New insights into host adaptation to swine respiratory disease revealed by genetic differentiation and RNA sequencing analyses

Abstract

Swine respiratory disease (SRD) causes massive economic losses in the swine industry and is difficult to control and eradicate on pig farms. Here, we employed population genetics and transcriptomics approaches to decipher the molecular mechanism of host adaptation to swine respiratory disease. We recorded two SRD‐related traits, the enzootic pneumonia‐like (EPL) score and lung lesion (LL) levels, and performed four body weight measurements, at ages of 150, 180, 240, and 300 days, in a Chinese Bamaxiang pig herd ( n = 314) raised under consistent indoor rearing conditions. We divided these animals into disease‐resistant and disease‐susceptible groups based on the most likely effects of both SRD‐related traits on their weight gain, and performed genetic differentiation analyses in these two groups. Significant loci showing the top 1% of genetic differentiation values, exceeding the threshold of p = 0.005 set based on 1,000‐times permutation tests, were defined as candidate regions related to host resistance or susceptibility to SRD. We identified 107 candidate genes within these regions, which are mainly involved in the biological processes of immune response, fatty acid metabolism, lipid metabolism, and growth factor signaling pathways. Among these candidate genes, TRAF6 , CD44 , CD22 , TGFB1 , CYP2B6, and SNRPA were highlighted due to their central regulatory roles in host immune response or fat metabolism and their differential expression between healthy lung tissues and lung lesions. These findings advance our understanding of the molecular mechanisms of host resistance or susceptibility to respiratory disease in pigs and are of significance for the breeding pigs resistant to respiratory disease in the swine industry.

Estimation of the prevalence of respiratory diseases in pigs in north-eastern Poland: Survey of pulmonary lesions in pigs at a slaughterhouse

“…The most frequent findings in pig lungs at the abattoir are cranioventral pulmonary consolidation, categorised as enzootic pneumonia-like lesions, particularly caused by M. hyopneumoniae. Despite all the efforts performed to reduce economic losses caused by these pathogens, M. hyopneumoniae continues to be an important concern to worldwide swine herds (Zhang et al 2018). The prevalence of M. hyopneumoniae, PRRSV and SIV infections was high in this research (Table 4), though similar to other reported European studies (Falk and Lium 1991;Lium and Falk 1991;Grest et al 1997;Cleveland-Nielsen et al 2002;Fraile et al 2010;Meyns et al 2011;Fablet et al 2012;Merialdi et al 2012).…”

Identification of Anti-SNRPA as a Novel Serological Biomarker for Systemic Sclerosis Diagnosis

“…found that SNRPA is highly expressed in swine respiratory diseases, which supports the hypothesis that it has a role in susceptibility to respiratory diseases. 38 However, some studies reported that anti-U1 snRNP was associated with reduced PAH risk. 39 , 40 Therefore, this controversial issue requires more research to be fully addressed.…”

Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology

“…To elucidate whether there is genetic differentiation exist in scrotal hernia pigs and health pigs, we divided the affected pigs and the unaffected pigs into two groups, as the method did by Zhang et al (2019) then assessed allele frequency differentiation using the unbiased genetic differentiation estimated of the fixation index (Fst). Akey et al have fully described estimation of unbiased Fst fixation index in his paper using SNP dataset (Akey et al, 2002).…”

“…The negative Fst didn’t have any biological interpretation and were set to 0 to fit the definition of Fst ranging from between 0 and 1 (Wright, 1951). The top 1% of loci according to genetic differentiation values was served as candidate regions to host resistance or susceptibility to pig scrotal hernia (Zhang et al, 2019).…”