Confirmation of genotypic effects for the bovine APM1 gene on marbling in Hanwoo cattle

Kwon, Anam; Srikanth, Krishnamoorthy; Lee, Eun-Jin; Kim, Seonkwan

doi:10.1186/s40781-016-0096-2

Cited by 6 publications

(6 citation statements)

References 19 publications

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“…A genome-wide association study (GWAS) was performed using a mixed linear model implemented in GCTA v.1.91.4 beta3 [39]. Farm (1419), birth year (2006-2016), birth month (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12), slaughter year (2008-2018), slaughter month (1-12), age (17-62 months), slaughter place (53), sire (324), and dam (8331) were tested for fixed effects. Fixed effects that were significant for all the traits were fitted in the model; this included farm, birth year, slaughter year, slaughter place, age, and sire.…”

Section: Genome-wide Association Analysis Heritability and Variancementioning

confidence: 99%

“…Our finding provides insight into the effects of regulatory SNPs on carcass traits.Genes 2020, 11, 316 2 of 22 and eye muscle area (EMA) [4]. Though substantial improvement in carcass and meat quality have been achieved, due to market requirement for higher quality, and for improving the economic value of Hanwoo, continuous improvement of economically important trait is required [5,6]. A genome-wide association study (GWAS) is an affordable and powerful tool to discover candidate genes and loci associated with quantitative traits [7].…”

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confidence: 99%

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A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

Srikanth

Lee

Chung³

et al. 2020

Genes

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Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10 −7 ) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.Genes 2020, 11, 316 2 of 22 and eye muscle area (EMA) [4]. Though substantial improvement in carcass and meat quality have been achieved, due to market requirement for higher quality, and for improving the economic value of Hanwoo, continuous improvement of economically important trait is required [5,6]. A genome-wide association study (GWAS) is an affordable and powerful tool to discover candidate genes and loci associated with quantitative traits [7]. GWASs in livestock, including in Hanwoo [8][9][10][11], have resulted in remarkable insights into the genetic architecture of carcass traits. Genetic variation in complex traits such as carcass and meat quality traits are, however, due to the contribution of many mutations with small effects [1,12] (polygenic effect). Though some of these mutations have been successfully identified through GWASs, the high significance thresholds required to correct for the multiple testing problem results in the identification of only SNPs with a large effect size [7,12]. Further, a GWAS does not make use of the fact that genes work together in a network, and multi-allelic QTL might not be captured due to the bi-allelic nature of SNPs [13]. Moreover, epistasis is an important genetic component underlying phenotypic variation that also accounts for missing heritability [14]. Therefore, a GWAS alone might result in only limited understanding of the nature of complex traits [13]. Suggested solutions to overcome this limitation and understand the genetic complexities regulating complex traits are to complement a GWAS with gene-set enrichment, a protein-protein interaction network (PPIN), and pathway analyses [15][16][17][18]. In GSEA and pathway analysis, a g...

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Section: Genome-wide Association Analysis Heritability and Variancementioning

confidence: 99%

mentioning

confidence: 99%

A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

Srikanth

Lee

Chung³

et al. 2020

Genes

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“…Particularly in Korea and Japan, producers have attempted to increase IMF to enhance the economic value of beef ( Sasaki et al, 2009 ; Kim et al, 2020 ). Experts use genetic methods to screen related genes and single nucleotide polymorphisms (SNP)( Sasaki et al, 2009 ; Kwon et al, 2016 ). In addition, various nutritional methods are also used, such as oil supplements, vitamin A supplementation and high-grain diet feeding ( Schmid et al, 2006 ; Gorocica-Buenfil et al, 2007 ; Pickworth et al, 2012 ; Kim et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Association between rumen microbiota and marbling grade in Hu sheep

et al. 2022

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The marbling fat regulates the flavor of mutton and measures the fat density in the loin eye and is the most important parameter of carcass grading. The objective of this study was to explore the relationship of rumen microbiota and mutton marbling grade. One hundred and eighty-seven feedlot-finished Hu male lambs (Age: 180 day; Final BW: 46.32 ± 6.03 kg) were slaughtered, and ruminal contents and marbling grade were collected. Ruminal microbial DNA extraction and 16S rRNA gene sequencing was performed to investigate microbial composition and to predict microbial metabolic pathways. The animal cohort was then grouped based on marbling grades [low marbling (LM), marbling grade ≤ 1; Medium marbling (MM), 1 < marbling grade ≤ 3; High Marbling (HM), 3 < marbling grade ≤ 5] and intramuscular fat-associated microorganisms were pinpointed using LEfSe and random forest classification model. Intramuscular fat content had significantly differences among the three groups (P < 0.05), and was significantly correlated with VFAs profiling. HM sheep showed a higher abundance of one bacterial taxon (Kandleria), and two taxa were overrepresented in the MM sheep (Pseudobutyrivibrio and Monoglobus), respectively. In addition, the main intramuscular fat deposition pathway was found to involve peroxisome proliferator-activated receptor (PPAR) fatty acid synthesis. By studying the effect of the ruminal microbiome on the marbling of sheep, the present study provides insights into the production of high-quality mutton.

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“…Intramuscular fat, known as "marbling," is highly correlated with meat quality traits (e.g., flavor, tenderness, and juiciness); thus, producers require higher marbling scores to achieve greater economic benefits. By using genetic approaches to detect single-nucleotide polymorphisms potentially related to meat quality [4][5][6], many researchers have attempted to increase marbling in beef. Further to this, various dietary oil supplements have been widely used to reduce levels of saturated fatty acids in adipose tissues [7][8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle

Kim

Park

Jeong

et al. 2020

Animals

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This study demonstrated the potential effects of the rumen microbiota on the deposition of intramuscular fat, known as marbling. Previous studies on fatty acid metabolism in beef cattle have mostly focused on biohydrogenating rumen bacteria, whereas those on the overall rumen microbiota—to understand their roles in marbling—have not been systematically performed. The rumen microbiota of 14 Korean beef cattle (Hanwoo), which showed similar carcass characteristics and blood metabolites but different marbling scores, were analyzed by 16S rRNA gene sequencing. The rumen samples were grouped into two extreme marbling score groups of host animals as follows: LMS, marbling score≤ 4 or HMS, marbling score ≥7. Species richness tended to be higher in the HMS group, whereas the overall microbiota differed between LMS and HMS groups. RFP12, Verrucomicrobia, Oscillospira, Porphyromonadaceae, and Paludibacter were differentially abundant in the HMS group, whereas Olsenella was abundant in the LMS group. Some marbling-associated bacterial taxa also contributed to the enrichment of two lipid metabolic pathways including “alpha-linolenic acid metabolism” and “fatty acid biosynthesis” in the HMS microbiome. Taxonomic drivers of fatty acid biosynthesis, particularly in the rumen microbiome of high-marbled meat, could thus be further studied to increase the intramuscular fat content.

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Confirmation of genotypic effects for the bovine APM1 gene on marbling in Hanwoo cattle

Cited by 6 publications

References 19 publications

A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

Association between rumen microbiota and marbling grade in Hu sheep

Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle

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