Truseq library kits

RNA libraries were prepared using standard Illumina TruSeq library kits. A PolyA selection step was performed as part of the library protocol to enrich for messenger RNA. Prepared libraries were then sequenced on an Illumina HiSeq 2000 instrument to generate 50nt single end reads. Raw sequence reads were post-processed to remove Illumina adapters/primer sequences. Sequence data generated has been deposited at NCBI under bioproject number PRJNA338054.

Library construction and sequencing was identical for all samples and was performed by the company Macrogen (Seoul, South Korea). RNA‐seq libraries were constructed using Illumina TruSeq library kits. Illumina HiSeq4000 (San Diego, CA, USA) instrument was used for paired‐end sequencing with 101‐bp read length resulting in 48‐79 million reads per library.

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.