Characterization of a newly developed chicken 44K Agilent microarray

Li, Xianyao; Chiang, Hung‐Ting; Zhu, James; Dowd, Scot E.; Zhou, Huaijun

doi:10.1186/1471-2164-9-60

Cited by 70 publications

(68 citation statements)

References 58 publications

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“…The data were generated by Ark-Genomics (Talbot et al 2012). Details of the characteristics of the microarrays can be found in Li et al (2008). To compare the 24 selected birds for the two alternative homozygous genotypes at the QTL, 12 arrays were used in a dye-balanced design in a way that on each array one QQ and one qq sample were hybridized and then the red/green color were randomly assigned such that 6 red and 6 green were assigned to each genotype group.…”

Section: Gene Expression Analysesmentioning

confidence: 99%

An Expression QTL of Closely Linked Candidate Genes Affects pH of Meat in Chickens

et al. 2014

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Genetical genomics has been suggested as a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfillment of its promise, especially for loci (QTL) of moderate effects.One strategy with which to overcome the issue is to use a targeted approach. It has two clear advantages: (i) it reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point from which to investigate downstream effects of the QTL. In this study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 birds with divergent homozygous QTL genotypes were investigated. The targeted QTL was on chromosome 1 and affected initial pH of breast muscle. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in humans. The gene expression study identified 10 strong local signals that were markedly more significant compared to any genes on the rest of the genome. The differentially expressed genes all mapped to a region ,1 Mb, suggesting a remarkable reduction of the QTL interval. These results, combined with analysis of downstream effect of the QTL using gene network analysis, suggest that the QTL is controlling pH by governing oxidative stress. The results were reproducible with use of as few as four microarrays on pooled samples (with lower significance level). The results demonstrate that this cost-effective approach is promising for characterization of QTL. EXISTING genetic variation provides a valuable resource for dissection of the genetic architecture of complex traits. Despite rapid developments in genetic and genomic tools, fine dissection of complex traits has remained challenging (Ron and Weller 2007). Many genetic studies have successfully mapped and identified chromosomal regions controlling these traits, but very few succeeded in further characterization and identification of genes and causative mutations. The extent to which protein-coding changes vs. regulatory changes contribute to the variation in complex traits is not clear. However, much of the naturally occurring variation in complex traits is believed to be partially controlled by regulatory elements. Changes in these regulatory elements, either at a single nucleotide level or more complex structural changes in the region, may underlie variations in gene expression (Guryev et al. 2008). Since its formal description (Jansen and Nap 2001), genetical genomics, the combined use of genetic mapping and expression profile (or other genomic information) in segregating populations, has shown to have great potential in addressing the issue. However, the successes to date do not match the original promise. One of the main reasons is the low power of the experiments linked to the low sample size due to high cost of such experiments, especially the genomic part of the study (De Koning and Haley 2005). One of the solutions proposed to address...

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Section: Gene Expression Analysesmentioning

confidence: 99%

An Expression QTL of Closely Linked Candidate Genes Affects pH of Meat in Chickens

et al. 2014

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“…Signal intensities were normalized by LOWESS within the R statistics package (90). To correct for background signal, median signal intensity and median background intensity were used to normalize the data by LOWESS (58 (15,42). DAVID was utilized to annotate biological themes in response to day of pregnancy (day 9 vs. day 12 in CO-treated ewes) or P4 treatment (CO vs. P4) within day of pregnancy.…”

Section: Animals Mature Suffolk Ewes (Ovis Aries)mentioning

confidence: 99%

Discovery of candidate genes and pathways in the endometrium regulating ovine blastocyst growth and conceptus elongation

Satterfield

Song

Kochan

et al. 2009

Physiological Genomics

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Establishment of pregnancy in ruminants requires blastocyst growth to form an elongated conceptus that produces interferon tau, the pregnancy recognition signal, and initiates implantation. Blastocyst growth and development requires secretions from the uterine endometrium. An early increase in circulating concentrations of progesterone (P4) stimulates blastocyst growth and elongation in ruminants. This study utilized sheep as a model to identify candidate genes and regulatory networks in the endometrium that govern preimplantation blastocyst growth and development. Ewes were treated daily with either P4 or corn oil vehicle from day 1.5 after mating to either day 9 or day 12 of pregnancy when endometrium was obtained by hysterectomy. Microarray analyses revealed many differentially expressed genes in the endometria affected by day of pregnancy and early P4 treatment. In situ hybridization analyses revealed that many differentially expressed genes were expressed in a cell-specific manner within the endometrium. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to identify functional groups of genes and biological processes in the endometrium that are associated with growth and development of preimplantation blastocysts. Notably, biological processes affected by day of pregnancy and/or early P4 treatment included lipid biosynthesis and metabolism, angiogenesis, transport, extracellular space, defense and inflammatory response, proteolysis, amino acid transport and metabolism, and hormone metabolism. This transcriptomic data provides novel insights into the biology of endometrial function and preimplantation blastocyst growth and development in sheep.

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“…One obvious application of microarray technology is the transcriptional profiling in species that have neither their own genome sequenced nor a reference genome from a closely related species. For some of these species a commercial microarray based on an existing own-design are available (Agilent, Affimetrix, Nimblegen, etc) (Close et al 2004;Li et al 2008;Martinez-Godoy et al 2008;Mascarrell-Creus et al 2009;Trick et al 2009;Booman et al 2010;Curtiss et al 2011). Sunflower is a species that fits into this framework, even though a genome sequence initiative is in progress (Kane et al 2011), there is no reference genome available.…”

Section: Concerted Gene Expression Studies To Elucidate Sunflower Senmentioning

confidence: 99%

Functional Approaches to Study Leaf Senescence in Sunflower

Fernández¹,

Moschen²,

Paniego³

et al. 2012

Senescence

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Characterization of a newly developed chicken 44K Agilent microarray

Cited by 70 publications

References 58 publications

An Expression QTL of Closely Linked Candidate Genes Affects pH of Meat in Chickens

An Expression QTL of Closely Linked Candidate Genes Affects pH of Meat in Chickens

Discovery of candidate genes and pathways in the endometrium regulating ovine blastocyst growth and conceptus elongation

Functional Approaches to Study Leaf Senescence in Sunflower

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