Investigation of genetic susceptibility to nonspecific digestive disorder between TYK2, JAK1, and STAT3 genes in rabbits

Fu, Lu; Zhao, Mingde; Chen, Shiyi; Jia, Xianbo; Lai, Songjia

doi:10.1016/j.livsci.2015.08.014

Cited by 4 publications

(7 citation statements)

References 41 publications

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“…And as an important gut-associated lymphoid tissue, RSR plays key roles in the development of an immune response or immune tolerance to the antigens and pathogens in the intestinal tract (Haasz et al, 1974). Recently, several genes have been discovered to be related to the genetic determination of susceptibility to NSDD in rabbit, including MyD88, TLR4, NOD2, NLRP3, NLRP12, TYK2, JAK1 and STAT3 (Zhang et al, 2011;Chen et al, 2013a;Liu et al, 2013;Yang et al, 2013b;Zhang et al, 2013;Fu et al, 2014Fu et al, , 2015. It is also proved that several miRNAs play an important role in the pathogenesis of experimental colitis and human IBD.…”

Section: Discussionmentioning

confidence: 99%

“…IBD or NSDD-related 25 genes and 25 miRNAs were retrieved from published papers Feng et al, 2012;Ghorpade et al, 2013;Koukos et al, 2013;Liu et al, 2013;Nata et al, 2013;Yang et al, 2013aYang et al, , 2013b Zhang et al, 2013;Fu et al, 2014;Lu et al, 2014;Carethers et al, 2015;Fu et al, 2015;Kalla et al, 2015), and their expression levels were then detected by RT-qPCR method in ileum, RSR and colon tissues. The relative expression level of the genes and miRNAs are shown in Figure 1 and Figure 2, in which the highest expression one is set to 1.…”

Section: Differentially Expressed Mrnas and Mirnasmentioning

confidence: 99%

“…Recently, using multifactor dimensionality reduction method, researchers showed that Tyrosine Kinase 2 (TYK2), Janus kinase 1 (JAK1), and signal transducer and activator of transcription 3 (STAT3) genes and their gene-gene interactions play an important role in the genetic susceptibility to NSDD in rabbit (Fu et al, 2014(Fu et al, , 2015. In addition, some immunogenic biomarkers illustrated in inflammatory bowel diseases (IBD) may also be considered as related to NSDD-susceptibility genes.…”

Section: Introductionmentioning

confidence: 99%

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Investigation of significant microRNA-mRNA pairs associated with nonspecific digestive disorder in rabbits

et al. 2017

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Nonspecific digestive disorders (NSDD) are one of the major intestinal problems in rabbit, with considerable economic losses in industrial rabbit farms. MicroRNAs (miRNAs), as small non-coding RNAs, have significant biological involvement in intestinal disorders. In this study, we investigated the expression levels of 25 genes and 25 miRNAs in ileum, rabbit sacculus rotundus (RSR) and colon tissues from 9 rabbits with different severity of NSDD. These molecules have been found to be related to NSDD or inflammatory bowel disease, which will help recognise the miRNA-mRNA pairs. Finally, 108 possible pairs of miRNAmRNA pairs with an anti-correlation were identified by Pearson's correlation analysis between differentially expressed 25 miRNAs and 23 mRNAs. Ninety-five of these miRNA-mRNA pairs were hitherto unexplored, and their roles in NSDD biology require further elucidation. Our results give a clue to the potential miRNAmRNA pairs for the NSDD that can further improve the understanding of the pathogenesis of NSDD in rabbit.

