• Title, Summary, Keyword: candidate genes

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Identification of Candidate Genes Associated with Beef Marbling Using QTL and Pathway Analysis in Hanwoo (Korean Cattle)

  • Park, Hye-Sun;Seo, Seong-Won;Cho, Yong-Min;Oh, Sung-Jong;Seong, Hwan-Hoo;Lee, Seung-Hwan;Lim, Da-Jeong
    • Asian-Australasian Journal of Animal Sciences
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    • v.25 no.5
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    • pp.613-620
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    • 2012
  • Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

Functional Prediction of Imprinted Genes in Chicken Based on a Mammalian Comparative Expression Network

  • Kim, Hyo-Young;Moon, Sun-Jin;Kim, Hee-Bal
    • Genomics & Informatics
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    • v.6 no.1
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    • pp.32-35
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    • 2008
  • Little evidence supports the existence of imprinted genes in chicken. Imprinted genes are thought to be intimately connected with the acquisition of parental resources in mammals; thus, the predicted lack of this type of gene in chicken is not surprising, given that they leave their offspring to their own heritance after conception. In this study, we identified several imprinted genes and their orthologs in human, mouse, and zebrafish, including 30 previously identified human and mouse imprinted genes. Next, using the HomoloGene database, we identified six orthologous genes in human, mouse, and chicken; however, no orthologs were identified for SLC22A18, and mouse Ppp1r9a was not included in the HomoloGene database. Thus, from our analysis, four candidate chicken imprinted genes (IGF2, UBE3A, PHLDA2, and GRB10) were identified. To expand our analysis, zebrafish was included, but no probe ID for UBE3A exists in this species. Thus, ultimately, three candidate imprinted genes (IGF2, PHLDA2, and GRB10) in chicken were identified. GRB10 was not significant in chicken and zebrafish based on the Wilcoxon-Mann-Whitney test, whereas a weak correlation between PHLDA2 in chicken and human was identified from the Spearman's rank correlation coefficient. Significant associations between human, mouse, chicken, and zebrafish were found for IGF2 and GRB10 using the Friedman's test. Based on our results, IGF2, PHLDA2, and GRB10 are candidate imprinted genes in chicken. Importantly, the strongest candidate was PHLDA2.

Statistical Method of Ranking Candidate Genes for the Biomarker

  • Kim, Byung-Soo;Kim, In-Young;Lee, Sun-Ho;Rha, Sun-Young
    • Communications for Statistical Applications and Methods
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    • v.14 no.1
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    • pp.169-182
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    • 2007
  • Receive operating characteristic (ROC) approach can be employed to rank candidate genes from a microarray experiment, in particular, for the biomarker development with the purpose of population screening of a cancer. In the cancer microarray experiment based on n patients the researcher often wants to compare the tumor tissue with the normal tissue within the same individual using a common reference RNA. Ideally, this experiment produces n pairs of microarray data. However, it is often the case that there are missing values either in the normal or tumor tissue data. Practically, we have $n_1$ pairs of complete observations, $n_2$ "normal only" and $n_3$ "tumor only" data for the microarray. We refer to this data set as a mixed data set. We develop a ROC approach on the mixed data set to rank candidate genes for the biomarker development for the colorectal cancer screening. It turns out that the correlation between two ranks in terms of ROC and t statistics based on the top 50 genes of ROC rank is less than 0.6. This result indicates that employing a right approach of ranking candidate genes for the biomarker development is important for the allocation of resources.

Association of SNP Marker in IGF-I and MYF5 Candidate Genes with Growth Traits in Korean Cattle

