Mechanistic insight into the progressive retinal atrophy disease in dogs via pathway-based genome-wide association analysis

Sheet, Sunirmal; Srikanth, Krishnamoorthy; Park, Woncheoul; Lim, Dajeong; Park, Jong-Eun; Ko, Min-Jeong; Choi, Bong Hwan

doi:10.5187/jast.2020.62.6.765

Cited by 4 publications

(5 citation statements)

References 46 publications

(65 reference statements)

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“…The moderate heritability estimate of 0.47 was quite similar to those in various studies that have reported heritability estimates of BW at different growth stages in a range from 0.15 to 0.55 in different native chicken breeds [20]. Moreover, the estimate was also in agreement with the results of Cahyadi et al [8], who estimated genetic parameters for growth-related traits in KNCs and showed that the BW at age 8 weeks had a genetic heritability of 0.45.…”

Section: Discussionsupporting

confidence: 86%

“…The latest version of the Gallus gallus (chicken) genome assembly 6 was used as the reference genome. When we first performed the GSEA based on the GWAS data, we referred to several published studies that have reported relevant similar analyses [18][19][20][21][22][23][24]. Based on these related reports, the p-value threshold for filtering GWAS SNPs to be used in GSEA differed between 0.05 and 0.005 among reports.…”

Section: Snp Annotation and Gene Set Enrichment Analysismentioning

confidence: 99%

“…The EASE score refers to the modified fisher exact p-value and is calculated by penalizing (removing) one gene within the given category from the list and calculating the resulting Fisher exact probability for that category [27]. Based on the EASE score, the enrichment p-value in the Functional Annotation chart was calculated, and we defined the p value threshold (p < 0.05) for significantly enriched GO/KEGG term [20,21].…”

Section: Snp Annotation and Gene Set Enrichment Analysismentioning

confidence: 99%

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Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

Cha

Choo

Srikanth

et al. 2021

Genes

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Meat from Korean native chickens (KNCs) has high consumer demand; however, slow growth performance and high variation in body weight (BW) of KNCs remain an issue. Genome-wide association study (GWAS) is a powerful method to identify quantitative trait-associated genomic loci. A GWAS, based on a large-scale KNC population, is needed to identify underlying genetic mechanisms related to its growth traits. To identify BW-associated genomic regions, we performed a GWAS using the chicken 60K single nucleotide polymorphism (SNP) panel for 1328 KNCs. BW was measured at 8 weeks of age, from 2018 to 2020. Twelve SNPs were associated with BW at the suggestive significance level (p < 2.95 × 10−5) and located near or within 11 candidate genes, including WDR37, KCNIP4, SLIT2, PPARGC1A, MYOCD and ADGRA3. Gene set enrichment analysis based on the GWAS results at p < 0.05 (1680 SNPs) showed that 32 Gene Ontology terms and two Kyoto Encyclopedia of Genes and Genomes pathways, including regulation of transcription, motor activity, the mitogen-activated protein kinase signaling pathway, and tight junction, were significantly enriched (p < 0.05) for BW-associated genes. These pathways are involved in cell growth and development, related to BW gain. The identified SNPs are potential biomarkers in KNC breeding.

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Section: Discussionsupporting

confidence: 86%

Section: Snp Annotation and Gene Set Enrichment Analysismentioning

confidence: 99%

Section: Snp Annotation and Gene Set Enrichment Analysismentioning

confidence: 99%

See 1 more Smart Citation

Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

Cha

Choo

Srikanth

et al. 2021

Genes

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“…Thus, periodic evaluations are recommended to monitor possible complications (BALICKI et al, 2021), such as retinal detachment and vascular degeneration, loss of pigmentation and optic atrophy (SHEET et al, 2020). With disease progression, complete retinal atrophy may occur, in addition to changes in vitreous and asteroid hyalosis (BALICKA et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Progressive retinal atrophy in a poodle dog: Case report

