Veterinary College, University of Passo Fundo, Passo Fundo, Brazil.
Embrapa Suínos e Aves, Concórdia, Brazil.
Sex Dev. 2023;17(1):56-66. doi: 10.1159/000528360. Epub 2023 Feb 9.
Cryptorchidism is a hereditary anomaly characterized by the incomplete descent of one or both testicles to the scrotum. One of the challenges of this anomaly is that the retained testicle maintains its endocrine function. As a consequence, cryptorchid animals produce hormone-tainted meat in comparison to castrated animals and are likely to be more aggressive. Cryptorchidism can lead to reduced animal welfare outcomes and cause economic losses. Identifying genetic markers for cryptorchidism is an essential step toward mitigating these negative outcomes and may facilitate genome manipulation to reduce the occurrence of cryptorchidism. Attempts to identify such markers have used genome-wide association studies. Using whole-exome sequencing, we aimed to identify single nucleotide polymorphisms (SNPs) in the coding regions of cryptorchid pigs and to characterize functional pathways concerning these SNPs.
DNA was extracted and sequenced from 5 healthy and 5 cryptorchid animals from the Landrace breed, using the Illumina HiSeq 2500 platform. Data were pre-processed using the SeqyClean tool and further mapped against the swine reference genome (Sus scrofa 11.1) using BWA software. GATK was used to identify polymorphisms (SNPs and InDels), which were annotated using the VEP tool. Network prediction and gene ontology enrichment analysis were conducted using the Cytoscape platform, and STRING software was used for visualization.
A total of 63 SNPs were identified across the genes PIGB, CCPG1, COMMD9, LDLRAD3, TRIM44, MYLPF, SEPTIN, ZNF48, TIA1, FAIM2, KRT18, FBP1, FBP2, CTSL, DAPK1, DHX8, GPR179, DEPDC1B, ENSSSCG00000049573, ENSSSCG00000016384, ENSSSCG00000022657, ENSSSCG00000038825, and ENSSSCG00000001229. Using pathway enrichment analyses and network prospection, we have identified the following significant adjusted p value threshold of 0.001 involved with the biological function pathways of estrogen signaling, cytoskeleton organization, and the pentose phosphate pathway.
Our data suggest the involvement of new SNPs and genes in developing cryptorchidism in pigs. However, further studies are needed to validate our results in a larger cohort population. Variations in the GPR179 gene, with implications at the protein level, may be associated with the appearance of this anomaly in the swine. Finally, we are showing that the estrogen signaling pathway may be involved in the pathophysiological mechanisms of this congenital anomaly as previously reported in GWAS.
隐睾症是一种遗传性异常，其特征是一个或两个睾丸不完全下降到阴囊。这种异常的挑战之一是保留的睾丸保持其内分泌功能。因此，与去势动物相比，隐睾动物产生激素污染的肉，并且可能更具攻击性。隐睾症会导致动物福利结果下降，并造成经济损失。确定隐睾症的遗传标记是减轻这些负面结果的重要步骤，并且可能有助于通过基因组操作来减少隐睾症的发生。已经使用全基因组关联研究来尝试识别此类标记。使用全外显子组测序，我们旨在鉴定来自长白品种的 5 只健康和 5 只隐睾猪的编码区中的单核苷酸多态性（SNP），并对这些 SNP 相关的功能途径进行特征描述。
使用 Illumina HiSeq 2500 平台从 5 只健康猪和 5 只隐睾猪中提取和测序 DNA，使用 SeqyClean 工具进行预处理，然后使用 BWA 软件将其进一步映射到猪参考基因组（Sus scrofa 11.1）。使用 GATK 识别多态性（SNP 和 InDels），并使用 VEP 工具进行注释。使用 Cytoscape 平台进行网络预测和基因本体富集分析，并使用 STRING 软件进行可视化。
总共在 PIGB、CCPG1、COMMD9、LDLRAD3、TRIM44、MYLPF、SEPTIN、ZNF48、TIA1、FAIM2、KRT18、FBP1、FBP2、CTSL、DAPK1、DHX8、GPR179、DEPDC1B、ENSSSCG00000049573、ENSSSCG00000016384、ENSSSCG00000022657、ENSSSCG00000038825 和 ENSSSCG00000001229 基因中鉴定出 63 个 SNP。通过通路富集分析和网络预测，我们确定了以下具有显著调整后 p 值阈值 0.001 的生物功能途径，包括雌激素信号转导、细胞骨架组织和戊糖磷酸途径。
我们的数据表明，新的 SNP 和基因可能参与了猪隐睾症的发生。然而，需要进一步的研究来在更大的队列人群中验证我们的结果。GPR179 基因的变异，在蛋白质水平上具有影响，可能与猪的这种异常表现有关。最后，我们表明雌激素信号通路可能与之前 GWAS 报道的这种先天性异常的病理生理机制有关。
