IPG, PO Box 43, 6640AA Beuningen, The Netherlands
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15
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Screening of microsatellite markers associated with cold tolerance of large yellow croaker ( Pseudosciaena crocea R.). YI CHUAN = HEREDITAS 2010; 32:248-53. [DOI: 10.3724/sp.j.1005.2010.00248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Ma J, Ren J, Guo Y, Duan Y, Ding N, Zhou L, Li L, Yan X, Yang K, Huang L, Song Y, Xie J, Milan D, Huang L. Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc x Chinese Erhualian resource population. Anim Genet 2009; 40:637-47. [PMID: 19397518 DOI: 10.1111/j.1365-2052.2009.01892.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F(2) animals from a White Duroc x Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.
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Affiliation(s)
- J Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, China
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17
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Reiner DJ, Jan TA, Boughter JD, Li CX, Lu L, Williams RW, Waters RS. Genetic analysis of tongue size and taste papillae number and size in recombinant inbred strains of mice. Chem Senses 2008; 33:693-707. [PMID: 18653645 DOI: 10.1093/chemse/bjn025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Quantitative trait loci (QTLs) analysis has been used to examine natural variation of phenotypes in the mouse somatosensory cortex, hippocampus, cerebellum, and amygdala. QTL analysis has also been utilized to map and identify genes underlying anatomical features such as muscle, organ, and body weights. However, this methodology has not been previously applied to identification of anatomical structures related to gustatory phenotypes. In this study, we used QTL analysis to map and characterize genes underlying tongue size, papillae number, and papillae area. In a set of 43 BXD recombinant inbred (RI) mice (n = 111) and 2 parental strains (C57BL/6J and DBA/2J; n = 7), we measured tongue length, width, and weight. In a subset of 23 BXD RI mice and the parental mice, we measured filiform and fungiform papillae number and fungiform papillae area. Using QTL linkage analysis (through WebQTL), we detected 2 significant and noninteracting QTLs influencing tongue length on chromosomes 5 and 7. We also found a significant QTL on chromosome 19 underlying fungiform papillae area and a suggestive QTL on chromosome 2 linked to fungiform papillae number. From these QTLs, we identified a number of candidate genes within the QTL intervals that include SRY-box containing gene, nebulin-related anchoring protein, and actin-binding LIM protein 1. This study is an important first step in identifying genetic factors underlying tongue size, papillae size, and papillae number using QTL analysis.
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Affiliation(s)
- David J Reiner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, College of Medicine, 855 Monroe Avenue, Memphis, TN 38163, USA
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