In:
Sexual Development, S. Karger AG, Vol. 17, No. 1 ( 2023), p. 56-66
Abstract:
〈 b 〉 〈 i 〉 Introduction: 〈 /i 〉 〈 /b 〉 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. 〈 b 〉 〈 i 〉 Methods: 〈 /i 〉 〈 /b 〉 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 ( 〈 i 〉 Sus scrofa 〈 /i 〉 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. 〈 b 〉 〈 i 〉 Results: 〈 /i 〉 〈 /b 〉 A total of 63 SNPs were identified across the genes 〈 i 〉 PIGB 〈 /i 〉 , 〈 i 〉 CCPG1 〈 /i 〉 , 〈 i 〉 COMMD9 〈 /i 〉 , 〈 i 〉 LDLRAD3 〈 /i 〉 , 〈 i 〉 TRIM44 〈 /i 〉 , 〈 i 〉 MYLPF 〈 /i 〉 , 〈 i 〉 SEPTIN 〈 /i 〉 , 〈 i 〉 ZNF48 〈 /i 〉 , 〈 i 〉 TIA1 〈 /i 〉 , 〈 i 〉 FAIM2 〈 /i 〉 , 〈 i 〉 KRT18 〈 /i 〉 , 〈 i 〉 FBP1 〈 /i 〉 , 〈 i 〉 FBP2 〈 /i 〉 , 〈 i 〉 CTSL 〈 /i 〉 , 〈 i 〉 DAPK1 〈 /i 〉 , 〈 i 〉 DHX8 〈 /i 〉 , 〈 i 〉 GPR179 〈 /i 〉 , 〈 i 〉 DEPDC1B 〈 /i 〉 , ENSSSCG00000049573, ENSSSCG00000016384, ENSSSCG00000022657, ENSSSCG00000038825, and ENSSSCG00000001229. Using pathway enrichment analyses and network prospection, we have identified the following significant adjusted 〈 i 〉 p 〈 /i 〉 value threshold of 0.001 involved with the biological function pathways of estrogen signaling, cytoskeleton organization, and the pentose phosphate pathway. 〈 b 〉 〈 i 〉 Conclusion: 〈 /i 〉 〈 /b 〉 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 〈 i 〉 GPR179 〈 /i 〉 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.
Type of Medium:
Online Resource
ISSN:
1661-5425
,
1661-5433
Language:
English
Publisher:
S. Karger AG
Publication Date:
2023
detail.hit.zdb_id:
2261528-3
Bookmarklink
