Dataset Information

Genome-wide profiling to identify unique immune markers in Indigenous cattle (Kangayam, Gir, Tharparkar, Sahiwal) vs. exotic (Holstein Friesian), and crossbred cattle (Karan Fries)

ABSTRACT: This study aims to identify immune signatures in Indigenous cattle breeds (Kangayam, Gir, Tharparkar, and Sahiwal) compared to exotic (Holstein Friesian) and crossbred (Karan Fries) cattle. A total of 6 samples were collected for three different location of each breed, resulting 108 samples (6 breeds x 6 samples x 3 locations) and these samples were pooled into 18 samples (6 breeds x 1 pooled sample x 3 locations) based on locations for whole genome sequencing. Sequencing was performed using an Illumina short-read platform NovoSeq 6000, with quality assessment and preprocessing conducted using FASTQC and Trimmomatic. Reads were mapped to the Bos taurus reference genome (ARS-UCD2.0) using BWA-Mem, and variants were identified using DELLY (structural variants) and FreeBayes (SNPs, MNPs, and indels). The study focuses on detecting common immune-related genomic variations across breeds.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Bos

SUBMITTER: SASTRA Deemed University

PROVIDER: PRJEB88461 | EVA | 2025-04-14

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	GirL1_delly.accessioned.vcf.gz	Vcf
	GirL1_delly.accessioned.vcf.gz.csi	Vcf
	GirL1_delly.vcf.csi	Other
	GirL1_delly.vcf.gz	Vcf
	GirL1_freebayes.accessioned.vcf.gz	Vcf

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Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.

Dataset Information

Genome-wide profiling to identify unique immune markers in Indigenous cattle (Kangayam, Gir, Tharparkar, Sahiwal) vs. exotic (Holstein Friesian), and crossbred cattle (Karan Fries)

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