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Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks. Genes (Basel) 2022; 13:genes13060986. [PMID: 35741748 PMCID: PMC9222319 DOI: 10.3390/genes13060986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 12/10/2022] Open
Abstract
With continuously increasing living standards and health requirements of consumers, meat quality is becoming an important consideration while buying meat products. To date, no genome-wide association study (GWAS) for copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) has been conducted to reveal the genetic effects on meat quality in ducks. This study analyzed the phenotypic correlation and heritability of fat, water, collagen, and protein content of duck breast muscle. To identify the candidate variants for meat quality, we performed a GWAS using 273 ducks from an F2 population. The results of the SNP GWAS showed that the BARHL2, COPS7B, and CCDC50 genes were associated with fat content; BLM, WDR76, and EOMES with water content; CAMTA1, FGD5, GRM7, and RAPGEF5 with collagen production; and RIMS2, HNRNPU, and SPTBN1 with protein content. Additionally, 3, 7, 1, and 3 CNVs were associated with fat, water, collagen, and protein content, respectively, in duck breast muscle. The genes identified in this study can serve as markers for meat quality. Furthermore, our findings may help devise effective breeding plans and selection strategies to improve meat quality.
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Gao G, Gao N, Li S, Kuang W, Zhu L, Jiang W, Yu W, Guo J, Li Z, Yang C, Zhao Y. Genome-Wide Association Study of Meat Quality Traits in a Three-Way Crossbred Commercial Pig Population. Front Genet 2021; 12:614087. [PMID: 33815461 PMCID: PMC8010252 DOI: 10.3389/fgene.2021.614087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/12/2021] [Indexed: 01/12/2023] Open
Abstract
Meat quality is an important trait for pig-breeding programs aiming to meet consumers' demands. Geneticists must improve meat quality based on their understanding of the underlying genetic mechanisms. Previous studies showed that most meat-quality indicators were low-to-moderate heritability traits; therefore, improving meat quality using conventional techniques remains a challenge. Here, we performed a genome-wide association study of meat-quality traits using the GeneSeek Porcine SNP50K BeadChip in 582 crossbred Duroc × (Landrace × Yorkshire) commercial pigs (249 males and 333 females). Meat conductivity, marbling score, moisture, meat color, pH, and intramuscular fat (IMF) content were investigated. The genome-wide association study was performed using both fixed and random model Circulating Probability Unification (FarmCPU) and a mixed linear model (MLM) with the rMVP software. The genomic heritability of the studied traits ranged from 0.13 ± 0.07 to 0.55 ± 0.08 for conductivity and meat color, respectively. Thirty-two single-nucleotide polymorphisms (SNPs) were identified for meat quality in the crossbred pigs using both FarmCPU and MLM. Among the detected SNPs, five, nine, seven, four, six, and five were significantly associated with conductivity, IMF, marbling score, meat color, moisture, and pH, respectively. Several candidate genes for meat quality were identified in the detected genomic regions. These findings will contribute to the ongoing improvement of meat quality, meeting consumer demands and improving the economic outlook for the swine industry.
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Affiliation(s)
- Guangxiong Gao
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Ning Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangxi Yangxiang Co., Ltd., Guigang, China
| | - Sicheng Li
- Guangxi Yangxiang Co., Ltd., Guigang, China
| | - Weijian Kuang
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Lin Zhu
- Guangxi Yangxiang Co., Ltd., Guigang, China
| | - Wei Jiang
- Guangxi Yangxiang Co., Ltd., Guigang, China
| | - Weiwei Yu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jinbiao Guo
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Zhili Li
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Chengzhong Yang
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Yunxiang Zhao
- School of Life Sciences and Engineering, Foshan University, Foshan, China
- Guangxi Yangxiang Co., Ltd., Guigang, China
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Li Z, Lu J, Chen J, Pang Q, Nan R, Zhu Z. Expression and localization of guanine nucleotide-binding protein alpha S in the testis and epididymis of rams at different developmental stages. Anim Reprod Sci 2017; 178:31-39. [PMID: 28108049 DOI: 10.1016/j.anireprosci.2017.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/14/2017] [Indexed: 11/19/2022]
Abstract
The guanine nucleotide-binding alpha S subunit (Gαs) is an important element of key signaling pathways, which is widely expressed in mammalian tissues; however, its role in the reproductive system is still unclear. In this study, we investigated the expression and localization of Gαs in the testes and epididymis of rams at different developmental stages using quantitative RT-PCR, immunohistochemistry, and western blotting. In 1-, 6-, and 12-month-old rams, the transcription of Gαs-encoding gene (Gnαs) was significantly upregulated in the corpus and cauda epididymis compared to the testes and caput epididymis (P<0.05). At 12 months, the level of Gnαs mRNA was higher than that at 1 and 6 months for all tested tissues (P<0.05). The Gαs protein was detected in the principal cells and interstitial epididymal cells, including Sertoli and Leydig cells, as well as in testicular cells, spermatogonial stem cells, and spermatocytes. Gαs expression was the highest in the cauda epididymis (P<0.05), followed by the corpus epididymis, caput epididymis, and testes. The results indicate that in the reproductive organs of rams, Gαs is expressed in a tissue-specific and age-dependent manner. The high levels of Gαs observed in the epididymis suggest that Gαs may influence the composition of the epididymal lumen fluid and, consequently, the microenvironment for spermatozoa maturation. Thus, Gαs could play an important role in spermatogenesis and the development of the testes and epididymis in the reproductive system of rams.
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Affiliation(s)
- Zhen Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, PR China
| | - Jieli Lu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, PR China
| | - Jia Chen
- Institute of Farm Product Storage and Fresh-keeping, Shanxi Academy of Agriculture Science, Taiyuan, PR China
| | - Quanhai Pang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, PR China.
| | - Ruipeng Nan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, PR China
| | - Zhiwei Zhu
- College of Life Science, Shanxi Agricultural University, Taigu, Shanxi, PR China
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Liu X, Xiong X, Yang J, Zhou L, Yang B, Ai H, Ma H, Xie X, Huang Y, Fang S, Xiao S, Ren J, Ma J, Huang L. Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population. Genet Sel Evol 2015; 47:44. [PMID: 25962760 PMCID: PMC4427942 DOI: 10.1186/s12711-015-0120-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population. METHODS Three hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F2 and Sutai pig populations. RESULTS We detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several relevant candidate genes. CONCLUSIONS These findings provide valuable insights into the molecular basis of convergent evolution of meat quality traits in Chinese and Western breeds that show divergent phenotypes. They may contribute to genetic improvement of purebreds for crossbred performance.
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Affiliation(s)
- Xianxian Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xinwei Xiong
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jie Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lisheng Zhou
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Bin Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huashui Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huanban Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xianhua Xie
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Yixuan Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shaoming Fang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shijun Xiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- 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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