Genome-wide Association Analysis For Diverticula Of Carpal Gland In Shanxia Black Pig

As one of the main farm animals in China,pigs play an important role in improving people’s living standard and economic development.As a large and concentrated skin gland in pigs,the carpal gland has important roles in marked territories,mating behavior,and communicating information of pigs through its secreting mucus.However,until now,People know very few about the carpal gland,especially its genetic mechanism,which has not been reported.In this study,971 Shanxia black pigs and 89 Bama Xiang pigs were used to study the effects of population,gender and left and right hoofs on the number of carpal diverticula,calculate the correlation coefficient between the number of carpal diverticula and carcass and meat quality traits,and identify the QTL loci for the number of carpal diverticula through a genome-wide association analysis in Shanxia black pigs.Finally,according to the physical location of the top SNP,queried the annotated genes in the region on the ensemble website,and search the functions of annotated genes in the GENECARD database,so as to provide a reference for subsequent candidate gene research.The main results are as follows:Except that the sum and difference of the number of diverticula in both hooves were not correlated,all other numbers of diverticula were significantly correlated(|r| ≥ 0.2376,P≤ 0.0250).The numbers of diverticula were significantly and weakly correlated with thoracic vertebrae number,thoracic vertebrae length,45 min a value,24 h p H,24 h meat color score,24 h marbling score,fat,moisture,sodium salt content,saturated fatty acid and cannon circumference(|r|≤ 0.1775).Except that the difference of diverticular numbers between two front hooves was not significant different between populations(P = 0.6757),the diverticular numbers of left,right and both hoofs were highly significant between populations(P ≤0.0002).Sex also had a significant effect on the number of diverticula.The diverticular number of left,right and both hoofs in castrated boars were 0.2549(P = 0.0391),0.4058(P= 0.0016)and 0.6635(P = 0.0048)more than those in sows,respectively.The diverticular number of right hoof were 0.0949 ± 1.3596 and 0.1910 ± 1.1162 more than that of left hoof in Shanxia black pig and Bama Xiang,respectively.It was significant(P = 0.0301)in Shanxia black pig,but not(P = 0.1291)in Bama Xiang due to its small population size.Genome wide association analysis(GWAS)identified only one genome-wide significant QTL,which was significantly associated with the numbers of diverticula on left,right and two hoofs.The top SNP of the QTL was CNC10010837,which locates at 37.057 Mb on chromosome 1.It associated with the three traits with P values of 2.52e-07,8.31e-10 and 1.83e-09,respectively.Besides the top SNP,there were another six SNPs associated with the three traits at genome-wide significant level,which are mapped in a region of 1.78Mb(35.347 ～ 37.129 MB)on chromosome 1.This study analyzed the effects of population,gender and left and right hoofs on the number of diverticula,and identified genomic loci for the number of diverticula through GWAS,and provided a reference for the subsequent genetic analysis of carpal diverticula.