Variation in gene expression is an essential mechanism for the formation of complex traits and susceptibility to complex diseases (Hormozdiari et al., 2018; Nikpay et al., 2019). Identification of expression quantitative trait loci (eQTLs), which are genetic variants that regulate gene expression, provides a powerful means of dissecting the molecular events that contribute to various phenotypes and diseases (Albert and Kruglyak, 2015; Hormozdiari et al., 2018). Furthermore, given that most quantitative trait loci (QTLs) found by genome-wide association studies (GWASs) point to regulatory regions of the genome, the study of eQTLs can help elucidate causal mechanisms underlying complex traits.

MicroRNAs (miRNAs) are a class of conserved small (∼22 nt) noncoding RNA molecules generated by a multistep biogenetic pathway. They target the 3′ untranslated region (UTR) of specific target mRNAs for endonucleolytic cleavage or translational repression, which is a well-known mechanism of gene expression regulation. It has been estimated that more than 30% of animal genes may be targets of miRNAs (Bushati and Cohen, 2007). Biochemical, genetic, and computational studies have shown that in multicellular organisms miRNAs play vital and diverse roles, including in cell proliferation, differentiation, apoptosis, metabolism, stress resistance, and cancer development (Mok et al., 2017; DeVeale et al., 2021). Although miRNAs are of great significance for development and physiology, relatively little research has been done on the mapping of eQTLs for miRNAs (miR-eQTLs) compared to the mapping of mRNAs (Sonehara et al., 2022). To date, most studies on miR-eQTLs have primarily focused on human diseases and have been carried out for several human tissues, such as peripheral blood, liver, brain, adipose, and tumor tissues (Gamazon et al., 2012). These studies not only identified some cis- and trans-miR-eQTLs but also found that some of these eQTLs were indeed associated with human complex traits or diseases. However, such work has less frequently been performed in the context of other animals and tissues.

The current understanding of the genetic basis of miRNA expression changes in animal skeletal muscle is still limited, although skeletal muscle is the single largest tissue in the body and plays an indispensable role in regulating metabolic homeostasis and determining meat quantity and quality in livestock. Many studies have focused on examining the impact of miRNAs on traits of economic interest, including muscle growth and meat quality traits, in agricultural animals, perhaps on the basis of the recognition that miRNAs play a critical role in many important biological processes (Lee et al., 2013; Siengdee et al., 2015; Zhang et al., 2017a). In contrast, only two recent studies have detected the genetic loci for miRNA expression in skeletal muscle (i.e., the porcine longissimus dorsi muscle), both using an F2 intercross between two Western commercial pig lines (Duroc × Pietrain [Daza et al., 2021] and Landrace × Pietrain [Ponsuksili et al., 2022]) and data from Porcine SNP60 BeadChip.

There are significant phenotypic and genetic differences between Chinese locally-developed pig breeds and Western commercial pig breeds (Ai et al., 2015). Obviously, the growth rate and weight of skeletal muscle in pigs of Chinese local breeds are much lower than those of Western commercial pigs, but they have a smaller muscle fiber cross-sectional area, a higher oxidative (red) fiber percentage, and thus a more favorable meat quality (Gil et al., 2008; Dai et al., 2009; Wang et al., 2011). Additionally, many local pig breeds in China have their own unique skeletal muscle characteristics due to long-term natural and artificial selection (Huang et al., 2020). Thus, we constructed an eight-breed crossed mosaic pig population by using four Western commercial lines and four Chinese local breeds to reveal the genetic architecture of swine complex traits more comprehensively and efficiently. Here, we mainly aimed to precisely map cis- and trans-eQTLs for miRNA expression in porcine longissimus thoracis (LT) muscle by whole-genome sequencing-based GWAS using the mosaic pig F6 population and to deeply investigate the mechanism underlying cis-regulation of miRNA expression.