Performing Department
ANIMAL SCIENCES
Non Technical Summary
In U.S. Hereford cattle, hypotrichosis is a non-lethal defect with a simple autosomal recessive mode of inheritance which is often referred to in the literature as viable hypotrichosis, congenital hypotrichosis, or semi-hairless. In afflicted Herefords, the hair coat can be very short, fine, kinky, curly, or appear frosted and the tail switch can be underdeveloped. Abnormal hair can appear over all or parts of the body, often on the poll, brisket, neck and legs. Affected animals can be born with abnormal hair that shortly falls out, or are born hairless and develop a short curly coat with age. The condition may vary in expression as the animal matures, thus becoming less noticeable with age. Congenital hair defects are detrimental to all segments of the livestock industry since affected animals are more vulnerable to environmental stress, skin infections, pests, sunburn, cold stress, and have a decreased economic value independently of where they are raised. A genetic
diagnostic test is needed to effectively identify carrier animals and to allow the design of breeding programs to minimize the economic disadvantage caused by the disease. By analyzing a pedigree of Hereford cattle that segregates for hypotrichosis and genotyping 47 animals from the pedigree with the Illumina BovineSNP50 Whole Genome SNP Genotyping assay we shall identify the region of the genome that harbors the disease mutation by homozygosity mapping. We anticipate that this interval will be no larger than 1 Mb in size and that by either sequencing candidate genes within the region or by sequencing the entire region, if necessary, we shall be able to identify the mutation responsible for hypotrichosis. This will allow us to develop a commercial test for the mutation that beef producers can use to identify breeding stock that are carriers for hypotrichosis and develop breeding decisions with this knowledge.
Animal Health Component
100%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Goals / Objectives
The objective of this proposal is to identify the mutation that is responsible for hypotrichosis in Hereford cattle and to develop a molecular test to diagnose the genotypes of animals which may be at risk for the disease or for being carriers of the disease allele.
Project Methods
DNA will be provided for 47 Hereford animals in a pedigree segregating for hypotrichosis by Dr. Johnathan Beever from the University of Illinois Urbana-Champaign A high resolution genome scan will be performed at the University of Missouri-Columbia using the BovineSNP50 assay on hypotrichosis affected Hereford calves, their unaffected obligate carrier parents, and other close relatives. The BovineSNP50 kit allows the simultaneous assay of 51,386 single nucleotide polymorphisms (SNPs) that are approximately evenly spaced at intervals of 45 kb throughout the bovine genome. Missing genotypes will be estimated and corrected for any apparent genotyping errors using GENOPROB. Analysis of the data for concordance of SNP and inferred disease locus genotypes will identify the region of the bovine genome that harbors the hypotrichosis causing mutation. Because hypotrichosis is inherited as a fully penetrant autosomal recessive disease, we will look for a genomic region (GR)
where all SNPs are homozygous for the same allele in the affected calves and are heterozygous in their obligate carrier relatives. This GR will harbor the causal mutation for hypotrichosis under the autosomal recessive model of inheritance. Since linkage disequilibrium extends up to 500 kb in cattle our use of the BovineSNP50 Kit should result in the identification of ~22 SNPs in a 1 Mb region centered on the Hereford hypotrichosis locus. SNPs towards the center of this interval should be completely concordant with the disease locus genotype (homozygous in the affected calves and heterozygous in the carrier parents) and the extent of concordance will decay for more distant SNPs. Thus, we expect to have sufficient SNPs in the BovineSNP50 assay to resolve the size of the GR to much less than 1 Mb. Next, the Btau4.0 sequence (from a Hereford cow) flanking the GR will be analyzed for candidate genes and also for repetitive elements and duplications by repeat masking and BLAST analysis
against the NCBI bovine trace file archives to identify regions that might be problematic for PCR amplification. Based upon these analyses, primers will be designed for long PCR (~6 kb) within the 1 Mb region harboring the GR and any suitable candidate genes. This strategy allows the entire 1 Mb region for 4 affected and 4 obligate carrier animals to be amplified in two 96 well plates. Finally, 1 Mb region of genomic DNA that harbors the GR will be sequenced from 4 affected calves and 4 unaffected parents using an Illumina 1G Genome Analyzer to identify the causal mutation. The gene content in the vicinity of the GR will also be analyzed to identify candidate genes that should first be sequenced. For example, LIPH, EDA, DSG4, HR, and ED1 have been shown to have mutations causal for human or mouse forms of hypotrichosis. Consequently, if one of these genes is located in or close to the GR, we will focus our sequencing on the region that contains the GR and the candidate gene.