Genomic Analysis Reveals Pleiotropic Alleles at EDN3 and BMP7 Involved in Chicken Comb Color and Egg Production
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PROVIDER: PRJNA514277 | ENA |
REPOSITORIES: ENA
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Project description:Dongxiang blue-shelled chicken, an indigenous chicken breed in China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The recent selection has also resulted in a significant difference in egg production. The red comb line (RCL) chicken produces significantly higher number of eggs than that by the dark comb line (DCL) chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. We performed genome-wide association study to identify candidate genes associated with chicken comb color using SNP array data, and we conducted selective sweep analysis to identify putative regions of selection harboring pleiotropic genes affecting both comb color and egg production.
2019-06-04 | GSE124906 | GEO
Project description:Artificial selection is often associated with numerous changes in seemingly unrelated phenotypic traits. The genetic mechanisms of correlated phenotypes probably involve pleiotropy or linkage of genes related to such phenotypes. Dongxiang blue-shelled chicken, an indigenous chicken breed of China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The red comb line chicken produces significantly higher number of eggs than the dark comb line chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. Based on the genome-wide association study results, we identified a genomic region on chromosome 20 involving EDN3 and BMP7, which is associated with hyperpigmentation of chicken comb. Further analyses by selection signatures in the two divergent lines revealed that several candidate genes, including EDN3, BMP7, BPIFB3, and PCK1, closely located on chromosome 20 are involved in the development of neural crest cell and reproductive system. The two genes EDN3 and BMP7 have known roles in regulating both ovarian function and melanogenesis, indicating the pleiotropic effect on hyperpigmentation and egg production in blue-shelled chickens. Association analysis for egg production confirmed the pleiotropic effect of selected loci identified by selection signatures. The study provides insights into phenotypic evolution due to genetic variation across the genome. The information might be useful in the current breeding efforts to develop improved breeds for egg production.
| S-EPMC6611142 | biostudies-literature
Project description:Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. After conducting a genome-wide association study (GWAS), a 36.5-kb candidate genomic region (chromosome 19:757,754-794,200) related to the Antler-comb phenotype was identified, which wholly and partially encompassed heat shock factor 5 (HSF5) and ring finger protein 43 (RNF43), respectively. HSF5 was ectopically expressed and RNF43 was up-regulated in Antler-comb chickens at embryo ages 7 and 9 (E7 and E9). We further genotyped the most significant single-nucleotide polymorphism (SNP) site, Chr19:794200, across 222 chickens of 16 breeds. We found that the major allele G in Antler-comb chickens remained highly significant across different breeds, and each Antler-comb chicken harbored an allele G. Whole-genome re-sequencing (WGS) involving 10 Hetian Antler-comb and 10 Wildtype-comb chickens reaffirmed the 36.5-kb candidate genomic region, and revealed a genomic duplication, which was 15.7 kb in length and pertained to the 5’-untranslated region and 5’-flanking region of HSF5 (Chr19:784,335-800,034), suggesting its possible role in inducing ectopic expression of HSF5 and altering expression of RNF43 during comb development (E7 and E9). The present study furthers our understanding of this novel chicken comb phenotype, and likely gives another example regarding interactions between genetic variation and phenotype.
2023-12-31 | GSE145948 | GEO
Project description:Comparison of untreated and BMP7 treated GSC We used microarrays to identify gene profiles of GSC modulated by BMP7 treatment
2015-10-01 | GSE68030 | GEO
Project description:Multipotent C3H10T1/2 cells can be induced to differentiate into mature brown adipocytes by 3-days BMP7 pretreatment followed by standard adipogenic induction. In this study, we used microRNA array to identify the microRNAs that were regulated by 3-days BMP7 treatment in C3H10T1/2 cells. One BMP7-treated sample and one vehicle-treated sample were used in this study to obtain the fold expression of microRNAs between BMP7 vs vehicle.
2015-07-22 | E-GEOD-71157 | biostudies-arrayexpress
Project description:To gain understanding in the tissue engineering of a human auricle, neocartilages generated from microtia and normal surgical remnants were compared by microarray anlaysis. Comparison of these two groups after 10 weeks development in vivo (nude mouse) revealed no statistically significant differences Comparison of normal and microtia cells, each seeded on nanoPGA and supplemented with BMP7 in a slow-release hydrogel, showed statistically significant differences in certain genes identified by microarray analysis. Such differences were also noted in several analyses comparing counterpart seeded cells without BMP7. Normal cells with and without growth factor showed several transcription and proliferative genes upregulated with addition of BMP7. Microtia with added BMP7 compared to normal neocartilage with added BMP7 was statistically significantly increased in gene levels of homeobox A10, DEAD box polypeptide 17, and arginine vasopressin.
2020-01-03 | GSE136198 | GEO
Project description:Bone morphogenetic proteins (BMPs) are members of the TGF-β superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP7, in particular, has been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We therefore explored the effects of BMP7 treatment on global gene transcription in five breast cancer cell lines during a 6-point time series. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. BMP7 had a strong effect on gene expression. The cellular functions most strongly affected were regulation of transcription and development. The observed transcriptional response followed a temporal sequence. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMP7, but also highlighted a synexpression group of genes. Finally, this study provides a list of potential novel BMP target genes relevant in breast cancer.
2012-03-22 | GSE31604 | GEO
Project description:Bone morphogenetic proteins (BMPs) are members of the TGF-β superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP7, in particular, has been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We therefore explored the effects of BMP7 treatment on global gene transcription in five breast cancer cell lines during a 6-point time series. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. BMP7 had a strong effect on gene expression. The cellular functions most strongly affected were regulation of transcription and development. The observed transcriptional response followed a temporal sequence. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMP7, but also highlighted a synexpression group of genes. Finally, this study provides a list of potential novel BMP target genes relevant in breast cancer. Two-condition experiment, vehicle-treated vs. BMP7-treated. Five cell lines were tested at six time points each, what makes a total of 30 samples. RNA samples from three biological replicates were pooled before hybridization.
2012-03-22 | E-GEOD-31604 | biostudies-arrayexpress
Project description:In this study, RNA sequencing (RNA-seq) was employed to compare the whole transcriptomic differences between six Partridge Shank chickens that are divergent in comb sizes and divided into two groups. A total of 563 differentially expressed genes (DEGs) were found in the two groups. Among these DGEs, 277 were up-regulated and 286 were down-regulated in the big comb group. According to the animal QTL database, eight DEGs including BMP2 and CHADL matched the QTLs associated with the chicken comb traits. Functional annotation analysis revealed that the DEGs were involved in cell communication and calcium signaling. Protein-protein interaction network analysis showed that STK32A, PI3KR1, EDN1, HSPA5 and HSPA8 might have great impact on comb growth. Moreover, potential alternative splicing (AS) events and single nucleotide polymorphisms (SNP) were also identified.
2017-12-08 | GSE107815 | GEO
Project description:Multipotent C3H10T1/2 cells can be induced to differentiate into mature brown adipocytes by 3-days BMP7 pretreatment followed by standard adipogenic induction. We used microarrays to detail the global programme of gene expression in C3H10T1/2 cells after 3-day BMP7 (3.3 nM) treatment.
2015-07-21 | GSE71101 | GEO