Identification of Putative SNPs in Bovine Pituitary Gland Transcriptome Using RNA-Seq

Bovine pituitary gland transcriptome was investigated by RNA-seq to identify the putative SNPs that contribute to body growth trait. Investigated experimental design include young growing bulls of Polish Holstein-Friesian (P-HF), Polish Red (PR) and Hereford breeds at three developmental ages viz., 6 months, 9 months and 12 months. RNA-seq libraries were constructed from 18 young bulls, and sequenced using illumina NextSeq 500 platform. The distribution (n) of sequenced samples was as follows: six pituitary gland transcriptome samples for each breed and two pituitary gland transcriptome samples for each developmental age. Bioinformatics analysis was performed to detect SNPs, using mPileUp samtools package. The constructed database for three breeds yielded at 13 775 885 SNPs. The obtained results identified SNPs unique to a particular breed and age, and also randomly repetitive or completely unrelated to each other. The criteria of SNP filtering include two rigorous filtering conducted in parallel: at least ten reads in the locus with the probability of A ≥ 90% (598 815 SNPs), and B = 100% (495 626 SNPs). The final results comprise only a common part (A∩B), so results are valid for the whole range of 90% -100%. Using an appropriate categorization, the final results were obtained with great accuracy. Highly possible candidates for further study include:  53 nucleotides to map de novo  Bos taurus specie, 567 annotation candidates, 98 single nucleotide polymorphisms specific to Hereford breed, 14 SNPs for Polish Holstein-Frisian and one polymorphism specific and unique to young bulls of all breeds.