Genome-Wide Association Study Towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats
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PROVIDER: PRJNA607190 | ENA |
REPOSITORIES: ENA
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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.
2020-02-19 | GSE145419 | GEO
Project description:This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. 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 criterion was a call rate ≥ 0.95. The initial dataset was composed of ~60,000 rows of SNPs and 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 50K BeadChip 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 provides precision breeding methods will thereby increase the breeding value.
| S-EPMC7403911 | biostudies-literature
Project description:Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats
| PRJEB33356 | ENA
Project description:Using WGBS we investigated blood DNA methylation profiles of Cooinda the Alpine dingo and determined putative regulatory elements (unmethylated regions, UMRs, and lowly methylated regions, LMRs).
2023-02-24 | GSE212509 | GEO
Project description:Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner-Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time. Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05). RNA-seq results showed that a total of 10,633 genes were differentially expressed (5,194 up regulated; 5,439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis. The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.
2022-08-14 | GSE210823 | GEO
Project description:Land cover change has long been recognized that marked effect the amount of soil organic carbon. However, little is known about microbial-mediated effect processes and mechanism on soil organic carbon. In this study, the soil samples in a degenerated succession from alpine meadow to alpine steppe meadow in Qinghai-Tibetan Plateau degenerated, were analyzed by using GeoChip functional gene arrays.
2017-01-05 | GSE93158 | GEO
Project description:Robust human-goat chimerism was achieved by transplanting human CD34+Lin- cord blood cells into fetal goats. We observed a broad distribution of GFP-marked human cells in non-hematopoietic organs including kidney, muscle, lung, and heart of transplant goats. Various marker techniques indicated that human genes were expressed in chimeric livers and blood.
2007-07-19 | E-GEOD-1801 | biostudies-arrayexpress
Project description:Transportation stress causes significant changes in physiological responses in goats; however, studies exploring the transcriptome of stress are very limited. This study was conducted to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control). Blood samples were collected before and after treatment for stress hormone, metabolite, and transcriptomic analysis. RNA-Seq technology was used to obtain the transcriptome profiles of blood. Analysis of physiological data using SAS showed that plasma cortisol concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group. A similar effect was noticed in plasma non-esterified fatty acid concentrations. Glucose concentrations were the lowest in the control group, highest in the 180 min group, and intermediate in the 30 min group (P < 0.01, while plasma creatine kinase concentrations were not significantly influenced by TRT. Neutrophil counts were higher (P < 0.01) and lymphocyte counts were lower (P < 0.01) in 180 min group compared to 30 min or control groups. The DESeq2 software identified a total of 430 DEGs for control vs. 30 min comparison, of which 127 genes were upregulated. For 180 min vs. control comparison, 741 DEGs were upregulated. Enrichment analysis of DEGs related to transportation stress through Gene Ontology and KEGG databases revealed that the DEGs related to inflammatory pathways, caspases, and apoptosis such as IL1R2, CASP14, CD14, TLR4, and MAPK14 were highly expressed in the transported group of goats compared to non-transported goats. Stress in goats leads to a sequence of events at cellular and molecular levels that causes inflammation and apoptosis and is also reflected in blood metabolites and leukocyte counts.
2022-08-14 | GSE210841 | GEO
Project description:power plant metagenome Raw sequence reads
| PRJNA407460 | ENA