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Comparative transcriptome analysis reveals genetic basis of the annual Pashmina fiber cycle in Changthangi Pashmina goats

ABSTRACT: Comparative transcriptome analysis reveals genetic basis of the annual Pashmina fiber cycle in Changthangi Pashmina goats

PROVIDER: PRJNA480975 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7518400_1.fastq.gz	Fastqsanger.gz
	SRR7518400_2.fastq.gz	Fastqsanger.gz
	SRR7518401_1.fastq.gz	Fastqsanger.gz
	SRR7518401_2.fastq.gz	Fastqsanger.gz
	SRR7518402_1.fastq.gz	Fastqsanger.gz

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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.

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Comparative transcriptome analysis reveals genetic basis of the annual Pashmina fiber cycle in Changthangi Pashmina goats

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