Won, Sohyoung
(Department of Agricultural Biotechnology and Research Institute of Population Genomics, Seoul National University)
,
Jung, Jaehoon
(Department of Agricultural Biotechnology and Research Institute of Population Genomics, Seoul National University)
,
Park, Eungwoo
(Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration)
,
Kim, Heebal
(Department of Agricultural Biotechnology and Research Institute of Population Genomics, Seoul National University)
Objective: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). Methods: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreedi...
Objective: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). Methods: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF quantitative trait loci (QTL) regions and functional classification of the identified genes were also performed. Heritability of IMF was estimated by GCTA tool. Results: Total 365 SNPs were found to be significant from a cutoff of p-value <0.01 and the 365 significant SNPs were annotated across 120 genes. Twenty five genes were on pig IMF QTL regions. Bone morphogenetic protein-binding endothelial cell precursor-derived regulator, forkhead box protein O1, ectodysplasin A receptor, ring finger protein 149, cluster of differentiation, tyrosine-protein phosphatase non-receptor type 1, SRY (sex determining region Y)-box 9 (SOX9), MYC proto-oncogene, and macrophage migration inhibitory factor were related to mitogen-activated protein kinase pathway, which regulates the differentiation to adipocytes. These genes and the genes mapped on QTLs could be the candidate genes affecting IMF. Heritability of IMF was estimated as 0.52, which was relatively high, suggesting that a considerable portion of the total variance of IMF is explained by the SNP information. Conclusion: Our results can contribute to breeding pigs with better IMF and therefore, producing pork with better sensory qualities.
Objective: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). Methods: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF quantitative trait loci (QTL) regions and functional classification of the identified genes were also performed. Heritability of IMF was estimated by GCTA tool. Results: Total 365 SNPs were found to be significant from a cutoff of p-value <0.01 and the 365 significant SNPs were annotated across 120 genes. Twenty five genes were on pig IMF QTL regions. Bone morphogenetic protein-binding endothelial cell precursor-derived regulator, forkhead box protein O1, ectodysplasin A receptor, ring finger protein 149, cluster of differentiation, tyrosine-protein phosphatase non-receptor type 1, SRY (sex determining region Y)-box 9 (SOX9), MYC proto-oncogene, and macrophage migration inhibitory factor were related to mitogen-activated protein kinase pathway, which regulates the differentiation to adipocytes. These genes and the genes mapped on QTLs could be the candidate genes affecting IMF. Heritability of IMF was estimated as 0.52, which was relatively high, suggesting that a considerable portion of the total variance of IMF is explained by the SNP information. Conclusion: Our results can contribute to breeding pigs with better IMF and therefore, producing pork with better sensory qualities.
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문제 정의
We also estimated the heritability of IMF using the data. This study aims to search genes associated to IMF of pig and furthermore, to provide knowledge for breeding pigs having better IMF consequently, better sensory qualities.
제안 방법
In this study, we analyzed the SNP data and IMF of pigs using GWAS to identify SNPs associated with IMF. To adjust the effect of inbreeding, a genetic relationship matrix was constructed and used during GWAS.
The phenotype (IMF) was standardized to z-scores by subtracting the mean and then dividing by the standard deviation, in each sex group (male, female, unknown) separately. Single trait, univariate linear mixed model was used for the analysis assuming additive effect of SNPs. SNP effects were treated as random effects and sex was added as a covariate.
대상 데이터
An inbred Berkshire population was used for analysis, and IMF of the Berkshire sample was measured. Seven hundred and four samples were examined. Among them, 367 samples were male, 204 samples were female and the sex of 133 samples was unknown.
이론/모형
The GCTA tool [9] was used to calculate heritability for IMF. We calculated the genetic relationship matrix between all pairs of samples using all the autosomal SNPs.
성능/효과
A total of 365 SNPs from all 19 chromosomes were identified as significant SNPs as the result of GWAS. Chromosome 14 contained 53 significant SNPs which was the largest number among all chromosomes.
Pork containing more than 3% IMF tends to have higher sensory qualities including juiciness, tenderness and taste [29]. As IMF of pork increased from a range of 2.01% to 3.0% to higher than 3%, juiciness, tenderness, and both the intensity and desirability of taste increased. Since the current average of IMF measured from the Berkshire sample was 2.
Identified genes were compared with IMF QTL regions base on the Pig QTLdb. Total 25 genes from the 120 significant genes, which is 20.8%, were included in reported pig IMF QTL regions. Seven genes on chromosome 9, 6 genes on both chromosome 2 and 6, and 2 genes on chromosome 4, 7, and 17 each were mapped on QTLs (Figure 2).
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