Lusa,

Roz,

Diaz

et al. 2023

Iii Seven International Multidisciplinary Congress

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The aim of this study was to report a case of Progressive Retinal Atrophy (PRA) in a Poodle dog. A female canine Poodle, approximately 12 years old, was treated. According to the report of her guardian, the animal had been presenting visual difficulties for some months. Ophthalmologic examination revealed bilateral mydriasis, positive palpebral reflex, glare reflex, negative direct and consensual pupillary reflexes, and absence of response to threat. In the evaluation of the posterior segment, absence of retinal vascularization was noted, as well as hyperreflective spots in the tapetal region and depigmentation of the non-tapetal region, both bilateral. In the "maze test" in light and dark rooms, the patient collided with objects and was diagnosed with advanced stage RPA. As it is a hereditary and degenerative ophthalmopathy, with no specific treatment, periodic evaluations were recommended in order to monitor the progression of the disease, in addition to ruling out possible future changes. It is essential that these animals are removed from breeding programs, since clinical manifestations will occur only as adults and, probably, new offspring will have already been generated.

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“…A complex microbial community resides in the gastrointestinal tract of animals, and healthy canines and felines have been demonstrated to exhibit an abundance of Bifidobacterium , Lactobacillus , Enterococcus , Mogibactera , Clostridium , and more ( 13 – 15 ); clinical trials of those canine- and feline-origin probiotics were successful in improving the digestibility and overall health of senior dogs ( 16 , 17 ), relieving diarrhea ( 18 ), lowering serum glucose and cholesterol levels, and decreasing systemic inflammation ( 19 , 20 ).…”

Section: Introductionmentioning

confidence: 99%

Dietary supplementation with probiotics promotes weight loss by reshaping the gut microbiome and energy metabolism in obese dogs

Kang,

Kwak,

Lee

et al. 2024

Microbiol Spectr

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Obesity and overweight among companion animals are significant concerns, paralleling the issues observed in human populations. Recent research has highlighted the potential benefits of various probiotics in addressing weight-related changes, obesity, and associated pathologies. In this study, we delved into the beneficial probiotic mechanisms in high-fat-induced obese canines, revealing that Enterococcus faecium IDCC 2102 (IDCC 2102) and Bifidobacterium lactis IDCC 4301 (IDCC 4301) have the capacity to mitigate the increase in body weight and lipid accumulation in obese canines subjected to a high-fat diet and hyperlipidemic Caenorhabditis elegans ( C. elegans ) strain VS29. Both IDCC 2102 and IDCC 4301 demonstrated the ability to reduce systemic inflammation and hormonal disruptions induced by obesity. Notably, these probiotics induced modifications in the microbiota by promoting lactic acid bacteria, including Lactobacillaceae , Ruminococcaceae , and S24-7 , with concomitant activation of pyruvate metabolism. IDCC 4301, through the generation of bacterial short-chain fatty acids and carboxylic acids, facilitated glycolysis and contributed to ATP synthesis. Meanwhile, IDCC 2102 produced bacterial metabolites such as acetic acid and butyric acid, exhibiting a particular ability to stimulate dopamine synthesis in a canine model. This stimulation led to the restoration of eating behavior and improvements in glucose and insulin tolerance. In summary, we propose novel probiotics for the treatment of obese animals based on the modifications induced by IDCC 2102 and IDCC 4301. These probiotics enhanced systemic energy utilization in response to high caloric intake, thereby preventing lipid accumulation and restoring stability to the fecal microbiota. Consequently, this intervention resulted in a reduction in systemic inflammation caused by the high-fat diet. IMPORTANCE Probiotic supplementation affected commensal bacterial proliferation, and administering probiotics increased glycolysis and activated pyruvate metabolism in the body, which is related to propanate metabolism as a result of pyruvate metabolism activation boosting bacterial fatty acid production via dopamine and carboxylic acid specialized pathways, hence contributing to increased ATP synthesis and energy metabolism activity.

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Mechanistic insight into the progressive retinal atrophy disease in dogs via pathway-based genome-wide association analysis

Cited by 4 publications

References 46 publications

Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

Progressive retinal atrophy in a poodle dog: Case report

Dietary supplementation with probiotics promotes weight loss by reshaping the gut microbiome and energy metabolism in obese dogs

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