  • Chung, E.R.;Kim, W.T.
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.8
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    • pp.1061-1065
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    • 2005
  • Growth rate is one of the economically important quantitative traits that affect carcass quantity in beef cattle. Two genes, bovine insulin-like growth factor I (IGF-I) and myogenic factor 5 (MYF5), were chosen as candidate genes for growth traits due to their important role in growth and development of mammals. The objectives of this study were to determine gene-specific single nucleotide polymorphism (SNP) markers of the IGF-I and MYF5 positional candidate genes and to investigate their associations with growth traits in Korean cattle. Genotyping of the SNP markers in these candidate genes was carried out using the single strand conformation polymorphism (SSCP) analysis. The frequencies of A and B alleles were 0.72 and 0.28 for IGF-I gene and 0.39 and 0.61 for MYF5 gene, respectively, in Korean cattle population examined. The gene-specific SNP marker association analysis indicated that the SNP genotype in IGF-I gene showed a significant association (p<0.05) with weight at 3 months (W3), and cows with AB genotype had higher W3 than BB genotype cows. The SNP genotype of MYF5 gene was found to have a significant effect (p<0.05) on the weight at 12 months (W12) and average daily gain (ADG), and cows with BB and AB genotypes had higher W12 and ADG compared with cows with AA genotype, respectively. However, no significant association between the SNP genotypes and any other growth traits was detected. The gene-specific SNP markers in the IGF-I and MYF5 candidate genes may be useful for selection on growth traits in Korean cattle.

Current Research Status for Economically Important and Disease Related Genes in Major Livestock Species (주요 가축들의 유용유전자 및 질병관련 유전자 연구현황)

  • Lee, J.H.;Park, Chan-Kyu
    • Journal of Animal Science and Technology
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    • v.47 no.3
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    • pp.325-340
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    • 2005
  • Great success has been being achieved in identification and utilization of candidate genes affecting economically important as well as disease related traits in animals for the past two decades. This article reviews the current status of candidate genes in animals, with particular emphasis on the disease causing genes in livestock. Two different types of phenotypes, monogenic and polygenic, are also described. Finally, commercialized animal DNA markers, which can be used for the molecular breeding in near future, are discussed.

StrokeBase: A Database of Cerebrovascular Disease-related Candidate Genes

  • Kim, Young-Uk;Kim, Il-Hyun;Bang, Ok-Sun;Kim, Young-Joo
    • Genomics & Informatics
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    • v.6 no.3
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    • pp.153-156
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    • 2008
  • Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome-wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.

Signatures of positive selection underlying beef production traits in Korean cattle breeds

  • Edea, Zewdu;Jung, Kyoung Sub;Shin, Sung-Sub;Yoo, Song-Won;Choi, Jae Won;Kim, Kwan-Suk
    • Journal of Animal Science and Technology
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    • v.62 no.3
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    • pp.293-305
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    • 2020
  • The difference in the breeding programs and population history may have diversely shaped the genomes of Korean native cattle breeds. In the absence of phenotypic data, comparisons of breeds that have been subjected to different selective pressures can aid to identify genomic regions and genes controlling qualitative and complex traits. In this study to decipher genetic variation and identify evidence of divergent selection, 3 Korean cattle breeds were genotyped using the recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array. The three Korean cattle breeds clustered according to their coat color phenotypes and breeding programs. The Heugu breed reliably showed smaller effective population size at all generations considered. Across the autosomal chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the two pairwise comparisons. The most important signals of selection were detected on bovine chromosomes 14 (24.39-25.13 Mb) and 18 (13.34-15.07 Mb), containing genes related to body size, and coat color (XKR4, LYN, PLAG1, SDR16C5, TMEM68, CDH15, MC1R, and GALNS). Some of the candidate genes are also associated with meat quality traits (ACSF3, EIF2B1, BANP, APCDD1, and GALM) and harbor quantitative trait locus (QTL) for beef production traits. Further functional analysis revealed that the candidate genes (DBI, ACSF3, HINT2, GBA2, AGPAT5, SCAP, ELP6, APOB, and RBL1) were involved in gene ontology (GO) terms relevant to meat quality including fatty acid oxidation, biosynthesis, and lipid storage. Candidate genes previously known to affect beef production and quality traits could be used in the beef cattle selection strategies.

