Dataset Information

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

ABSTRACT: Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.

SUBMITTER: Low WY

PROVIDER: S-EPMC7190621 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

Low Wai Yee WY Tearle Rick R Liu Ruijie R Koren Sergey S Rhie Arang A Bickhart Derek M DM Rosen Benjamin D BD Kronenberg Zev N ZN Kingan Sarah B SB Tseng Elizabeth E Thibaud-Nissen Françoise F Martin Fergal J FJ Billis Konstantinos K Ghurye Jay J Hastie Alex R AR Lee Joyce J Pang Andy W C AWC Heaton Michael P MP Phillippy Adam M AM Hiendleder Stefan S Smith Timothy P L TPL Williams John L JL

Nature communications 20200429 1

Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that dif ...[more]

PMID: 32350247

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Project description:Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.

Dataset Information

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

Publications

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

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