Differential Gene Expression from Genome-Wide Microarray Analyses Distinguishes Lohmann Selected Leghorn and Lohmann Brown Layers

Habig, Christin; Geffers, Robert; Distl, O.

doi:10.1371/journal.pone.0046787

Cited by 24 publications

(28 citation statements)

References 33 publications

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“…They are excellent candidate genes for functional studies in animal sciences. Differential expression of ANK2 , which encodes a member of the ankyrin proteins required for targeting and stability of Na + /Ca ++ exchanger 1 in cardiomyocytes during cardiac muscle contraction (Mohler 2006; Hashemi et al 2009), between two layer lines, Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB), has also been found in one study using genome-wide microarray analyses (Habig et al 2012). …”

Section: Discussionmentioning

confidence: 87%

Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

Fan

Chen

et al. 2013

Genome Biology and Evolution

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Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.

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Section: Discussionmentioning

confidence: 87%

Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

Fan

Chen

et al. 2013

Genome Biology and Evolution

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“…A 2-fold or greater change in gene expression was identified on 151 probe sets in the previous experiment [14]. These 151 probe sets could be assigned to 79 different genes.…”

Section: Resultsmentioning

confidence: 99%

A Replication Study for Genome-Wide Gene Expression Levels in Two Layer Lines Elucidates Differentially Expressed Genes of Pathways Involved in Bone Remodeling and Immune Responsiveness

2014

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The current replication study confirmed significant differences in gene expression profiles of the cerebrum among the two commercial layer lines Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB). Microarray analyses were performed for 30 LSL and another 30 LB laying hens kept in the small group housing system Eurovent German. A total of 14,103 microarray probe sets using customized Affymetrix ChiGene-1_0-st Arrays with 20,399 probe sets were differentially expressed among the two layer lines LSL and LB (FDR adjusted P-value <0.05). An at least 2-fold change in expression levels could be observed for 388 of these probe sets. In LSL, 214 of the 388 probe sets were down- and 174 were up-regulated and vice versa for the LB layer line. Among the 174 up-regulated probe sets in LSL, we identified 51 significantly enriched Gene ontology (GO) terms of the biological process category. A total of 63 enriched GO-terms could be identified for the 214 down-regulated probe sets of the layer line LSL. We identified nine genes significantly differentially expressed between the two layer lines in both microarray experiments. These genes play a crucial role in protection of neuronal cells from oxidative stress, bone mineral density and immune response among the two layer lines LSL and LB. Thus, the different regulation of these genes may significantly contribute to phenotypic trait differences among these layer lines. In conclusion, these novel findings provide a basis for further research to improve animal welfare in laying hens and these layer lines may be of general interest as an animal model.

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“…The results of these studies provide valuable insight into the gene expression and the cellular basis of FE in broilers. (Habig et al, 2012) Affymetrix GeneChip Chicken Genome Array…”

Section: Referencementioning

confidence: 99%

Microarray resources for genetic and genomic studies in chicken: A review

Gheyas

Burt

2013

Genesis

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Summary: Advent of microarray technologies revolutionized the nature and scope of genetic and genomic research in human and other species by allowing massively parallel analysis of thousands of genomic sites. They have been used for diverse purposes such as for transcriptome analysis, CNV detection, SNP and CNV genotyping, studying DNA-protein interaction, and detection of genome methylation. Microarrays have also made invaluable contributions to research in chicken which is an important model organism for studying embryology, immunology, oncology, virology, evolution, genetics, and genomics and also for other avian species. Despite their huge contributions in life science research, the future of microarrays is now being questioned with the advent of massively parallel next generation sequencing (NGS) technologies, which promise to overcome some of the limitations of microarray platforms. In this article we review the various microarray resources developed for chicken and their past and potential future applications. We also discuss about the future of microarrays in the NGS era particularly in the context of livestock genetics. We argue that even though NGS promises some major advantages-in particular, offers the opportunity to discover novel elements in the genome-microarrays will continue to be major tools for research and practice in the field of livestock genetics/genomics due to their affordability, high throughput nature, mature established technologies and ease of application. Moreover, with advent of new microarray technologies like capture arrays, the NGS and microarrays are expected to complement each other in future research in life science. genesis 51:337-356. V C 2013 Wiley Periodicals, Inc.

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Differential Gene Expression from Genome-Wide Microarray Analyses Distinguishes Lohmann Selected Leghorn and Lohmann Brown Layers

Cited by 24 publications

References 33 publications

Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

A Replication Study for Genome-Wide Gene Expression Levels in Two Layer Lines Elucidates Differentially Expressed Genes of Pathways Involved in Bone Remodeling and Immune Responsiveness

Microarray resources for genetic and genomic studies in chicken: A review

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