Whole genome and transcriptome analyses identify genetic markers associated with growth traits in Qinchuan black pig

Growth traits are economically important traits in pig breeding. However, the genetic mechanism of growth traits is still unclear. Qinchuan Black (QCB) pigs are crossbred and produced by hybridizing Guanzhong Black (GZB) pigs and Large White (LW) pigs, its characteristics include fast growth and excellent meat quality. In this study, whole genome and transcriptome analyses revealed the candidate genes associated with growth traits in QCB pigs based on imputed low-coverage whole-genome resequencing data.

In total, we used 197 low-depth whole-genome resequencing data with an average depth of 3.5X, and then the data were imputed to resequencing data using SWIM reference panel, the imputation accuracy parameters, allele frequency r² and concordance rate were 0.86 and 95.83%, respectively. We used two methods to investigate the candidate genes affecting the growth traits of QCB pigs, a total of 371 PSGs were identified, which related to muscle tissue development, tissue development and system development. A total of 30,489,782 SNPs were retained. A GWAS of ten growth traits by using fixed and random model circulating probability unification (FarmCPU) model, was performed in QCB pigs. We discovered seven genome wide significant SNPs and eight genome wide suggestive significant SNPs associated with body weight at 2 months (2-BW), body length at 2 months (2-BL), body height at 2 months (2-BH) and body height at 4 months (4-BH), and eighteen potential candidate genes were discovered. Transcriptomic data revealed that 18 differentially expression genes related to muscle and growth and development. Additionally, whole genome and transcriptome analyses found six genes (TENM3, CTNND2, RIMS1, PCDH7, ADGRL3 and CTNNA3) may affect the growth traits in Qinchuan Black pigs.

Our study shows that more candidate genes associated with pig growth traits can be identified by whole genome and transcriptome analyses. We found that six genes may be new key candidate genes affecting pig growth traits. In conclusion, this study elucidated the molecular genetic mechanisms of growth traits and identified new molecular breeding targets, offering a robust scientific basis for advancing breeding strategies and genetic investigations within this breed.