Dataset Information

Whole genome sequencing of Red Chittagong Cattle (RCC) cattle and insight into candidate gene mutations associated with disease resistance

ABSTRACT: The aim of this research is to investigate Red Chittagong Cattle (RCC) genome to create a morecomplete catalog of genetic variants, a resource for future studies to understand variationunderlying important phenotypes (disease resistance and beef production)

INSTRUMENT(S): -

ORGANISM(S): Bos Indicus

SUBMITTER: Chattogram Veterinary and Animal Sciences University

PROVIDER: PRJEB55361 | EVA | 2022-08-14

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	RCC_variants_BD_CVASU_Ashutosh.accessioned.vcf.gz	Vcf
	RCC_variants_BD_CVASU_Ashutosh.accessioned.vcf.gz.csi	Vcf
	RCC_variants_BD_CVASU_Ashutosh.vcf.csi	Other
	RCC_variants_BD_CVASU_Ashutosh.vcf.gz	Vcf
	Y_variants.accessioned.vcf.gz	Vcf

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Project description:BackgroundIf unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population.ResultsSeven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Following the imputation, no variants were identified that were fully concordant with the marker-based diplotypes.ConclusionsSelective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.

Dataset Information

Whole genome sequencing of Red Chittagong Cattle (RCC) cattle and insight into candidate gene mutations associated with disease resistance

Dataset's files

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