Genetical genomics of growth in a chicken model

Johnsson, Martin; Henriksen, Rie; Höglund, Andrey; Fogelholm, Jesper; Jensen, Per; Wright, I. A.

doi:10.1186/s12864-018-4441-3

Cited by 31 publications

(32 citation statements)

References 63 publications

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“…Conversely, the data structure in our research did not reveal a significant influence on abdominal fat weight between different genotypes carrying the novel SNP. This contrasting result may come from the fact that different determinants including hormonal levels, nutrition, genotypes, and even data structure are responsible for phenotypic plasticity (De-Jong and Bijma 2002;Johnsson et al, 2018). The strategy of using UCP3 polymorphism as a DNA marker would increase body weight, improve production quality and decrease abdominal fat next will cause low production costs in the poultry industry (Liu et al, 2007;Moazeni et al, 2016;An et al, 2018;Jin et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

A Novel Mutation in the Promoter Region of Avian Uncoupling Protein3 Associated with Feed Efficiency and Body Composition Traits in Broiler Chicken.

Niarami¹,

Masoudi²,

Torshizi³

et al. 2020

jwpr

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The Avian Uncoupling Protein (avUCP) belongs to the mitochondrial anion transporter family. It has a pivotal homeostatic mechanism that associated with energy regulation and lipid metabolism. The avUCP considered as a candidate gene for chicken growth-related traits according to its predominant expression is in skeletal muscle. To address genetic distance pattern of UCP3 between mammalian and avian species, sequence similarity analysis using the protein alignment of UCP3 identified the high amino acid identity between the species and complementarily detected two protein conserved regions which are known as the ADP/ATP transporter translocase and the Mitochondria-carrier. Likewise, for mutation detection, samples were genotyped, afterward PCR-SSCP method implemented. In addition, association analysis was performed for investigating single nucleotide polymorphism within the UCP3 gene relating to the given economic traits. A detected polymorphic site, on the promoter region of UCP3 (-40 T/A substitution), has displayed significant influences on the Feed Conversion Rate (FCR), Residual Feed Intake (RFI), Average Daily Gain (ADG), and Carcass Weight (CW%). In the case that, birds with genotype AA had better FCR, ADG, RFI as compared to the genotype BB and birds with genotype AA revealed a higher CW% as compared to the genotype BB. According to the obtained results from the in-silico survey, Myoblast determination protein (MyoD) was predicted as a best-matched transcription factor with a consensus sequence harboring the-40 T/A-novel SNP-in the promoter region of UCP3, where might be responsible for phenotypic variation between two genotypes. In conclusion, the result suggests important roles for UCP3 polymorphism in feed efficiency and growth traits which is better to be used in broiler chicken breeding programs.

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Section: Discussionmentioning

confidence: 99%

A Novel Mutation in the Promoter Region of Avian Uncoupling Protein3 Associated with Feed Efficiency and Body Composition Traits in Broiler Chicken.

Niarami¹,

Masoudi²,

Torshizi³

et al. 2020

jwpr

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“…These birds have been previously demonstrated to be an excellent model for the genetic regulation of brain size variation due to the large differences in brain size and composition generated via domestication [5]. By combining these results with previous analyses of the genetic regulation of the hypothalamus [17] and liver transcriptomes [18] in the same chicken intercross, we can compare the regulation of gene expression in both brain regions, as well as between the brain and distant somatic tissue. This allows a comparison of the transcriptomic regulation of these different tissues and the relative similarity between them, that can help shed light on the evolutionary pattern of brain evolution.…”

Section: Introductionmentioning

confidence: 86%

“…The microarray probesets were based on Ensembl transcripts and RefSeq mRNA sequences, with a total of 20,771 probesets representing 11,776 annotated genes. For further details about the microarray design see Johnsson et al (2018) [ 18 ]. 2–3 probes were used for each probeset and summarised to one value per probeset using the R-package ‘preprocessCore’ [ 38 ].…”

Section: Methodsmentioning

confidence: 99%

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The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution

et al. 2020

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Background: Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to their wild progenitor, the Red jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene expression in other regions of the brain (the hypothalamus) and somatic tissue (liver). Results: We identify one candidate gene that putatively regulates cerebrum size (MTF2) as well as a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being transacting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus). Conclusion: The candidate gene for cerebrum size (MTF2) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that coevolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.

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“…From previous studies done on the same intercross 1123 eQTL have been identified for the hypothalamus (17) and 1462 eQTL for liver (18). These eQTL was used to compare gene expression profiles between the tissues.…”

Section: Cerebrum Gene Profile Compared To Neuronal-and Non-neuronal mentioning

confidence: 99%

The Genetic Regulation of size Variation in the Transcriptome of the Cerebrum in the Chicken and its role in domestication and brain size evolution

Höglund

Strempfl

Fogelholm

et al. 2020

Preprint

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Background: Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power. During domestication chickens developed a larger cerebrum compared to their wild progeny, the Red Jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene-expression in other regions of the brain (the hypothalamus) and somatic tissue (liver). Results: We identify one candidate gene that putatively regulates cerebrum size ( MTF2 ) as well as identified a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being trans-acting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus). Conclusion: The candidate gene for cerebrum size ( MTF2 ) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that co-evolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.

show abstract

Genetical genomics of growth in a chicken model

Cited by 31 publications

References 63 publications

A Novel Mutation in the Promoter Region of Avian Uncoupling Protein3 Associated with Feed Efficiency and Body Composition Traits in Broiler Chicken.

A Novel Mutation in the Promoter Region of Avian Uncoupling Protein3 Associated with Feed Efficiency and Body Composition Traits in Broiler Chicken.

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution

The Genetic Regulation of size Variation in the Transcriptome of the Cerebrum in the Chicken and its role in domestication and brain size evolution

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