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Gao X, Zhou S, Liu Z, Ruan D, Wu J, Quan J, Zheng E, Yang J, Cai G, Wu Z, Yang M. Genome-Wide Association Study for Somatic Skeletal Traits in Duroc × (Landrace × Yorkshire) Pigs. Animals (Basel) 2023; 14:37. [PMID: 38200769 PMCID: PMC10778498 DOI: 10.3390/ani14010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits.
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Affiliation(s)
- Xin Gao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.G.); (S.Z.); (Z.L.)
| | - Shenping Zhou
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.G.); (S.Z.); (Z.L.)
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Zhihong Liu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.G.); (S.Z.); (Z.L.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (X.G.); (S.Z.); (Z.L.)
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Steinerova M, Horecky C, Knoll A, Nedomova S, Slama P, Pavlik A. Study of genes polymorphisms in RANK/RANKL/OPG and WNT signaling pathways and their associations with bone parameters in broiler chicken. Heliyon 2023; 9:e22371. [PMID: 38053912 PMCID: PMC10694325 DOI: 10.1016/j.heliyon.2023.e22371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 09/22/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Limb problems are one of the most common problems with fast-growing meat-type chickens. Various bone abnormalities, which can lead to limping, bone weakness, or even fractures, bring overall discomfort to birds and a loss of production. Genetic aspects are often associated with these side effects on bone stability and are also cited as the dominant cause. These points to a close negative relationship of genetic selection for rapid growth with traits involved in bone integrity. Due to the assumption of an additive genetic background, improvements through genetic tools can be used. Our study is focused on selected genes of important signaling pathways for bone metabolism. We tried to detect polymorphisms that would show associations with selected bone parameters in a total of 48 broilers. Those were fast-growing Ross 308 hybrids and slow-growing Hubbard M22BxJA87A hybrids. The TNFRSF11A and WISP1 genes were tested. A total of fourteen polymorphisms were found, three of them were synonymous and five in the intron. In the case of four polymorphisms found in exons of the TNFRSF11A gene (c.11G > T, c.31G > A, c.37C > G, c.514G > A), associations with the observed bone parameters (bone strength, bone dimensions and bone mass) were demonstrated. The genetic architecture of bone traits is not fully understood, therefore the present study and the knowledge gained can help to increase the potential in poultry breeding processes and thus reduce the death of individuals.
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Affiliation(s)
- Michala Steinerova
- Department of Animal Morphology, Physiology and Genetics, Mendel University in Brno, Faculty of AgriSciences, Zemedelska 1/1665, 613 00, Brno, Czech Republic
| | - Cenek Horecky
- Department of Animal Morphology, Physiology and Genetics, Mendel University in Brno, Faculty of AgriSciences, Zemedelska 1/1665, 613 00, Brno, Czech Republic
| | - Ales Knoll
- Department of Animal Morphology, Physiology and Genetics, Mendel University in Brno, Faculty of AgriSciences, Zemedelska 1/1665, 613 00, Brno, Czech Republic
| | - Sarka Nedomova
- Department of Food Technology, Mendel University in Brno, Faculty of AgriSciences, Zemedelska 1/1665, 613 00, Brno, Czech Republic
| | - Petr Slama
- Department of Animal Morphology, Physiology and Genetics, Mendel University in Brno, Faculty of AgriSciences, Zemedelska 1/1665, 613 00, Brno, Czech Republic
| | - Ales Pavlik
- Department of Animal Morphology, Physiology and Genetics, Mendel University in Brno, Faculty of AgriSciences, Zemedelska 1/1665, 613 00, Brno, Czech Republic
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Hu L, Lu J, Guo L, Tan J, Sun H, Zhou Y, Wu Y, Wei H, Jiang S, Peng J. Factors influencing the bone mineral density in Duroc boars. Porcine Health Manag 2023; 9:22. [PMID: 37221632 DOI: 10.1186/s40813-023-00318-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Leg weakness affects animal welfare and is one of the primary reasons for culling of boars. Low bone mineral density (BMD) is one of the primary factors contributing to leg weakness. Low BMD also appeared to be associated with severe bone pain and has the highest risk of skeletal fragility. Surprisingly, few studies have been performed on the factors influencing BMD in pigs. Therefore, the primary aim of this study was to identify the influencing factors on boar BMD. Herein, the BMD data were determined through the use of ultrasonography from 893 Duroc boars. Logistic regression model was utilized in the analysis of BMD, in which the explanatory variables in the model were lines, ages, body weights, backfat thicknesses and serum mineral element concentrations (Ca, P, Mg, Cu, Fe, Zn, Mn, Se, Pb and Cd). RESULTS Results showed that factors significantly influencing BMD included serum Ca, P concentrations, ages and backfat thicknesses (P < 0.05), in which serum Ca concentrations were positively correlated with BMD (P < 0.01), whereas increasing concentrations of serum P decreased BMD (P < 0.01). The serum Ca/P ratio showed significant quadratic effects on BMD (r = 0.28, P < 0.01), and the Ca/P ratio to achieve the best BMD was determined to be 3.7. Furthermore, BMD also changed with age quadratically (r = 0.40, P < 0.01), and reached a peak value around 47 months. Interestingly, a quadratic (r = 0.26, P < 0.01) increase in the BMD was observed as backfat thickness increased, and the inflection point was calculated at around 17 mm. CONCLUSION In conclusion, BMD characteristics of boars could be detected by ultrasonic method, and serum Ca, serum P, age, and backfat thickness contributed to the greatest effect on BMD.
