Genome Sequencing of Limonero Cattle

Genome sequence for individuals of the Limonero breed (n = 9) animals were obtained using Illumina Short Read Sequence technology (Bentley et al., 2008 (link)). The set of individuals included seven slick, one normal, and one long hair phenotype. Barcoded sequencing libraries were prepared from hair samples using Illumina TruSeq library kits and run as 6-plex pools on an Illumina HiSeq 2000. Sequence data quality was assessed with FastQC, and was aligned to the UMD3.1 (Zimin et al., 2009 (link)) reference genome (Ensembl release 73) using BWA MEM v0.7.9 (Li and Durbin, 2009 (link)). SNP and INDEL calls were generated using samtools v0.2.0 (Li et al., 2009 (link)) and the functional annotation of variant calls was accomplished using SNPeff 3.6c (build 2014-05-20) (Cingolani et al., 2012 (link)). The whole-genome sequences of the Limonero cattle including the metadata on the coat phenotype were deposited at https://www.ncbi.nlm.nih.gov/bioproject/ under BioProject PRJNA422135. The SNP called using these sequences within the critical genomic interval are available as downloads from https://github.com/USDA-ARS-AGIL/bos-taurus-slick-coat-variations.

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Porto-Neto L.R., Bickhart D.M., Landaeta-Hernandez A.J., Utsunomiya Y.T., Pagan M., Jimenez E., Hansen P.J., Dikmen S., Schroeder S.G., Kim E.S., Sun J., Crespo E., Amati N., Cole J.B., Null D.J., Garcia J.F., Reverter A., Barendse W, & Sonstegard T.S. (2018). Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor. Frontiers in Genetics, 9, 57.

Publication 2018

TruSeq library kits HiSeq 2000

Animals Bos taurus Cattle Genomic Hair Indel Library Phenotype

Corresponding Organization :

Other organizations : Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, U.S. Dairy Forage Research Center, United States Department of Agriculture, Agricultural Research Service, University of Zulia, Universidade Estadual Paulista (Unesp), University of Puerto Rico-Mayaguez, University of Florida, Bursa Uludağ Üni̇versi̇tesi̇, South China Agricultural University

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Variable analysis

independent variables

Genome sequence for individuals of the Limonero breed

dependent variables

Coat phenotype (slick, normal, long hair)

control variables

Illumina Short Read Sequence technology
Barcoded sequencing libraries prepared from hair samples using Illumina TruSeq library kits
Sequence data quality assessed with FastQC
Sequence data aligned to the UMD3.1 reference genome using BWA MEM v0.7.9
SNP and INDEL calls generated using samtools v0.2.0
Functional annotation of variant calls using SNPeff 3.6c

Annotations

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