Genetic analysis of growth, visual scores, height, and carcass traits in Nelore cattle.

Covariance components were estimated for growth traits (BW, birth weight; WW, weaning weight; YW, yearling weight), visual scores (BQ, breed quality; CS, conformation; MS, muscling; NS, navel; PS, finishing precocity), hip height (HH), and carcass traits (BF, backfat thickness; LMA, longissimus muscle area) measured at yearling. Genetic gains were obtained and validation models on direct and maternal effects for BW and WW were fitted. Genetic correlations of growth traits with CS, PS, MS, and HH ranged from 0.20 ± 0.01 to 0.94 ± 0.01 and were positive and low with NS (0.11 ± 0.01 to 0.20 ± 0.01) and favorable with BQ (0.14 ± 0.02 to 0.37 ± 0.02). Null to moderate genetic correlations were obtained between growth and carcass traits. Genetic gains were positive and significant, except for BW. An increase of 0.76 and 0.72 kg is expected for BW and WW, respectively, per unit increase in estimated breeding value (EBV) for direct effect and an additional 0.74 and 1.43, respectively, kg per unit increase in EBV for the maternal effect. Monitoring genetic gains for HH and NS is relevant to maintain an adequate body size and a navel morphological correction, if necessary. Simultaneous selection for growth, morphological, and carcass traits in line with improve maternal performance is a feasible strategy to increase herd productivity.

Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers.

The aim of this study was to determine the extent (r2) of linkage disequilibrium (LD) in the genome of Nellore cattle, and to examine associations between single nucleotide polymorphisms (SNP) and age at first calving (AFC) and early pregnancy (EP) using a panel of high-density SNPs and data from 1182 Nellore females. A total of 13 contemporary groups (CG) were used consisting of farm, season, and year of birth. For genome-wide association analysis, SNPs with a minor allele frequency (MAF)<0.05 and animals with a call rate<0.90 were excluded, totaling 431,885 SNPs. For statistical analysis, a linear model was used for AFC and a threshold model for EP. To estimate the significance of the associations for the two traits, the model included the categorical fixed effects of CG, SNPs, and sire. In addition, the polygenic effect was included in the analysis. The additive effects and dominance deviations of Bonferroni-adjusted significant SNPs for AFC and EP were estimated using orthogonal contrasts. The average estimate of r2 for all autosomes was 0.18 at a distance of 4.8kb and the mean MAF was 0.25±0.13. The LD decreased as the distance between markers increased: 0.35 (1kb) to 0.12 (100kb). Eleven significant associations were detected in seven different chromosomes. Seven SNPs were associated with AFC and four were associated with EP. Three SNPs were significant for both traits. The identification of SNPs associated with AFC and EP may contribute for selecting sexually precocious animals.

Expression of genes related to mitochondrial function in Nellore cattle divergently ranked on residual feed intake.

Several measures have been proposed to investigate and improve feed efficiency in cattle. One of the most commonly used measure of feed efficiency is residual feed intake (RFI), which is estimated as the difference between actual feed intake and expected feed intake based on the animal's average live weight. This measure permits to identify and select the most efficient animals without selecting for higher mature weight. Mitochondrial function has been indicated as a major factor that influences RFI. The analysis of genes involved in mitochondrial function is therefore an alternative to identify molecular markers associated with higher feed efficiency. This study analyzed the expression of PGC1α, TFAM, UCP2 and UCP3 genes by quantitative real-time PCR in liver and muscle tissues of two groups of Nellore cattle divergently ranked on RFI values in order to evaluate the relationship of these genes with RFI. In liver tissue, higher expression of TFAM and UCP2 genes was observed in the negative RFI group. Expression of PGC1α gene did not differ significantly between the two groups, whereas UCP3 gene was not expressed in liver tissue. In muscle tissue, higher expression of TFAM gene was observed in the positive RFI group. Expression of PGC1α, UCP2 and UCP3 genes did not differ significantly between the two groups. These results suggest the use of TFAM and UCP2 as possible candidate gene markers in breeding programs designed to increase the feed efficiency of Nellore cattle.

Polymorphism analysis in genes of the somatotropic axis in Nellore cattle selected for growth.

The somatotropic axis consists of genes that are involved in muscular development. These genes are potential regions of study to identify possible QTL for economically important traits in beef cattle. The aim of this study was to verify the existence of GH1, POU1F1, and GHR polymorphisms in Nellore cattle to verify the influence of selection in these mutations and to analyse the association between molecular markers and body weight at different ages, yearling hip height, carcass fat thickness and loin eye area. Six hundred forty-five animals from the Centro APTA Bovinos de Corte, were genotyped by PCR-RFLP techniques. The association analyses were performed with general mixed models taking into consideration the effect of one marker, and other model taking into consideration interactions between two molecular markers. Only the molecular markers rs81109601 on GH1 and rs109136815 on GHR were polymorphic; however, they were not found to be under selection. The association of the GHR rs109136815 marker and loin eye area was observed (p<0.05), as well as the effect of interaction between the markers and the female body weight at 550 days of age (p<0.04). The interaction effect should be considered in situations where the interactivity between two genes is known.

