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Zeng H, Zhong Z, Xu Z, Teng J, Wei C, Chen Z, Zhang W, Ding X, Li J, Zhang Z. Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait. BMC Genomics 2022; 23:786. [DOI: 10.1186/s12864-022-09036-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Abstract
Background
Average backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population. Alternatively, meta-analysis of GWAS (metaGWAS) is an attractive method to increase the statistical power by integrating data from multiple breeds and populations. The aim of this study is to identify shared genetic characterization of BFT across breeds in pigs via metaGWAS.
Results
In this study, we performed metaGWAS on BFT using 15,353 pigs (5,143 Duroc, 7,275 Yorkshire, and 2,935 Landrace) from 19 populations. We detected 40 genome-wide significant SNPs (Bonferroni corrected P < 0.05) and defined five breed-shared QTLs in across-breed metaGWAS. Markers within the five QTL regions explained 7 ~ 9% additive genetic variance and showed strong heritability enrichment. Furthermore, by integrating information from multiple bioinformatics databases, we annotated 46 candidate genes located in the five QTLs. Among them, three important (MC4R, PPARD, and SLC27A1) and seven suggestive candidate genes (PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3) were identified.
Conclusion
QTLs and candidate genes underlying BFT across breeds were identified via metaGWAS from multiple populations. Our findings contribute to the understanding of the genetic architecture of BFT and the regulating mechanism underlying fat deposition in pigs.
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Li W, Zhang XY, Du J, Li YF, Chen YJ, Cao Y. RNA-seq-based quanitative transcriptome analysis of meat color and taste from chickens administered by eucalyptus leaf polyphenols extract. J Food Sci 2020; 85:1319-1327. [PMID: 32175699 DOI: 10.1111/1750-3841.15082] [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: 11/14/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 01/13/2023]
Abstract
To evaluate how eucalyptus leaf polyphenol extract (EPE) affects chicken meat color and taste, we added different levels of EPE (0%, 0.06%, 0.09%, and 0.12%) to chicken feed. The redness (a* value) and the myoglobin content of breast muscle in EPE group were remarkably higher. Furthermore, the guanosine monophosphate, histidine, and glycine muscle contents were also enhanced. Transcriptome analysis showed that 10 candidate genes related to meat quality were affected by EPE treatment. The identified genes, with functions critical to chicken meat color and taste, will help to determine the molecular mechanisms of EPE.
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Affiliation(s)
- Wei Li
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangdong Research Center for Engineering Technology in Bioactive Natural Products, Guangzhou, 510642, China
| | - Xiao-Ying Zhang
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangdong Research Center for Engineering Technology in Bioactive Natural Products, Guangzhou, 510642, China
| | - Jie Du
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangdong Research Center for Engineering Technology in Bioactive Natural Products, Guangzhou, 510642, China
| | - Yi-Feng Li
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangdong Research Center for Engineering Technology in Bioactive Natural Products, Guangzhou, 510642, China
| | - Yun-Jiao Chen
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangdong Research Center for Engineering Technology in Bioactive Natural Products, Guangzhou, 510642, China
| | - Yong Cao
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangdong Research Center for Engineering Technology in Bioactive Natural Products, Guangzhou, 510642, China
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