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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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Dias, M. M. [1] ; Canovas, A. [2] ; Mantilla-Rojas, C. [3] ; Riley, D. G. [3] ; Luna-Nevarez, P. [4] ; Coleman, S. J. [5] ; Speidel, S. E. [5] ; Enns, R. M. [5] ; Islas-Trejo, A. [6] ; Medrano, J. F. [6] ; Moore, S. S. [7] ; Fortes, M. R. S. [8] ; Nguyen, L. T. [8, 9] ; Venus, B. [7] ; Diaz, I. S. D. P. [1] ; Souza, F. R. P. [10] ; Fonseca, L. F. S. [1] ; Baldi, F. [1] ; Albuquerque, L. G. [1] ; Thomas, M. G. [5] ; Oliveira, H. N. [1]
Total Authors: 21
Affiliation:
[1] Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, Jaboticabal, SP - Brazil
[2] Univ Guelph, Ctr Genet Improvement Livestock, Dept Anim Biosci, Guelph, ON - Canada
[3] Texas A&M Univ, Dept Anim Sci, College Stn, TX - USA
[4] Inst Tecnol Sonora, Dept Ciencias Agron & Vet, Obregon, Son - Mexico
[5] Colorado State Univ, Dept Anim Sci, Ft Collins, CO 80523 - USA
[6] Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 - USA
[7] Univ Queensland, Queensland Alliance Agr & Food Innovat, Brisbane, Qld - Australia
[8] Univ Queensland, Sch Chem & Mol Biosci, St Lucia, Qld - Australia
[9] Vietnam Natl Univ Agr, Fac Biotechnol, Hanoi - Vietnam
[10] Univ Fed Pelotas, Dept Ecol Zool & Genet, Pelotas, RS - Brazil
Total Affiliations: 10
Document type: Journal article
Source: Genetics and Molecular Research; v. 16, n. 1 MAR 24 2017.
Web of Science Citations: 8
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. (AU)

FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
Grantee:Lucia Galvão de Albuquerque
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 11/21241-0 - Study of the genetic variability of meat fatty acid profile in Nelore cattle finished in feedlot
Grantee:Fernando Sebastián Baldi Rey
Support Opportunities: Research Grants - Young Investigators Grants