An atlas of expression quantitative trait loci of microRNAs in <i>longissimus</i> muscle of eight-way crossbred pigs

Liepeng Zhong; Min Zheng; Yizhong Huang; Tao Jiang; Bin Yang; Lusheng Huang; Junwu Ma

doi:10.1016/j.jgg.2023.02.007

Volume 50 Issue 6

Jun. 2023

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Article Navigation > Journal of Genetics and Genomics > 2023 > 50(6): 398-409

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An atlas of expression quantitative trait loci of microRNAs in longissimus muscle of eight-way crossbred pigs

doi: 10.1016/j.jgg.2023.02.007

State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China

Funds:

We sincerely thank all the people from the State Key Laboratory for Pig Genetic Improvement and Production Technology (Jiangxi Agricultural University) for their help in sample and data collection. This study was supported by the National Natural Science Foundation of China (31790413 and 31872339).

Received Date: 2022-10-10
Accepted Date: 2023-02-05
Rev Recd Date: 2023-02-03
Publish Date: 2023-02-22

Abstract

Abstract

MicroRNAs (miRNAs) are key regulators of myocyte development and traits, yet insight into the genetic basis of variation in miRNA expression is still limited. Here, we present a systematic analysis of expression quantitative trait loci (eQTL) for miRNA profiling in longissimus muscle of pigs from an eight-breed crossed heterogeneous population. By integrating the whole-genome sequencing and miRNAomics data, we map 54 cis- and 292 trans-eQTLs at high resolution that are associated with the expression of 54 and 92 miRNAs, respectively. Twenty-three trans-acting loci are identified to affect the expression of nine myomiRs (known muscle-specific miRNAs). MiRNAs in mammalian conserved miRNA clusters are found to be subjected to regulation by shared cis-eQTLs, while the expression of mature miRNA-5p/-3p counterparts is more likely to be regulated by different cis-eQTLs. Fine mapping and bioinformatics analyses pinpoint the peak cis-eSNP of miR-4331-5p, rs344650810, which is located in its seed region, as a causal variant for the changes in expression and function of this miRNA. Additionally, rs344650810 is significantly (P < 0.01) correlated with the density and percentage of type I muscle fibers. Altogether, this study provides a comprehensive atlas of miRNA-eQTLs in porcine skeletal muscle and new insights into regulatory mechanisms of miRNA expression.
- miRNA,
- eQTL,
- Pig,
- Muscle,
- Causal variant,
- Regulatory mechanism

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References(54)

References

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