Analysis of protein-protein interaction network based on transcriptome profiling of ovine granulosa cells identifies candidate genes in cyclic recruitment of ovarian follicles

  • Talebi, Reza;Ahmadi, Ahmad;Afraz, Fazlollah
    • Journal of Animal Science and Technology
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    • v.60 no.6
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    • pp.11.1-11.7
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    • 2018
  • After pubertal, cohort of small antral follicles enters to gonadotrophin-sensitive development, called recruited follicles. This study was aimed to identify candidate genes in follicular cyclic recruitment via analysis of protein-protein interaction (PPI) network. Differentially expressed genes (DEGs) in ovine granulosa cells of small antral follicles between follicular and luteal phases were accumulated among gene/protein symbols of the Ensembl annotation. Following directed graphs, PTPN6 and FYN have the highest indegree and outdegree, respectively. Since, these hubs being up-regulated in ovine granulosa cells of small antral follicles during the follicular phase, it represents an accumulation of blood immune cells in follicular phase in comparison with luteal phase. By contrast, the up-regulated hubs in the luteal phase including CDK1, INSRR and TOP2A which stimulated DNA replication and proliferation of granulosa cells, they known as candidate genes of the cyclic recruitment.

New Evidences of Effect of Melanocortin-4 Receptor and Insulin-like Growth Factor 2 Genes on Fat Deposition and Carcass Traits in Different Pig Populations

  • Chen, J.F.;Xiong, Y.Z.;Zuo, B.;Zheng, R.;Li, F.E.;Lei, M.G.;Li, J.L.;Deng, C.Y.;Jiang, S.W.
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.11
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    • pp.1542-1547
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    • 2005
  • The Melanocortin-4 Receptor (MC4R) and Insulin-like Growth Factor 2 (IGF2) are two important candidate genes related to fat deposition and carcass traits. MC4R was found on study on human obesity and then was studied as candidate gene affecting food intake and fat deposition traits in mice and pigs. Insulin-like Growth Factor 2 (IGF2) gene plays an important role on tumor cell proliferation and muscle growth. It also affects fat traits and live weight in pigs. In this paper, MC4R and IGF2 were studied as two candidate genes associated with important economic traits such as fat deposition and carcass traits in five different pig populations. Taq I-PCR-RFLP and Bcn I-PCR-RFLP were respectively used to detect the polymorphism of genotypes of MC4R and IGF2 genes. Different MC4R genotype frequencies were observed in four populations. IGF2 genotype frequencies were also different in two populations. The results of association analysis show both MC4R and IGF2 genes were significantly associated with fat deposition and carcass traits in about 300 pigs. This work will add new evidence of MC4R and IGF2 affecting fat deposition and carcass traits in pigs and show that two genes can be used as important candidate genes for marker assistant selection (MAS) of growth and lean meat percentage in pigs.

Selection of candidate genes affecting meat quality and preliminary exploration of related molecular mechanisms in the Mashen pig

  • Gao, Pengfei;Cheng, Zhimin;Li, Meng;Zhang, Ningfang;Le, Baoyu;Zhang, Wanfeng;Song, Pengkang;Guo, Xiaohong;Li, Bugao;Cao, Guoqing
    • Asian-Australasian Journal of Animal Sciences
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    • v.32 no.8
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    • pp.1084-1094
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    • 2019
  • Objective: The aim of this study was to select the candidate genes affecting meat quality and preliminarily explore the related molecular mechanisms in the Mashen pig. Methods: The present study explored genetic factors affecting meat quality in the Mashen pig using RNA sequencing (RNA-Seq). We sequenced the transcriptomes of 180-day-old Mashen and Large White pigs using longissimus dorsi to select differentially expressed genes (DEGs). Results: The results indicated that a total of 425 genes were differentially expressed between Mashen and Large White pigs. A gene ontology enrichment analysis revealed that DEGs were mainly enriched for biological processes associated with metabolism and muscle development, while a Kyoto encyclopedia of genes and genomes analysis showed that DEGs mainly participated in signaling pathways associated with amino acid metabolism, fatty acid metabolism, and skeletal muscle differentiation. A MCODE analysis of the protein-protein interaction network indicated that the four identified subsets of genes were mainly associated with translational initiation, skeletal muscle differentiation, amino acid metabolism, and oxidative phosphorylation pathways. Conclusion: Based on the analysis results, we selected glutamic-oxaloacetic transaminase 1, malate dehydrogenase 1, pyruvate dehydrogenase 1, pyruvate dehydrogenase kinase 4, and activator protein-1 as candidate genes affecting meat quality in pigs. A discussion of the related molecular mechanisms is provided to offer a theoretical basis for future studies on the improvement of meat quality in pigs.