SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.

Abstract

Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.

DOI: 10.4238/gmr16019522

Cite this paper

@article{Dias2017SNPDU, title={SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.}, author={Marina Mortati Dias and {\'A}ngela C{\'a}novas and C Mantilla-Rojas and David G. Riley and Pablo Luna-Nevarez and Stephen J. Coleman and Silvia Speidel and Richard M Enns and Alma D Islas-Trejo and Juan F Medrano and Steve Moore and Marina R S Fortes and Luyen T Nguyen and Bronwyn Venus and Iara Del Pilar Solar Diaz and F{\'a}tima Pereira Souza and Larissa Fernanda Simielli da Fonseca and Fernando Baldi and L{\'u}cia Galv{\~a}o de Albuquerque and Manu G . Thomas and Henrique Nunes de Oliveira}, journal={Genetics and molecular research : GMR}, year={2017}, volume={16 1} }