Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb
Year: 2007
Type: dissertation
Abstract: Cattle are vitally important to American agriculture industry, generating over 24.6\nbillion pounds of beef (by carcass weight), and 79.5 billion dollars in 2005, and over 27\nbillion dollars in milk sales in 2004. As of July 2006, the U.S. beef and dairy industry is\ncomprised of 104.5 million head of cattle, 32.4 million of which were processed in 2005.\nThe health of the animals has always been an important concern for breeders, as healthy\nanimals grow faster and are more likely to reach market weight. Animals that exhibit\nnatural resistance to disease do not require chemicals to stimulate normal weight gain,\nand are less prone to disease related wasting.\nThe major histocompatibility complex (MHC) is a collection of genes, many of\nwhich function in antigen processing and presentation. The bovine MHC (BoLA) differs\nfrom typical mammalian MHCs in that the class II region was disrupted by a\nchromosomal inversion into two subregions, designated BoLA IIa and BoLA IIb. BoLA\nIIb was transposed to a position near the centromere on bovine chromosome 23,while\nBoLA IIa retains its position in BoLA. Comparative sequence analysis of BoLA IIb with\nthe human MHC revealed the location of the region containing the proximal inversion breakpoint. Gene content, order and orientation of BoLA IIb are consistent with the single\ninversion hypothesis when compared to the corresponding region of the human class II\nMHC (HLA class II). BoLA IIb spans approximately 450 kb.\nThe genomic sequence of BoLA IIb was used to detect sequence variation\nthrough comparison to other bovine sequences, including data from the bovine genome\nproject, and two regions in the BAC scaffold used to develop the BoLA IIb sequence.\nAnalysis of the bovine genome project sequence revealed a total of 10,408 mismatching\nbases, 30 out of 231 polymorphic microsatellites, and 15 sequences corresponding to the\nvalidated SNP panel generated by the bovine genome sequencing project. The two\noverlapping regions in the BoLA IIb BAC scaffold were found to have 888\npolymorphisms, including a total of 6 out of 42 polymorphic microsatellites indicating\nthat each BAC derived from a different chromosome.
Author: Christopher Childers
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
Funder: U.S. Department of Agriculture
OpenAlex ID: W2285755894