Allelic frequencies of NR6A1 and VRTN, two genes that affect vertebrae number in diverse pig breeds: A study of the effects of the VRTN insertion on phenotypic traits of a Duroc × Landrace–Large White cross Carmen Burgos a , Pedro Latorre a,c , Juan Altarriba b,c , José Alberto Carrodeguas c , Luis Varona b,c , Pascual López-Buesa a,c, ⁎ a Departamento de Producción Animal y Ciencia de los Alimentos, Spain b Departamento de Anatomía, Embriología y Genética, Spain c Instituto de Biocomputación y Física de Sistemas Complejos, Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain abstract article info Article history: Received 28 March 2014 Received in revised form 11 September 2014 Accepted 25 September 2014 Available online 5 October 2014 Keywords: VRTN NR6A1 Loin Quality Genes A SNP (748 C N T) in the NR6A1 gene and an insertion (g.20311_20312ins291) in the VRTN gene have been shown to affect vertebrae number in the pig. The allelic frequencies of both genes were investigated in six west- ern breeds and the effects of the VRTN insertion on some phenotypic traits in a Duroc × Landrace/Large White cross. The NR6A1 c. 748T allele, associated with higher number of vertebrae, appeared to be fixed in most studied breeds except in Iberians. The VRTN insertion (Ins allele) shows ample variability in all studied breeds although the allelic frequency of Ins seems to be larger in breeds with a greater history of genetic selection. Ins is associated with an increase in weight at slaughter, in loin and rib primal cut proportions, and with modified meat quality properties such as cooking loss, intramuscular fat content or yield after curing. We discuss the usefulness of both gene markers for pig selection. © 2014 Elsevier Ltd. All rights reserved. 1. Introduction The number of vertebrae in pigs varies considerably. It is an impor- tant trait in pig production because it directly determines the size of important meat cuts such as the loin and also has an overall effect on carcass conformation. One extra vertebra expands the carcass length up to 80 mm (King & Roberts, 1960). While wild boars and indigenous breeds have 19 vertebrae, western commercial breeds have a few more (n = 21–23) (King & Roberts, 1960) as a result of long-term selec- tion for enlarged size. Two quantitative trait loci (QTL) for vertebral number have been identified in pigs: one on chromosome 1 (SSC1) (Mikawa et al., 2005; Wada et al., 2000) and the other on chromosome 7 (SSC7) (Mikawa et al., 2005). The most likely causative mutation underlying the QTL on SSC1 is a base substitution in an orphan nuclear receptor, NR6A1 c. 748 C N T of GenBank sequence AB248749, which results in a proline to leucine substitution at codon 192 (Mikawa et al., 2007). Vertnin (VRTN), also known as “vertebrae development associated” gene (www.ncbi.nlm.nih.gov/gene/55237), was proposed as a strong candi- date for the gene underlying the QTL reported on SSC7 (Mikawa et al., 2011). Recently, Fan et al. (2013) have identified the most likely causal variant of this QTL; it is an insertion of one fragment of 291 bp in the promoter region of the VRTN gene, g.20311_20312ins291, located in one transcription factor-binding site. This insertion alters the normal expression of the VRTN gene leading to the VRTN effect on vertebrae number. The allele with the insertion is denominated “Ins” in the litera- ture whereas the wild type allele is denominated “Wt” or just “–”. The effect of each of these mutations on vertebrae number is an increase of 0.55 to 0.6 thoracic vertebrae per allele (Mikawa et al., 2007, 2011). While the allele of NR6A1 associated with increased vertebral num- ber, allele T, seems to be fixed in all western breeds analyzed (Yang, Ren, Zhang, & Huang, 2009), genetic variation of VRTN has been detected in some European commercial breeds, but it has not been investigated in all such breeds, including the Pietrian or Iberian. VRTN has several effects on other important traits besides vertebrae number. However, reports of its effects on other important traits are conflicting. For example, while Hirose et al. (2013) found that pigs with the Wt/Wt genotype had more intramuscular fat in the loin than those with the Ins/Ins genotype, Mikawa and Awata (2012) reported the opposite. Conflicting results have also been described on the influ- ence of this gene on loin muscle area; Mikawa and Awata (2012) ob- served a smaller loin area associated with the Ins allele, but Hirose et al. (2013) didn't detect any statistically significant differences be- tween the three genotypes for any loin traits. The effects of the vertnin Meat Science 100 (2015) 150–155 ⁎ Corresponding author at: Facultad de Veterinaria, c/Miguel Servet 177, 50013 Zaragoza, Spain. Tel.: +34 976762533; fax: +34 976761590. E-mail address: plopezbu@unizar.es (P. López-Buesa). http://dx.doi.org/10.1016/j.meatsci.2014.09.143 0309-1740/© 2014 Elsevier Ltd. All rights reserved. Contents lists available at ScienceDirect Meat Science journal homepage: www.elsevier.com/locate/meatsci