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Whole-Exome Sequencing Indicated New Candidate Genes Associated with Unilateral Cryptorchidism in Pigs.
- Source :
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Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation [Sex Dev] 2023; Vol. 17 (1), pp. 56-66. Date of Electronic Publication: 2023 Feb 09. - Publication Year :
- 2023
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Abstract
- Introduction: 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.<br />Methods: 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.<br />Results: 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.<br />Conclusion: 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.<br /> (© 2023 S. Karger AG, Basel.)
- Subjects :
- Male
Humans
Animals
Genome-Wide Association Study
Exome Sequencing
Signal Transduction
Polymorphism, Single Nucleotide genetics
Mannosyltransferases genetics
Mannosyltransferases metabolism
Tripartite Motif Proteins genetics
Tripartite Motif Proteins metabolism
Intracellular Signaling Peptides and Proteins genetics
Intracellular Signaling Peptides and Proteins metabolism
RNA Splicing Factors genetics
RNA Splicing Factors metabolism
DEAD-box RNA Helicases metabolism
GTPase-Activating Proteins genetics
Cryptorchidism genetics
Cryptorchidism veterinary
Subjects
Details
- Language :
- English
- ISSN :
- 1661-5433
- Volume :
- 17
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation
- Publication Type :
- Academic Journal
- Accession number :
- 36758533
- Full Text :
- https://doi.org/10.1159/000528360