First polymorphisms in JY-1 gene in cattle (Bos taurus indicus) and their association with sexual precocity and growth traits.

Protein JY-1 is a bovine oocyte-specific protein that regulates granulosa cell function and is involved in early embryonic development, influencing the chance of pregnancy. This study investigated molecular markers for the JY-1 gene. Seven SNPs were identified in exon 3 of the gene. The positions of the SNPs in the exon and the respective substitutions are: 163 (T/C), 281 (T/C), 321 (T/C), 532 (T/C), 652 (A/G), 679 (T/C), and 722 (G/C) (GenBank: JN592587 and JF262042.2). SNP 163 is located in a coding region and causes a proline-to-leucine substitution. The other SNPs are located in the 3'UTR region. SNPs 163, 281, 321, and 679 were genotyped in 297 Nellore heifers and the haplotypes were constructed. The haplotypes of JY-1 were not correlated with the traits studied at 5 %.

Associations of FASN gene polymorphisms with economical traits in Nellore cattle (Bos primigenius indicus).

The aim of this study was to identify molecular markers to be applied to marker-assisted selection. Three SNPs of the FASN gene were studied. PCR-RFLP was used for genotyping. The SNPs g.17924A>G, g.17860C>T and g.15603A>G all in the FASN gene were genotyped using the enzymes MscI, DdeI and Hae III, respectively. The animals were raised in extensive systems and belong to three lines selected for growth as part of the Selection Program of Zebu and Caracu Breeds, São Paulo, Brazil. Allele and genotype frequencies were compared between selection lines using the Genepop 3.4. Associations between polymorphisms and the traits studied were evaluated using the PROC MIXED procedure of the SAS/STAT 9.1.3. The G and C alleles were the most frequent alleles of the g.15603A>G and g.17860C>T loci, respectively. The g.17924A>G locus showed no polymorphism in the population studied. Allele and genotype frequencies differed significantly between the NeT line and the NeC and NeS lines. The g.15603A>G polymorphism tended to exert an additive effect on rump fat thickness and male yearling height. For g.17860C>T, an additive effect on male yearling height was observed. Genotype combination analysis revealed a significant effect on loin eye area. Although this study provided evidence of an association between the FASN gene and some traits, more detailed analyses are needed to obtain more efficient molecular markers.

MUC1 gene polymorphism in three Nelore lines selected for growth and its association with growth and carcass traits.

The objective of this study was to describe the VNTR polymorphism of the mucin 1 gene (MUC1) in three Nelore lines selected for yearling weight to determine whether allele and genotype frequencies of this polymorphism were affected by selection for growth. In addition, the effects of the polymorphism on growth and carcass traits were evaluated. Birth, weaning and yearling weights, rump height, Longissimus muscle area, backfat thickness, and rump fat thickness, were analyzed. A total of 295 Nelore heifers from the Beef Cattle Research Center, Instituto de Zootecnia de Sertãozinho, were used, including 41 of the control line, 102 of the selection line and 152 of the traditional. The selection and traditional lines comprise animals selected for higher yearling weight, whereas control line animals are selected for yearling weight close to the average. Five alleles were identified, with allele 1 being the most frequent in the three lines, especially in the lines selected for higher means for yearling weight. Heterozygosity was significantly higher in the control line. Association analyses showed significant effects of allele 1 on birth weight and weaning weight while the allele 3 exert significant effects on yearling weight and back fat thickness. Despite these findings, application of this marker to marker-assisted selection requires more consistent results based on the genotyping of a larger number of animals in order to increase the accuracy of the statistical analyses.

Association between MUC1 gene polymorphism and expected progeny differences in Nelore cattle (Bos primigenius indicus).

MUC1 is a heavily glycosylated mammalian transmembrane protein expressed by mucosal secretory tissues for both protection against microbial infection and lubrication. An important characteristic of MUC1 is its variable number of tandem repeats (VNTR) containing several sites for O-glycosylation. VNTR length has been associated with many human diseases and with certain economically important traits in domestic ruminants. The aim of the present study was to correlate the length of MUC1 gene VNTR with expected progeny differences (EPDs) obtained for growth, fertility and carcass traits. Five alleles were identified, with alleles containing short VNTRs being more frequent than those with long, thereby demonstrating that Brazilian Nelore cattle are characterized by high frequencies in short MUC1 VNTRs. Statistical analyses revealed there to be no significant association between VNTR length and EPDs for weight at 120 days (W(120) ), scrotal circumference at 365 (SC (365) ) and 450 (SC (450) ) days, age at first calving (AFC), and rib eye area (REA).