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

Dias, M. M., Cánovas, A, Mantilla-Rojas, C, Riley, D. G., Luna-Nevarez, P, Coleman, S. J., Speidel, S. E., Enns, R. M., Islas-Trejo, A., Medrano, J. F., Moore, S. S., Fortes, M. R. S., Nguyen, L. T., Venus, B., Diaz, I. S. D. P., Souza, F. R. P., Fonseca, L. F. S., Baldi, F., Albuquerque, L. G., Thomas, M. G. and Oliveira, H. N. (2017) SNP detection using RNA-sequences of candidate genes associated with puberty in cattle. Genetics and Molecular Research, 16 1: . doi:10.4238/gmr16019522

Author Dias, M. M.
Cánovas, A
Mantilla-Rojas, C
Riley, D. G.
Luna-Nevarez, P
Coleman, S. J.
Speidel, S. E.
Enns, R. M.
Islas-Trejo, A.
Medrano, J. F.
Moore, S. S.
Fortes, M. R. S.
Nguyen, L. T.
Venus, B.
Diaz, I. S. D. P.
Souza, F. R. P.
Fonseca, L. F. S.
Baldi, F.
Albuquerque, L. G.
Thomas, M. G.
Oliveira, H. N.
Title SNP detection using RNA-sequences of candidate genes associated with puberty in cattle
Journal name Genetics and Molecular Research   Check publisher's open access policy
ISSN 1676-5680
Publication date 2017-03-22
Sub-type Article (original research)
DOI 10.4238/gmr16019522
Open Access Status Not yet assessed
Volume 16
Issue 1
Total pages 17
Place of publication Ribeirao Preto, Brazil
Publisher Fundacao de Pesquisas Cientificas de Ribeirao Preto
Language eng
Formatted 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.
Keyword Bovine
Gene discovery
Transcript discovery
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Alliance for Agriculture and Food Innovation
School of Chemistry and Molecular Biosciences
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Created: Fri, 07 Apr 2017, 12:55:36 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences