scholarly journals Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data

2018 ◽  
Vol 9 ◽  
Author(s):  
Mohammad S. A. Bhuiyan ◽  
Dajeong Lim ◽  
Mina Park ◽  
Soohyun Lee ◽  
Yeongkuk Kim ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Carcass Traits ◽  
Genome Wide Association ◽  
Snp Data ◽  
Genome Wide ◽  
Genomic Variance ◽  
Hanwoo Cattle ◽  
Functional Partitioning

scholarly journals Haplotype-Based Genome-Wide Association Study and Identification of Candidate Genes Associated with Carcass Traits in Hanwoo Cattle

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 551
Author(s):  
Swati Srivastava ◽  
Krishnamoorthy Srikanth ◽  
Sohyoung Won ◽  
Ju-Hwan Son ◽  
Jong-Eun Park ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Haplotype Block ◽  
Genome Wide Association Study ◽  
Carcass Traits ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Hanwoo Cattle

Hanwoo, is the most popular native beef cattle in South Korea. Due to its extensive popularity, research is ongoing to enhance its carcass quality and marbling traits. In this study we conducted a haplotype-based genome-wide association study (GWAS) by constructing haplotype blocks by three methods: number of single nucleotide polymorphisms (SNPs) in a haplotype block (nsnp), length of genomic region in kb (Len) and linkage disequilibrium (LD). Significant haplotype blocks and genes associated with them were identified for carcass traits such as BFT (back fat thickness), EMA (eye Muscle area), CWT (carcass weight) and MS (marbling score). Gene-set enrichment analysis and functional annotation of genes in the significantly-associated loci revealed candidate genes, including PLCB1 and PLCB4 present on BTA13, coding for phospholipases, which might be important candidates for increasing fat deposition due to their role in lipid metabolism and adipogenesis. CEL (carboxyl ester lipase), a bile-salt activated lipase, responsible for lipid catabolic process was also identified within the significantly-associated haplotype block on BTA11. The results were validated in a different Hanwoo population. The genes and pathways identified in this study may serve as good candidates for improving carcass traits in Hanwoo cattle.

A genome-wide association study of meat and carcass traits in Australian cattle1

2011 ◽  
Vol 89 (8) ◽  
pp. 2297-2309 ◽  
Author(s):  
S. Bolormaa ◽  
L. R. Porto Neto ◽  
Y. D. Zhang ◽  
R. J. Bunch ◽  
B. E. Harrison ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Carcass Traits ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome–wide association study of carcass weight in commercial Hanwoo cattle

2018 ◽  
Vol 31 (3) ◽  
pp. 327-334 ◽  
Author(s):  
Zewdu Edea ◽  
Yeong Ho Jeoung ◽  
Sung-Sub Shin ◽  
Jaeul Ku ◽  
Sungbo Seo ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Carcass Weight ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Hanwoo Cattle

scholarly journals Genome-wide association study identifies the PLAG1-OXR1 region on BTA14 for carcass meat yield in cattle

2019 ◽  
Vol 51 (5) ◽  
pp. 137-144 ◽  
Author(s):  
Rui Zhang ◽  
Jian Miao ◽  
Yuxin Song ◽  
Wengang Zhang ◽  
Lingyang Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Carcass Traits ◽  
Coiled Coil ◽  
Genome Wide Association ◽  
Strong Linkage Disequilibrium ◽  
Meat Yield ◽  
Fatty Acid Binding ◽  
Genome Wide ◽  
A Genome

Carcass meat yield is an important carcass trait that contributes to the production efficiency and economic benefits in beef cattle. It is therefore critical to identify quantitative trait loci associated with carcass traits to enable selection. Our previous studies have identified several causal variants within the pleomorphic adenoma gene 1 ( PLAG1) and coiled-coil-helix-coiled-coil-helix domain-containing 7 ( CHCHD7) genes on BTA14 for carcass traits in Chinese Simmental. In the current study, we carried out a genome-wide association study for carcass meat yield in 472 Wagyu cattle with Bovine HD SNP array. Our results showed that 27 single nucleotide polymorphisms (SNPs) were identified for tenderloin weight (TDW), striploin weight (SPW), chuck roll weight (CRW), bicep weight (BPW), knuckle weight (KCW), and flank steak weight (FSW) in Wagyu cattle. Of these SNPs, 10 distinct SNPs were detected within the oxidation resistance 1 ( OXR1), fatty acid binding protein 5 ( FABP5), TNF receptor superfamily member 11b ( TNFRSF11B), and zinc finger CCCH-type containing 3 ( ZC3H3) genes on BTA14. Notably, three significant SNPs, BovineHD1400016738, BovineHD1400016743, and BovineHD1400016665 within OXR1, were shown strong linkage disequilibrium (r2 > 0.8) and significantly associated with CRW ( P = 1.37 × 10−8 ~ 1.94 × 10−8). Moreover, Ingenuity Pathway Analysis showed that OXR1, FABP5, and CAP1A genes were involved in a single network and FABP5 may regulate the expression of OXR1 gene via node gene, peroxisome proliferator-activated receptor gamma ( PPARG). Overall, this study suggests that OXR1 and FABP5 are candidate genes affecting carcass traits in Wagyu and the PLAG1-OXR1 region on BTA14 as a putative susceptibility locus for carcass meat yield for both Chinese Simmental and Wagyu.

