Qiu Zijian, Yin Yanzhen, Huang Ruihua, Zhou Jin, Liu Qian, Liu Kaiyue, Liu Chenxi, Li Pinghua, Zhao Qingbo
Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China.
College of Animal Science & Technology, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.
J Anim Sci. 2025 Jan 4;103. doi: 10.1093/jas/skaf145.
Milk is an essential source of nutrition for preweaning piglets. Therefore, in the breeding process, sows were expected to have sufficient teats to suckle their piglets. However, in Danish Landrace and Large White pigs, the number of piglets born currently exceeds the number of teats, making it urgent to select and breed for an increased teat number. In this study, the samples of 491 Danish Landrace pigs and 1,047 Danish Large White pigs with teat number phenotype were used to perform genome-wide association studies to identify SNPs associated with total teat number (TTN) based on SNP-chip data and data imputed to the level of whole-genome sequencing (iWGS), respectively. In Landrace pigs, the most significant SNP on SSC10 explains 5.14% of the phenotypic variance, while in Large White pigs, the most significant SNP on SSC7 explains 4.46% of the phenotypic variance. Additionally, linkage disequilibrium and linkage analysis (LDLA) were used to refine the regions of QTLs on SSC10 to 2.89 to 5.43 Mb in Danish Landrace pigs and to 96.00 to 97.95 Mb on SSC7 in Danish Large White pigs, respectively. To maximize the utility of information from 2 populations, meta-analysis was conducted across multiple populations. A total of 12 protein-coding genes were identified within the candidate QTL regions determined by LDLA and meta-analysis. To supplement the candidate gene set, transcriptome-wide association studies (TWAS) based on embryo and placenta tissues identified 7 protein-coding genes associated with TTN in Landrace and Large White pigs. Phenome-wide association studies (PheWAS) query was conducted for all the above genes, revealing that nearly all of them are associated with teat number traits. Additionally, some genes showed strong associations with carcass traits, suggesting a potential association between teat number and carcass traits. Through functional annotation and integrated analysis, BRINP3, LIN52, ABCD4, and UBE3B were determined as the functional candidate genes regulating TTN. These findings lay the foundation for identifying the genetic loci regulating teat number in Danish pigs, as well as for their molecular breeding.
牛奶是断奶前仔猪重要的营养来源。因此，在育种过程中，期望母猪有足够的乳头来哺育仔猪。然而，在丹麦长白猪和大白猪中，目前出生的仔猪数量超过了乳头数量，因此迫切需要选育增加乳头数量的猪。在本研究中，分别基于SNP芯片数据和推算至全基因组测序水平的数据（iWGS），使用491头具有乳头数量表型的丹麦长白猪和1047头丹麦大白猪的样本进行全基因组关联研究，以鉴定与总乳头数（TTN）相关的单核苷酸多态性（SNP）。在长白猪中，SSC10上最显著的SNP解释了5.14%的表型变异，而在大白猪中，SSC7上最显著的SNP解释了4.46%的表型变异。此外，连锁不平衡和连锁分析（LDLA）用于将丹麦长白猪SSC10上的数量性状基因座（QTL）区域分别精细定位到2.89至5.43 Mb，将丹麦大白猪SSC7上的QTL区域精细定位到96.00至97.95 Mb。为了最大限度地利用两个群体的信息，对多个群体进行了荟萃分析。在由LDLA和荟萃分析确定的候选QTL区域内共鉴定出12个蛋白质编码基因。为了补充候选基因集，基于胚胎和胎盘组织的全转录组关联研究（TWAS）在长白猪和大白猪中鉴定出7个与TTN相关的蛋白质编码基因。对上述所有基因进行了全表型组关联研究（PheWAS）查询，结果显示几乎所有基因都与乳头数量性状相关。此外，一些基因与胴体性状有很强的关联，表明乳头数量与胴体性状之间可能存在关联。通过功能注释和综合分析，确定BRINP3、LIN52、ABCD4和UBE3B为调节TTN的功能候选基因。这些发现为鉴定丹麦猪中调节乳头数量的遗传位点及其分子育种奠定了基础。
