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Expression quantitative loci (eQTL) analyses for bovine blood and liver

ABSTRACT: To identify expression quantitative loci (eQTL) operating in bovine blood and liver, 238 animals were genotyped uisng Illumina BovineHD genotyping arrary (777K SNPs). The genotypes were further imputed to whole genome level using 264 sequenced Holstein animals as reference.

INSTRUMENT(S): Illumina iScan

ORGANISM(S): Bos Taurus

SUBMITTER: GIGA Institute, University of Liege; Irish Cattle Breeding Federation Society Limited

PROVIDER: PRJEB66286 | EVA | 2023-09-24

REPOSITORIES: EVA

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			Action	DRS
	GplusE_SEQ_HD_raw_s1_uploaded.accessioned.vcf.gz	Vcf
	GplusE_SEQ_HD_raw_s1_uploaded.accessioned.vcf.gz.csi	Vcf
	GplusE_SEQ_HD_raw_s1_uploaded.vcf.csi	Other
	GplusE_SEQ_HD_raw_s1_uploaded.vcf.gz	Vcf

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Project description:Genetic dissection of the S rat genome has provided strong evidence for the presence of two interacting blood pressure (BP) quantitative trait loci (QTLs), termed QTL1 and QTL2, on rat chromosome 5. However, the identities of the underlying interacting genetic factors remain unknown. Further experiments targeted to identify the interacting genetic factors by the substitution mapping approach alone are difficult because of the interdependency of natural recombinations to occur at the two QTLs. We hypothesized that the interacting genetic factors underlying these two QTLs may interact at the level of gene transcription and thereby represent expression QTLs (eQTLs). To detect these interacting eQTLs, a custom QTL chip containing the annotated genes within QTL1 and QTL2 was developed and used to conduct a transcriptional profiling study of S and two congenic strains that retain either one or both the QTLs. The results uncovered an interaction between two transcription factors, DMRTA2 and NFIA. Further, the âbiological signatureâ elicited by these two transcription factors was differential between the congenic strain that retained LEW alleles at both QTL1 and 2 compared to the congenic strain that retained LEW alleles at QTL1 alone. A network of transcription factors potentially affecting BP could be traced, lending support to our hypothesis. Pairs of Cy5 and Cy3 labeled targets were co-hybridized onto either a custom long oligonucleotide microarray for the interrogation of 231 genes encompassed by QTL1 and QTL2, or a TIGR rat cDNA array consisting of 26,401 probe elements representing 20,465 unique non-QTL genes. A âflip-dyeâ or âbalanced blockâ design was used as the experimental method of choice to account for potential dye-bias labeling effects. Six âbalanced blockâ normalized files are submitted for the long oligonucleotide array interrogating the hearts from S versus S.LEW(5)x6x9 animals, fourteen âflip-dyeâ hybridizations are submitted for the cDNA array interrogating the hearts from S versus S.LEW(5)x6x9 animals, and twelve âflip-dyeâ hybridizations are submitted for the cDNA array interrogating the hearts from S versus S.LEW(5)x6x11 animals. GPR and MEV files cannot be located.

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Expression quantitative loci (eQTL) analyses for bovine blood and liver

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