Polymorphisms and expression analysis of SOX-6 in relation to porcine growth, carcass, and meat quality traits Rui Zhang a , Christine Große-Brinkhaus a , Hanna Heidt a , Muhammad Jasim Uddin a,b , Mehmet Ulas Cinar a,c , Dawit Tesfaye a , Ernst Tholen a , Christian Looft a , Karl Schellander a , Christiane Neuhoff a, ⁎ a Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany b Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh c Faculty of Agriculture, Department of Animal Science, Erciyes University, 38039 Kayseri, Turkey abstract article info Article history: Received 12 December 2014 Received in revised form 16 March 2015 Accepted 13 April 2015 Available online 22 April 2015 Keywords: SOX-6 Growth Carcass Meat quality Single nucleotide polymorphism MicroRNA The aim of the study was to investigate single nucleotide polymorphisms (SNPs) and expression of SOX-6 to support its candidacy for growth, carcass, and meat quality traits in pigs. The first SNP, rs81358375, was associated with pH 45 min post mortem in loin (pH1 L ), the thickness of backfat and side fat, and carcass length in Pietrain (Pi) population, and related with backfat thickness and daily gain in Duroc × Pietrain F 2 (DuPi) population. The other SNP, rs321666676, was associated with meat colour in Pi population. In DuPi population, the protein, not mRNA, level of SOX-6 in high pH1 L pigs was significantly less abundant compared with low pH1 L pigs, where microRNAs targeting SOX-6 were also differently regulated. This paper shows that SOX-6 could be a potential candidate gene for porcine growth, carcass, and meat quality traits based on genetic association and gene expression. © 2015 Elsevier Ltd. All rights reserved. 1. Introduction Pigs are one of the most important farm animals and serve as a valued source of food worldwide. Modern pork production system tries to balance the requirements of animal welfare, cost of production, and meat quality. Among diverse parameters of meat quality, pH during post-mortem period has been shown to be one of the best predictors according to the accuracy and precision (Monin, 1998) and influences many meat quality traits like tenderness, water holding capacity, and meat colour (Fernandez, Forslid, & Tornberg, 1994; Fernandez & Tornberg, 1994; van Laack, Stevens, & Stalder, 2001). Marker-assisted selection in pig breeding programmes has contributed to the improvement of many aspects of porcine production, including growth, carcass, meat quality, reproduction, and disease resistance (Ernst & Steibel, 2013). Application of porcine SNP chip and genome-wide asso- ciation study (GWAS) has accelerated the identification of SNP markers and candidate genes for traits of interest (Fontanesi et al., 2012; Ma et al., 2013). Many candidate genes, like a-1-microglobulin/bikunin precursor, triosephosphate isomerase 1, and long-chain acyl-CoA synthetase 4, have been suggested for pork traits (Corominas et al., 2012; Heidt et al., 2013). SOX-6 is a versatile transcription factor and plays an important role in muscle fiber differentiation. SOX-6 represses the specification of slow fiber type during skeletal muscle differentiation by inhibiting the transcription of multiple myosin and sarcomeric genes (Hagiwara, 2011; Quiat et al., 2011). Muscle fiber is an important determinant for meat quality (Karlsson, Klont, & Fernandez, 1999; Klont, Brocks, & Eikelenboom, 1998). The distinct biochemical and physiological proper- ties of slow- and fast-twitch muscle fiber lead to their divergent responses to pre-slaughter stress, varied post mortem (p.m.) pH decline, and different meat quality (Karlsson et al., 1999). As a key regulator of muscle fiber type specification, SOX-6 could be greatly associated with muscle growth and meat quality characteristics. Human population genetic studies revealed that the genetic polymorphisms in SOX-6 gene are associated with blood-pressure traits (Franceschini et al., 2013), bone mineral density (Rivadeneira et al., 2009), wrist bone mass (Tan et al., 2010), obesity phenotypes in males (Liu et al., 2009), and carotid plaque traits (Dong et al., 2010). Up to now, thousands of SNPs were identified in pig SOX-6 loci, including SOX-6 and SOX-6-like; however, there is no genetic association study about SOX-6 in pigs. MicroRNA (miRNA) is a post-transcriptional regulator and induces mRNA degradation or translation inhibition of target genes. The polymorphisms of miRNA and its binding sites have been proven to be Meat Science 107 (2015) 26–32 ⁎ Corresponding author. Tel.: +49 228 733583; fax: +49 228 732284. E-mail addresses: rzha@itw.uni-bonn.de (R. Zhang), cgro@itw.uni-bonn.de (C. Große-Brinkhaus), hhei@itw.uni-bonn.de (H. Heidt), judd@itw.uni-bonn.de (M.J. Uddin), ucin@itw.uni-bonn.de (M.U. Cinar), dtes@itw.uni-bonn.de (D. Tesfaye), etho@itw.uni-bonn.de (E. Tholen), cloo@itw.uni-bonn.de (C. Looft), ksch@itw.uni-bonn.de (K. Schellander), cneu@itw.uni-bonn.de (C. Neuhoff). http://dx.doi.org/10.1016/j.meatsci.2015.04.007 0309-1740/© 2015 Elsevier Ltd. All rights reserved. Contents lists available at ScienceDirect Meat Science journal homepage: www.elsevier.com/locate/meatsci