Anser sp.
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ABSTRACT:
PROVIDER: PRJNA1305644 | ENA |
REPOSITORIES: ENA
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Project description:Western commercial pig breeds have been intensively selected, resulting in a sizeable, rapid, and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA-sequencing (RNA-seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the differentially expressed genes may play important roles in determining meat quality traits. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmed the differential expression of twelve selected differentially expressed genes. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.
2015-11-30 | GSE75045 | GEO
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Project description:Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip. The analysis used a polygenic model where the dropping criteria was the Call Rate ≥ 0.95. The initial dataset was composed of ~ 60,000 rows of SNPs, 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50KBeadchip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provide precision breeding methods will thereby increase breeding value. Specific aims: 1) Improve on contributions to the phenotype repository, the Council on Dairy Cattle Breeding (CDCB) for milk quality traits that are economically important for goat production while developing a corresponding DNA repository for each of the animals with significant genotype-phenotype associations. 2) Develop genomic prediction tools and provide data for a better database for tools to predict phenotypic traits by initially using the high density Goat50KSNP BeadChip for the selection of more specific SNPs associated with select signatures (genes) for phenotypic traits in American Alpine goats. 3) To establish whether a low number of goat subjects (< 300 goats) will provide statistically significant (p < 0.05) predictive capabilities for desired breeding traits in American Alpine dairy goats.
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Project description:In order to establish the correlation between biological processes and the mechanisms of gene expression controlling beef traits formation in bovine, microarray analysis was performed to capture the differences in gene expression related to beef traits profile in Longissimus Dorsi muscle tissue between 1-month and 24-month Chinese Red Steppes. 1282 (5.6%) probes showed significant differences at the two stages in the experiment, and 1008 differential gene annotations were obtained using Capitalbio molecule annotation system. BLAST analysis revealed that 1001(78.1%) probe genes shared significant similarity in amino acid sequence with other functional genes (As of June 2009). 126 genes showing strong correlation with beef traits were gained by the GO analysis. With the KEGG analysis, 63 pathways were found to be related to beef traits which involved 73 genes. 28 genes were found in a single pathway, while 35 genes were found in 2-16 pathways respectively. The panels of transcripts and gene pathways analysis in different growth stages may be helpful for the study on beef traits formation, and the gene expression profile construction in Longissimus Dorsi muscle tissues, would make a foundation for screening candidate genes which have genetic effect on meat quality in bovine. Keywords: Microarray analysis; Beef traits; Differences of gene expression; Longissimus Dorsi muscle tissue; Chinese Red Steppe
2013-06-01 | GSE21782 | GEO
Project description:In order to establish the correlation between biological processes and the mechanisms of gene expression controlling beef traits formation in bovine, microarray analysis was performed to capture the differences in gene expression related to beef traits profile in Longissimus Dorsi muscle tissue between 1-month and 24-month Chinese Red Steppes. 1282 (5.6%) probes showed significant differences at the two stages in the experiment, and 1008 differential gene annotations were obtained using Capitalbio molecule annotation system. BLAST analysis revealed that 1001(78.1%) probe genes shared significant similarity in amino acid sequence with other functional genes (As of June 2009). 126 genes showing strong correlation with beef traits were gained by the GO analysis. With the KEGG analysis, 63 pathways were found to be related to beef traits which involved 73 genes. 28 genes were found in a single pathway, while 35 genes were found in 2-16 pathways respectively. The panels of transcripts and gene pathways analysis in different growth stages may be helpful for the study on beef traits formation, and the gene expression profile construction in Longissimus Dorsi muscle tissues, would make a foundation for screening candidate genes which have genetic effect on meat quality in bovine. Keywords: Microarray analysis; Beef traits; Differences of gene expression; Longissimus Dorsi muscle tissue; Chinese Red Steppe A total of 18 bulls of the same breed (Chinese Red Steppe) were included in the study; 9 were 1month old while another 9 were 24 months old and were provided by Jilin Academy of Agricultural Sciences. They were maintained in standard conditions and fed with standard diet. The bulls were humanely killed at the slaughter house of the academy, and fresh longissimus dorsi muscle tissues were obtained during slaughter, immediately frozen in liquid nitrogen and stored at -80M-BM-0C for microarray analysis.
2013-06-01 | E-GEOD-21782 | biostudies-arrayexpress