Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: 4/21/2005
Publication Date: 5/1/2005
Citation: Liu, G., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Shade, L.L. 2005. Comparative genomics:genomic variation between bovine and human genomes [abstract]. BARC Poster Day. p. 32.
Technical Abstract: Cattle researchers have accumulated hundreds of quantitative traits loci (QTL) waiting for the candidate gene identification. But only a few successful examples of gene cloning exist because the conventional process of gene discovery and functional verification is slow and tedious. Bovine Genome Project is working to sequence and annotate the genome of the cow, Bos taurus using a whole genome shotgun approach. It generates a promise to accelerate the gene cloning process in cattle. However, the whole genome shotgun assembly of the cow is less than perfect at the current coverage: it contains gaps and collapses of duplicated and repetitive sequences; the order and orientation of contigs are determined by overlay on human genome. We designed a combined computational strategy to overcome the above limitation. First, we plan to check the cow BAC span/orientation concordance or discordance after the optimal placement of cow BAC end pairs on the human genome. The pairing of cow BAC ends allows us to detect large-scale evolutionary events like insertion, deletion, inversions and rearrangements between bovine and human genomes. Next, we plan to perform a detailed comparative analysis directly on cattle-human genomic sequence alignment in individual genomic regions of high priorities. We will calculate mutation rates to screen for the genes under adaptive evolution or positive selection. We will compare cattle-human orthologous fragments to reveal the change of the genome sizes and the potential contribution from retrotranspositions. PCR, FISH and Southern blotting experiments will be planned to confirm these in silico predictions. We will exam the distribution of those events, investigate those genes which are altered and cluster them into functional groups. These studies could directly translate into candidate gene and mutation identification for economic traits and disease resistance in cattle. They would also provide insights regarding genome evolution and function, which could serve as the starting point for understanding how the genomic variation contributes to diverse phenotypes and diseases.