Jun 29, 2016

Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

BioRxiv : the Preprint Server for Biology
Lynsey K WhitacreJared E Decker

Abstract

Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by the absence of a variable distal portion of the hindlimbs. The limited genomic resources available for water buffalo, in conjunction with an unconfirmed inheritance pattern, required an original approach to identify genetic variants associated with this disease. The genomes of 4 bilaterally affected cases, 7 unilaterally affected cases, and 14 controls were sequenced. Variant calling identified 19.8 million high confidence single nucleotide polymorphisms (SNPs) and 2.8 million insertions/deletions (INDELs). A concordance analysis of SNPs and INDELs requiring all unilateral and bilateral cases and none of the controls to be homozygous for the same allele, revealed two genes, WNT7A and SMARCA4 , known to play a role in embryonic hindlimb development. Additionally, SNP alleles in NOTCH1 and RARB were homozygous exclusively in the bilaterally affected cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genome de novo assembly was then used to...Continue Reading

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Mentioned in this Paper

Embryo
Genome-Wide Association Study
Drug Carriers
Patterns
Genetic Disorders Screening
Genome
Genes
SMARCA4 gene
RARB wt Allele
SMARCA4 protein, human

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