RESUMO
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.
Assuntos
Puberdade/genética , Animais , Sequência de Bases , Bovinos , Feminino , Fertilidade/genética , Genoma , Masculino , Polimorfismo de Nucleotídeo Único , Gravidez , RNA/genética , Seleção Genética , Análise de Sequência de RNA/métodos , Maturidade SexualRESUMO
The aim of this study was to evaluate the effect of genetic variants on candidate genes corresponding to the sterol recognition element-binding protein-1 (SREBP-1) signaling pathway and stearoyl-CoA desaturases (SCD1 and SCD5) on muscle fatty acid (FA) composition of Brangus steers fattened on grass. FA profiles were measured on Longissimus lumborum muscle samples using a gas chromatography-flame ionization detection technique. A total of 43 tag single-nucleotide polymorphisms on the SCD1, SCD5, SREBP-1, SCAP, INSIG1, INSIG2, MBTPS1, MBTPS2, and SRPR genes were genotyped on 246 steers to perform a marker-trait association study. To evaluate the influence of the Indicine breed in the composite breed, additional groups of 48 Angus, 18 Hereford, 75 Hereford x Angus, and 36 Limousin x Hereford-Angus steers were also genotyped. To perform the association analysis, FA data were grouped according to the number of carbon atoms and/or number of double bonds (i.e. SFA, MUFA, PUFA, etc.). In addition, different indexes that reflect the activity of FA desaturase and elongase enzymes were calculated. SCD1 markers significantly affected C14:1/(C14:0 + C14:1) and C18:1/(C18:0 + C18:1) indexes, whereas one SNP in SCD5 was correlated with the C16:1/(C16:0 + C16:1) index. Polymorphisms in the signal recognition particle receptor (SRPR) gene were associated with all the estimated desaturase indexes. Because the evaluated markers showed no effect on total lipid content of beef, this work supports the potential utilization of these markers for the improvement of grass-fed beef without undesirable side effects.
Assuntos
Bovinos/genética , Variação Genética , Carne/análise , Valor Nutritivo/genética , Transdução de Sinais/genética , Proteína de Ligação a Elemento Regulador de Esterol 1/genética , Animais , Argentina , Cromatografia Gasosa/veterinária , Ácidos Graxos/análise , Marcadores Genéticos , Genótipo , Modelos Lineares , Músculo Esquelético/química , Poaceae , Receptores Citoplasmáticos e Nucleares/genética , Receptores de Peptídeos/genética , Estearoil-CoA Dessaturase/genéticaRESUMO
The somatotropic axis is a major regulatory pathway of energy metabolism during postnatal growth in mammals. Genes involved in this pathway influence many economically important traits. The association of selected SNPs in these genes with carcass traits was examined in grazing Brangus steers. These traits included final live weight, ultrasound backfat thickness (UBFT), rib-eye area, kidney fat weight, hot carcass weight, and intramuscular fat percentage (%IMF). Genomic DNA (N = 246) was genotyped for a panel of 15 tag SNPs located in the growth hormone receptor (GHR), insulin-like growth factor I, insulin-like growth factor-binding protein 6, pro-melanin-concentrating hormone, suppressor of cytokine signaling 2, and signal transducer and activator of transcription 6 (STAT6) genes. Allelic and haplotype frequencies were compared with those of a sample of European breeds (N = 177 steers). Two tag SNPs in the GHR affected %IMF; one of them (ss86273136) was also strongly associated with UBFT (P < 0.003). The frequency of the most favorable GHR haplotype for %IMF was lower in Brangus steers. Moreover, the haplotype carrying two unfavorable alleles was present at a frequency of 31% in this group. Four tag SNPs on STAT6 had a significant effect on UBFT. One of these, SNP ss115492467, was also associated with %IMF. The STAT6 haplotype, including all the alleles favoring UBFT, was the most abundant variant (34%) in the European cattle, while it had a frequency of 14% in the Brangus steers. The four less favorable variants (absent in the European cattle) were found at a frequency of 38% in the Brangus steers. These results support the association of GHR and STAT6 SNP with carcass traits in composite breeds, such as Brangus, under grazing conditions.
