A genome‐wide association study of copy number variations with umbilical hernia in swine

Yi, Long; Su, Ying; Ai, Huashui; Zhang, Zhiyan; Yang, Bin; Ruan, Guorong; Xiao, Shijun; Liao, Xinjun; Ren, Jun; Huang, Lusheng; Ding, Nengshui

doi:10.1111/age.12402

Cited by 32 publications

(37 citation statements)

References 39 publications

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“…Moreover, SNPs within the NUAK1 gene showed associations with only French Landrace but not with more pigs and it may be caused by the limited sample numbers. For the remaining three SNPs, the comparison in mixed or purebred groups did not uncover notable differences between inguinal/scrotal hernias and the polymorphisms of DEGS1, COL2A1 and MMP2 (p > 0.05) providing some evidence that numerous SNPs in pig inguinal/scrotal hernias were likely breed specific, which coincided with the former studies of pig inguinal/scrotal hernias [29][30][31].…”

Section: Confirmation Of Association Results In 270 Samplessupporting

confidence: 77%

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Zou¹,

Zuo²,

Zhu³

et al. 2017

Oncotarget

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Inguinal and scrotal hernias are the most frequent congenital disorders in pigs, and they may cause severe economic loss in the pig breeding industry. Genetic factors play a significant role in the susceptibility to hernias, but the genetic mechanisms of inguinal/scrotal hernia are poorly understood. In this study, we performed a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) on 120 (59 cases and 61 controls) full and half sib pigs to identify genetic loci underlying variations in inguinal/scrotal hernias. A total of 218,460 high-quality SNPs were generated for further statistical analysis with casecontrols and the farmCPU model. Based on these two methods, a total of 59 SNPs were significantly (P < 0.01) associated with inguinal/scrotal hernia. Finally, 14 novel candidate genes implicated in the defect were identified, and 5 genes (CPNE5, DEGS1, PLCG2, PRKCE and NUAK1) were related to cell apoptosis, which is one of the pivotal pathogenesis factors of inguinal/scrotal hernia. In addition, 4 of them were shown strong associations with the hernia were confirmed in 270 samples (P < 0.05). This finding provides new evidence that genes related to cell apoptosis may be associated with inguinal/scrotal hernias.

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Section: Confirmation Of Association Results In 270 Samplessupporting

confidence: 77%

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Zou¹,

Zuo²,

Zhu³

et al. 2017

Oncotarget

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“…Associations between CNVs and phenotypic performance have been documented in a whole multitude of species including dairy cattle [6], beef cattle [7,8], chickens [14], dogs [15], pigs [16] and humans [17][18][19]; thus CNVs are likely to contribute to some of the underlying genetic variability. The ability to estimate the genomic or phenotypic merit of individuals based on CNVs requires knowledge of the CNV genotypes of those animals.…”

Section: Discussionmentioning

confidence: 99%

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

et al. 2020

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Background: The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number.

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“…Several quantitative trait loci (QTL) associated with UH have already been reported for pigs. In a search in the pig QTLdb (https://www.animalgenome.org/cgi-bin/QTLdb/SS/index -11/02/2019), 54 QTLs for umbilical hernia have been found in several pig breeds, being located in chromosomes SSC1, SSC2, SSC3, SSC4, SSC6, SSC7, SSC8, SSC9, SSC10, SSC11, SSC13, SSC14, SSC15, SSC16 and SSC17 [11][12][13][14]. Ding et al (2009) [11] performed the first genomic study with UH and found some chromosomic regions related to the appearance of this condition.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs

Souza

Ibelli²,

Savoldi

et al. 2020

PLoS ONE

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Umbilical hernia (UH) is one of the most frequent defects affecting pig production, however, it also affects humans and other mammals. UH is characterized as an abnormal protrusion of the abdominal contents to the umbilical region, causing pain, discomfort and reduced performance in pigs. Some genomic regions associated to UH have already been identified, however, no study involving RNA sequencing was performed when umbilical tissue is considered. Therefore, here, we have sequenced the umbilical ring transcriptome of five normal and five UH-affected pigs to uncover genes and pathways involved with UH development. A total of 13,216 transcripts were expressed in the umbilical ring tissue. From those, 230 genes were differentially expressed (DE) between normal and UH-affected pigs (FDR <0.05), being 145 downregulated and 85 upregulated in the affected compared to the normal pigs. A total of 68 significant biological processes were identified and the most relevant were extracellular matrix, immune system, anatomical development, cell adhesion, membrane components, receptor activation, calcium binding and immune synapse. The results pointed out ACAN, MMPs, COLs, EPYC, VIT, CCBE1 and LGALS3 as strong candidates to trigger umbilical hernias in pigs since they act in the extracellular matrix remodeling and in the production, integrity and resistance of the collagen. We have generated the first transcriptome of the pig umbilical ring tissue, which allowed the identification of genes that had not yet been related to umbilical hernias in pigs. Nevertheless, further studies are needed to identify the causal mutations, SNPs and CNVs in these genes to improve our understanding of the mechanisms of gene regulation.

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A genome‐wide association study of copy number variations with umbilical hernia in swine

Cited by 32 publications

References 39 publications

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs

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