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Section: Discussionmentioning

confidence: 99%

Section: Differentially Expressed Mrnas and Mirnasmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Investigation of significant microRNA-mRNA pairs associated with nonspecific digestive disorder in rabbits

et al. 2017

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“…This evidence opened the possibility for the implementation of selection strategies to increase resistance against enteropathies and related pathogenic conditions in commercial meat rabbit populations and investigate the genetic factors involved in this complex pathogenic status (Garreau et al, 2008(Garreau et al, , 2012(Garreau et al, , 2021. Several studies reported that polymorphisms in candidate genes involved in host immunity might be associated with the susceptibility of non-specific digestive disorders in growing rabbits of a few lines (Chen, Zhang, et al, 2013;Fu et al, 2014Fu et al, , 2015Li et al, 2018;Liu et al, 2013Liu et al, , 2017Yang et al, 2013;Zhang et al, 2011; several genes that encode members of a family of immunoglobulin Fc receptors (FCER1G, FCRLA, FCRLB and FCGR2A) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.…”

Section: Introductionmentioning

confidence: 99%

“…This evidence opened the possibility for the implementation of selection strategies to increase resistance against enteropathies and related pathogenic conditions in commercial meat rabbit populations and investigate the genetic factors involved in this complex pathogenic status (Garreau et al., 2008, 2012, 2021). Several studies reported that polymorphisms in candidate genes involved in host immunity might be associated with the susceptibility of non‐specific digestive disorders in growing rabbits of a few lines (Chen, Zhang, et al., 2013; Fu et al., 2014, 2015; Li et al., 2018; Liu et al., 2013, 2017; Yang et al., 2013; Zhang et al., 2011; Zhang, Zhang, Chen, et al., 2013; Zhang, Zhang, Peng, et al., 2013). However, it seems clear that the association reported in these investigations should be validated and confirmed with other studies that can provide more comprehensive genome‐wide analyses, in different lines and in specifically defined environments, which could also assure that all involved animals have been in contact with the pathogenic agents or conditions.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits

Bovo,

Ribani,

Schiavo

et al. 2023

J Animal Breeding Genetics

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Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from the suckling period, with large negative economic impacts. In this study, from a commercial population of suckling rabbits (derived from 133 litters) that experienced an outbreak of enteropathy, we first selected a few animals that died with severe symptoms of diarrhoea and characterized their microbiota, using 16S rRNA gene sequencing data. Clostridium genus was consistently present in all affected specimens. In addition, with the aim to identify genetic markers in the rabbit genome that could be used as selection tools, we performed genome‐wide association studies for symptoms of diarrhoea in the same commercial rabbit population. These studies were also complemented with FST analyses between the same groups of rabbits. A total of 332 suckling rabbits (151 with severe symptoms of diarrhoea, 42 with mild symptoms and 129 without any symptoms till the weaning period), derived from 45 different litters (a subset of the 133 litters) were genotyped with the Affymetrix Axiom OrcunSNP Array. In both genomic approaches, rabbits within litters were paired to constitute two groups (susceptible and resistant, including the mildly affected in one or the other group) and run case and control genome‐wide association analyses. Genomic heritability estimated in the designed experimental structure integrated in a commercial breeding scheme was 0.19–0.21 (s.e. 0.09–0.10). A total of eight genomic regions on rabbit chromosome 2 (OCU2), OCU3, OCU7, OCU12, OCU13, OCU16 and in an unassembled scaffold had significant single nucleotide polymorphisms (SNPs) and/or markers that trespassed the FST percentile distribution. Among these regions, three main peaks of SNPs were identified on OCU12, OCU13 and OCU16. The QTL region on OCU13 encompasses several genes that encode members of a family of immunoglobulin Fc receptors (FCER1G, FCRLA, FCRLB and FCGR2A) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.

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Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

Sheriff,

Ahbara,

Haile

et al. 2024

Front. Genet.

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Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e−05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100–150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

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Investigation of genetic susceptibility to nonspecific digestive disorder between TYK2, JAK1, and STAT3 genes in rabbits

Cited by 4 publications

References 41 publications

Investigation of significant microRNA-mRNA pairs associated with nonspecific digestive disorder in rabbits

Investigation of significant microRNA-mRNA pairs associated with nonspecific digestive disorder in rabbits

Genome‐wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits

Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

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