Assuntos
Composição Corporal/genética , Bovinos/anatomia & histologia , Estudos de Associação Genética , Marcadores Genéticos , Aumento de Peso/genética , Tecido Adiposo/química , Alelos , Animais , Argentina , Pesos e Medidas Corporais , Cruzamento , Bovinos/genética , Genótipo , Haplótipos , Proteínas de Ligação a Fator de Crescimento Semelhante a Insulina/genética , Fator de Crescimento Insulin-Like I/genética , Carne , Músculo Esquelético/química , Fenótipo , Polimorfismo de Nucleotídeo Único , Receptores da Somatotropina/genética , Fator de Transcrição STAT6/genéticaRESUMO
Suppressor of cytokine signaling 2 (SOCS2) is a negative regulator of growth hormone signaling. The deletion of SOCS2 in mice results in a 30-50% increase in post-natal growth. In an effort to identify polymorphisms in the SOCS2 gene that may be associated with body size in dogs, we characterized the canine SOCS2 gene and analyzed its genetic diversity among small and large dog breeds. The study was carried out on a total of 520 dogs from 66 different breeds. Dogs were classified as large or small based on height and weight as determined by their respective American Kennel Club breed standards. The SH2 and SOCS domains of the canine SOCS2 gene were sequenced in 32 dogs from different breeds. Only one non-synonymous sequence variant (DQ415457:g.326G>T) was detected which corresponds to an amino acid change (Asp127Tyr). All samples were genotyped by PCR/RFLP and the allele frequencies were determined for each dog breed. The T allele was distributed primarily among European large dog breeds with a gene frequency ranging from 0.72 to 0.04. The nature of the nucleotide change and the effect on the protein together with the finding of a QTL related to body size in the same CFA15 region by other researchers suggest canine SOCS2 as a potential candidate gene for body size in dogs. Future studies will be needed to clarify the role of the 326G>T polymorphism and its interaction with genes like growth hormone and insulin-like growth factor 1.
Assuntos
Tamanho Corporal/genética , Cães/genética , Frequência do Gene/genética , Proteínas Supressoras da Sinalização de Citocina/genética , Animais , Genótipo , Humanos , Camundongos , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição , Ratos , Alinhamento de Sequência , Lobos/genéticaRESUMO
Suppressor of cytokine signaling 2 (SOCS2) is a negative regulator of growth hormone signaling. The deletion of SOCS2 in mice results in a 30-50% increase in post-natal growth. In an effort to identify polymorphisms in the SOCS2 gene that may be associated with body size in dogs, we characterized the canine SOCS2 gene and analyzed its genetic diversity among small and large dog breeds. The study was carried out on a total of 520 dogs from 66 different breeds. Dogs were classified as large or small based on height and weight as determined by their respective American Kennel Club breed standards. The SH2 and SOCS domains of the canine SOCS2 gene were sequenced in 32 dogs from different breeds. Only one non-synonymous sequence variant (DQ415457:g.326G>T) was detected which corresponds to an amino acid change (Asp127Tyr). All samples were genotyped by PCR/RFLP and the allele frequencies were determined for each dog breed. The T allele was distributed primarily among European large dog breeds with a gene frequency ranging from 0.72 to 0.04. The nature of the nucleotide change and the effect on the protein together with the finding of a QTL related to body size in the same CFA15 region by other researchers suggest canine SOCS2 as a potential candidate gene for body size in dogs. Future studies will be needed to clarify the role of the 326G>T polymorphism and its interaction with genes like growth hormone and insulin-like growth factor 1
Assuntos
Humanos , Animais , Bovinos , Cães , Camundongos , Ratos , Tamanho Corporal/genética , Cães/genética , Frequência do Gene/genética , Proteínas Supressoras da Sinalização de Citocina/genética , Genótipo , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição , Alinhamento de Sequência , SuínosRESUMO
This work describes the construction and characterization of a sequence characterized amplified DNA region (SCAR DNA), designated OmyP9, that was derived from a RAPD marker associated with the sex chromosomes in rainbow trout. A RsaI restriction fragment length polymorphism in OmyP9 identifies variants A, B and C. We found six OmyP9 variant phenotypes - A, B, C, AB, BC and ABC, in 186 individuals of seven different rainbow trout strains. The patterns of inheritance of OmyP9 in 139 fingerlings from 10 crosses of three strains of rainbow trout were studied. The males had a greater representation of the A variant (93.3%) suggesting an association with the Y chromosome. All male fingerlings analysed inherited the A variant from their male parents. These results support the hypothesis that OmyP9 is located on the sex chromosomes of rainbow trout, and that for the males studied the A variant is located on the Y chromosome in a region close to sex determinants and/or in a sector where the genetic recombination between X and Y is restricted. The present evidence also supports our previous hypothesis that OmyP9 is organized as a tandem repeated sequence in the sex chromosomes of rainbow trout. We feel that the OmyP9 RsaI marker can be used for sex identification in crosses where it is possible to determine the phenotype of the parents.