Wang Yaxin, Lv Guangquan, Liu Zhe, Cheng Ye, Ding Rongrong, Yang Gongshe, Yu Taiyong
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
BMC Genomics. 2025 May 12;26(1):469. doi: 10.1186/s12864-025-11627-5.
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 r 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.
生长性状是猪育种中重要的经济性状。然而，生长性状的遗传机制仍不清楚。秦川黑猪（QCB）是由关中黑猪（GZB）和大白猪（LW）杂交培育而成的杂交猪，其特点是生长速度快、肉质优良。在本研究中，基于估算的低覆盖度全基因组重测序数据，通过全基因组和转录组分析揭示了与秦川黑猪生长性状相关的候选基因。
我们总共使用了197个平均深度为3.5X的低深度全基因组重测序数据，然后使用SWIM参考面板将数据估算为重测序数据，估算准确性参数等位基因频率r和一致性率分别为0.86和95.83%。我们使用两种方法研究影响秦川黑猪生长性状的候选基因，共鉴定出371个PSG，它们与肌肉组织发育、组织发育和系统发育有关。总共保留了30489782个单核苷酸多态性（SNP）。利用固定和随机模型循环概率统一法（FarmCPU）模型对秦川黑猪的十个生长性状进行了全基因组关联研究（GWAS）。我们发现了七个全基因组显著的SNP和八个全基因组提示性显著的SNP，它们与2月龄体重（2-BW）、2月龄体长（2-BL）、2月龄体高（2-BH）和4月龄体高（4-BH）相关，并发现了18个潜在的候选基因。转录组数据显示有18个与肌肉及生长发育相关的差异表达基因。此外，全基因组和转录组分析发现六个基因（TENM3、CTNND2、RIMS1、PCDH7、ADGRL3和CTNNA3）可能影响秦川黑猪的生长性状。
我们的研究表明，通过全基因组和转录组分析可以鉴定出更多与猪生长性状相关的候选基因。我们发现六个基因可能是影响猪生长性状的新的关键候选基因。总之，本研究阐明了生长性状的分子遗传机制，确定了新的分子育种靶点，为推进该品种的育种策略和遗传研究提供了有力的科学依据。
