The SINE in CDR2 gene associated with the resistance to lung diseases in Xiang pigs

Xiang pig is a native inbred line originating from a warm and humid mountainous region and is prone to infections by pathogens causing lung lesions. However, the underlying genetic factors still remain unclear. Our previous genomic resequencing comparisons found a deletion type of structural variation (SV) within the intron of gene cerebellar degeneration related protein 2 (CDR2) with a higher frequency in Xiang pigs compared with European pig breeds. This study is aimed to explore the relationship between the SV and the lung injury in Xiang pig populations. It demonstrated that the deletion genotype (MM) was dominant in Xiang pig herds and with a higher percentage of allele M than that in Xiang pig with pulmonary lesions and Large White breeds. By Sanger sequencing and RepeatMasker analysis, a SINE in 277 bp (namely SINE-277) was detected and located in the opposite orientation of CDR2 gene. The inhibit effects of SINE-277 on transcription was confirmed by EGFP reporter gene after transfected into HEK-293T cells. And the expression levels of CDR2 was increased in the lungs with MM types (P < 0.05) via both RT-qPCR and Western blotting assays. Moreover, significant differences were estimated between the SV genotypes and the lung lesion severity scores, the antibody concentrations against pathogens, and expressions of nine inflammation factor genes including NFκB. It reinforced the effects of SINE on gene CDR2 expression and might be taken as a DNA marker for the resistance/susceptibility to lung diseases in pigs.