scholarly journals Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Heredity ◽  
2020 ◽  
Author(s):  
Yanhua Zhang ◽  
Yuzhe Wang ◽  
Yiyi Li ◽  
Junfeng Wu ◽  
Xinlei Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Carcass Traits ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Pathway Enrichment Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

scholarly journals An improved tree-based statistical method for genome-wide association study

2018 ◽  
Author(s):  
Dwueng-Chwuan Jhwueng
Keyword(s):  
Association Study ◽  
Evolutionary History ◽  
Genome Wide Association Study ◽  
Comparative Method ◽  
Genome Wide Association ◽  
Data Set ◽  
Phylogenetic Comparative Method ◽  
Snp Data ◽  
Genome Wide ◽  
Evolutionary Relatedness

In genetic studies, quantitative traits are found possibly associated with genetic data. Due to advanced sequencing technology, many methods have been proposed in genome wide association study (GWAS) to search the single nucleotide polymorphism (SNP) associated with the traits. Currently several methods that account for the evolutionary relatedness among individuals were developed. When comparing with conventional methods without evolutionary relatedness among individuals, tree based methods are found to have better performance when the population structure increases. In this work, we extend a couple of methods in previous studies by varying the magnitude of relatedness. The magnitude of relatedness of the evolutionary history is controlled by an Ornstein-Uhlenbeck (OU) process through its parameters. Our method combines a pertinent process and phylogenetic comparative method where the incorporated evolutionary history is built by SNP data. We perform simulation as well as analyze drosophila longevity data set.

scholarly journals An improved tree-based statistical method for genome-wide association study

2018 ◽  
Author(s):  
Dwueng-Chwuan Jhwueng
Keyword(s):  
Association Study ◽  
Evolutionary History ◽  
Genome Wide Association Study ◽  
Comparative Method ◽  
Genome Wide Association ◽  
Data Set ◽  
Phylogenetic Comparative Method ◽  
Snp Data ◽  
Genome Wide ◽  
Evolutionary Relatedness

In genetic studies, quantitative traits are found possibly associated with genetic data. Due to advanced sequencing technology, many methods have been proposed in genome wide association study (GWAS) to search the single nucleotide polymorphism (SNP) associated with the traits. Currently several methods that account for the evolutionary relatedness among individuals were developed. When comparing with conventional methods without evolutionary relatedness among individuals, tree based methods are found to have better performance when the population structure increases. In this work, we extend a couple of methods in previous studies by varying the magnitude of relatedness. The magnitude of relatedness of the evolutionary history is controlled by an Ornstein-Uhlenbeck (OU) process through its parameters. Our method combines a pertinent process and phylogenetic comparative method where the incorporated evolutionary history is built by SNP data. We perform simulation as well as analyze drosophila longevity data set.

scholarly journals An improved tree-based statistical method for genome-wide association study

2018 ◽  
Author(s):  
Dwueng-Chwuan Jhwueng
Keyword(s):  
Association Study ◽  
Evolutionary History ◽  
Genome Wide Association Study ◽  
Comparative Method ◽  
Genome Wide Association ◽  
Data Set ◽  
Phylogenetic Comparative Method ◽  
Snp Data ◽  
Genome Wide ◽  
Evolutionary Relatedness

In genetic studies, quantitative traits are found possibly associated with genetic data. Due to advanced sequencing technology, many methods have been proposed in genome wide association study (GWAS) to search the single nucleotide polymorphism (SNP) associated with the traits. Currently several methods that account for the evolutionary relatedness among individuals were developed. When comparing with conventional methods without evolutionary relatedness among individuals, tree based methods are found to have better performance when the population structure increases. In this work, we extend a couple of methods in previous studies by varying the magnitude of relatedness. The magnitude of relatedness of the evolutionary history is controlled by an Ornstein-Uhlenbeck (OU) process through its parameters. Our method combines a pertinent process and phylogenetic comparative method where the incorporated evolutionary history is built by SNP data. We perform simulation as well as analyze drosophila longevity data set.

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