Detection of coding sequence, mRNA expression and three insertions/deletions (indels) of KDM6A gene in male pig

Lysine demethylase 6A (KDM6A, also known as UTX), which belongs a type of histone demethylase, is essential for spermatogenesis and embryo development. However, in pig, the coding sequence, mRNA expression and insertion/deletion (indel) variants of KDM6A remain unclear. Herein, the open-reading frame (ORF) of pig KDM6A gene was cloned and characterized. The entire ORF sequence was 4206 bp in length encoding a deduced protein of 1401 amino acid residues. The phylogenetic tree and signatures of selection on the pig KDM6A gene were calculated, and the results revealed that the pig KDM6A gene has been under strong positively selection. Expression analysis results showed that KDM6A gene was expressed in all tissues tested both in male piglets and adult boars. Meanwhile, with testicular development, the KDM6A expression levels in testis were significantly increased. Additionally, three intronic indels of 11-bp insertion, 17-bp deletion and 16-bp insertion were identified. Association analyses revealed that the 11-bp indel was associated with testicular short perimeter (TSP) (P < 0.01), testicular long perimeter (TLP) (P < 0.01) and testicular weight (TW) (P < 0.01) in 15-day-old Yorkshire and TLP (P < 0.01) in 40-day-old Yorkshire. The 16-bp indel was associated with TLP, TSP and TW (P < 0.05) in 15-day-old Yorkshire. All these findings would provide a foundation for the further research of KDM6A gene and the application of marker-assisted selection to pig breeding.