SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.
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.
Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil marina.mortati@gmail.com.
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Dias
Centre for Genetic Improvement of Livestock, Department of Animal Bioscience, University of Guelph, Guelph, ON, Canada.
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Cánovas
Department of Animal Science, Texas A&M University, College Station, TX, USA.
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Mantilla-Rojas
Department of Animal Science, Texas A&M University, College Station, TX, USA.
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Riley
Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, SON, México.
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Luna-Nevarez
Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
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SJ
Coleman
Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
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Speidel
Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
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Enns
Department of Animal Science, University of California, Davis, CA, USA.
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Islas-Trejo
Department of Animal Science, University of California, Davis, CA, USA.
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Medrano
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia.
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Moore
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia, Australia.
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MR
Fortes
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia, Australia.|Faculty of Biotechnology, Vietnam National University of Agriculture, Vietnam.
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Nguyen
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia.
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Venus
Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
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Diaz
Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas, RS, Brasil.
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Souza
Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
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Fonseca
Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
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Baldi
Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
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Albuquerque
Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
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Thomas
Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
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Oliveira
D000818:Animals; D001483:Base Sequence; D002417:Cattle; D005260:Female; D005298:Fertility / Q000235:genetics; D016678:Genome; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D011627:Puberty / Q000235:genetics*; D012313:RNA / Q000235:genetics; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA / Q000379:methods; D012741:Sexual Maturation
D012313:RNA