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Affiliation(s)
- Lingling Hu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxin Lu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liangliang Guo
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiajian Tan
- YangXiang Joint Stock Company, Guigang, 537000, China
| | - Haiqing Sun
- YangXiang Joint Stock Company, Guigang, 537000, China
| | - Yuanfei Zhou
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yinghui Wu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongkui Wei
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Siwen Jiang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
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Liu Y, Fu Y, Yang Y, Yi G, Lian J, Xie B, Yao Y, Chen M, Niu Y, Liu L, Wang L, Zhang Y, Fan X, Tang Y, Yuan P, Zhu M, Li Q, Zhang S, Chen Y, Wang B, He J, Lu D, Liachko I, Sullivan ST, Pang B, Chen Y, He X, Li K, Tang Z. Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs. GENETICS SELECTION EVOLUTION 2022; 54:62. [PMID: 36104777 PMCID: PMC9476355 DOI: 10.1186/s12711-022-00754-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.
Results
We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.
Conclusions
Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.
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Wang FH, Zhang L, Gong G, Yan XC, Zhang LT, Zhang FT, Liu HF, Lv Q, Wang ZY, Wang RJ, Zhang YJ, Wang ZX, Liu ZH, He LB, Su R, Zhao YH, Li JQ. Genome-wide association study of fleece traits in Inner Mongolia Cashmere goats. Anim Genet 2021; 52:375-379. [PMID: 33778967 PMCID: PMC8251931 DOI: 10.1111/age.13053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
Inner Mongolia Cashmere goat is a well-known local cashmere goat breed in China. It is famous for excellent fleece quality and a significant advantage in cashmere yield compared to other cashmere goat breeds. In this study, a genome-wide association study was used to investigate fiber length, fiber diameter, and cashmere yield of 192 Inner Mongolia Cashmere goats using the Illumina GoatSNP52K Beadchip panel. We discovered that four single nucleotide polymorphisms (SNPs) reached genome-wide significance levels. These SNPs were located in some genes, e.g. FGF12, SEMA3D, EVPL, and SOX5, possibly related to fleece traits in Inner Mongolia Cashmere goat. Gene ontology enrichment analysis revealed that these genes were enriched in several biological pathways that were involved in hair follicle development in cashmere goats. In summary, the identified significant SNPs and genes provide useful information to explore genetic mechanisms underlying the variation in fleece traits and genomic selection of Chinese cashmere goat.
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Affiliation(s)
- F. H. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - L. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - G. Gong
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - X. C. Yan
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - L. T. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - F. T. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - H. F. Liu
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Q. Lv
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Z. Y. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - R. J. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Y. J. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Z. X. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
- Key Laboratory of Animal Genetics, Breeding and ReproductionHohhotInner Mongolia Autonomous Region010018China
| | - Z. H. Liu
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
- Key Laboratory of Mutton Sheep Genetics and BreedingMinistry of Agriculture and Rural AffairsHohhot010018China
| | - L. B. He
- Key Laboratory of Mutton Sheep Genetics and BreedingMinistry of Agriculture and Rural AffairsHohhot010018China
| | - R. Su
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Y. H. Zhao
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - J. Q. Li
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
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