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

Abstract Background 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-depth whole-genome resequencing data. Results 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. 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. Conclusion 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, our results help to clarify the genetic basis of growth traits and have laid a theoretical foundation for subsequent breeding and genetic research of this breed.