Genome‐wide association study identifies variants in the<i><scp>CAPN</scp>9</i>gene associated with umbilical hernia in pigs

Xu, Pao; Zhang, C.; Sun, Chang; Li, Xiuling; Han, Xuelei; Li, M.; Qiao, Ruimin

doi:10.1111/age.12760

Cited by 9 publications

(14 citation statements)

References 16 publications

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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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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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“…Some studies investigating genes involved with the occurrence of hernias have been performed using candidate genes and GWAS approaches [11,25,29,31,32,[57][58][59][60]. More recently, functional candidate genes were prospected for scrotal [6] and umbilical [7] hernias by our group using RNA-Seq approach.…”

Section: Discussionmentioning

confidence: 99%

Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs

Rodrigues

Ibelli

Peixoto

et al. 2021

Genes

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Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected pigs to discover genes and pathways involved with the development of both types of hernia. A total of 13,307 transcripts was expressed in the inguinal and 13,302 in the umbilical ring tissues with 94.91% of them present in both tissues. From those, 35 genes were differentially expressed in both groups, participating in 108 biological processes. A total of 67 polymorphisms was identified in the inguinal ring and 76 in the umbilical ring tissue, of which 11 and 14 were novel, respectively. A single nucleotide polymorphism (SNP) with deleterious function was identified in the integrin α M (ITGAM) gene. The microtubule associated protein 1 light chain 3 γ (MAP1LC3C), vitrin (VIT), aggrecan (ACAN), alkaline ceramidase 2 (ACER2), potassium calcium-activated channel subfamily M α 1 (KCNMA1) and synaptopodin 2 (SYNPO2) genes are highlighted as candidates to trigger both types of hernia. We generated the first comparative study of the pig umbilical and inguinal ring transcriptomes, contributing to the understanding of the genetic mechanism involved with these two types of hernia in pigs and probably in other mammals.

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“…The genomic regions indicated in previous publications were analyzed using polymerase chain reaction: (1) fragment (chr14:59603379-59604090) containing single SNP (rs321865883) in exon 10 of CAPN9 (Li et al, 2019);…”

Section: Pcr Amplificationmentioning

confidence: 99%

“…The encoded proteins belong to the interleukin‐6 family, which plays a role in cell differentiation, growth promotion, and inflammatory response to injury (Grindflek et al, 2018). A subsequent GWAS performed in an Erhualian × Shaziling F2 intercross population indicated a candidate SNP synonymous variant in the calpain‐9 ( CAPN9 ) gene, which is also located in SSC14 (Li et al, 2019). In a recent study of hernias in the Landrace breed, performed using RNA sequencing, a candidate SNP was described in the integrin α M ( ITGAM ) gene, which is involved in ectodermal cell differentiation (Rodrigues et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…

Hernias are a serious health problem in the swine industry and production system. They are one of the most common developmental disorders (Lago et al, 2018;Li et al, 2019), which together with splay leg, inguinal/ scrotal hernia, and atresia lead to significant economic losses of about one hundred million US dollars annually in world production, taking into account only the mortality rate (Walters, 2016). Pigs with hernias have retarded growth due to feeding problems.

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confidence: 99%

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A confirmed association betweenDNAvariants inCAPN9,OSM, andITGAMcandidate genes and the risk of umbilical hernia in pigs

Wozniak

Loba

Iskrzak³

et al. 2023

Animal Genetics

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Umbilical hernia (UH) is one of the most prevalent defects of swine, affecting their welfare and causing considerable economic loss. The molecular mechanisms behind UH in pigs remain poorly understood. The aim of this study was to verify the association between UH and previously reported DNA variants in the CAPN9, OSM, ITGAM, and NUGGC genes. A case/control study design was applied in two different crossbred cohorts of commercial fatteners containing 412 and 171 pigs, respectively. SNPs within CAPN9, OSM, and ITGAM were analyzed using Sanger sequencing, and 10 SNPs in CAPN9, five in OSM, and two in ITGAM were identified. A structural variant in the NUGGC gene was studied by droplet‐digital PCR, and an elevated copy number was detected in only a single individual. Significant differences in allele frequencies for four SNPs in CAPN9 were detected. The haplotype analysis showed the effect on the risk of UH for two genes. The CAGGA haplotype within OSM and AT haplotype in ITGAM reduced the relative risk of UH by 52% and 45%, respectively, confirming that variants in those genes are associated with the risk of UH in pigs. Moreover, the interaction between the CAPN9 haplotype and the sex of animals had also significant impact on UH risk.

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Genome‐wide association study identifies variants in theCAPN9gene associated with umbilical hernia in pigs

Cited by 9 publications

References 16 publications

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

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

Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs

A confirmed association betweenDNAvariants inCAPN9,OSM, andITGAMcandidate genes and the risk of umbilical hernia in pigs

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