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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #328136

Title: Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan

item UTSUNOMIYA, ADAM - Universidade Estadual Paulista (UNESP)
item DE ABREU SANTOS, DANIEL - Universidade Estadual Paulista (UNESP)
item BOISON, SOLOMON - Collaborator
item UTSUNOMIYA, YURI - Universidade Estadual Paulista (UNESP)
item MILANESI, MARCO - Collaborator
item Bickhart, Derek
item AJMONE-MARSAN, PAOLO - Collaborator
item SOLKNER, JOHANN - Collaborator
item GARCIA, JOSE - Universidade Estadual Paulista (UNESP)
item FONSECA, RICARDO - Universidade Estadual Paulista (UNESP)
item DA SILVA, MARCOS - Embrapa

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2016
Publication Date: 9/5/2016
Citation: Utsunomiya, A., De Abreu Santos, D.J., Boison, S.A., Utsunomiya, Y.T., Milanesi, M., Bickhart, D.M., Ajmone-Marsan, P., Solkner, J., Garcia, J.F., Fonseca, R., Da Silva, M.V. 2016. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics. 17:705.

Interpretive Summary: The current reference genome sequence that is used in analysis of cattle genetic sequence data has many mistakes. Often, these mistakes cause false positive signals within genome-wide association studies, which are frequently used to identify the association of alleles with productive traits. This study uses linkage disequilibrium -- the frequency of association of one marker with another -- to identify and correct cattle assembly mistakes, and shows that these corrections improve genome-wide association studies.

Technical Abstract: Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be easily seen by analyzing the unexpected behaviour of the linkage disequilibrium (LD) decay. A heuristic process was proposed to identify those misassembly signatures and presented the ones found in the bovine reference genome assembly UMD, release 3.1. We also discuss their implication presenting a genome wide association study case for Polled/Horned phenotype in Nellore (Bos indicus beef cattle) and the impact of misassembly on imputation accuracies in Nellore an Holstein (Bos taurus dairy cattle). We show superior resolution of local false positive signal within the Polled locus resulting from a rearrangement of SNP markers to a new location determined by our LD based signatures.