Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle.

BACKGROUND: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample. RESULTS: Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches. CONCLUSIONS: The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.

Detection of quantitative trait loci for mineral content of Nelore longissimus dorsi muscle.

BACKGROUND: Beef cattle require dietary minerals for optimal health, production and reproduction. Concentrations of minerals in tissues are at least partly genetically determined. Mapping genomic regions that affect the mineral content of bovine longissimus dorsi muscle can contribute to the identification of genes that control mineral balance, transportation, absorption and excretion and that could be associated to metabolic disorders. METHODS: We applied a genome-wide association strategy and genotyped 373 Nelore steers from 34 half-sib families with the Illumina BovineHD BeadChip. Genome-wide association analysis was performed for mineral content of longissimus dorsi muscle using a Bayesian approach implemented in the GenSel software. RESULTS: Muscle mineral content in Bos indicus cattle was moderately heritable, with estimates ranging from 0.29 to 0.36. Our results suggest that variation in mineral content is influenced by numerous small-effect QTL (quantitative trait loci) but a large-effect QTL that explained 6.5% of the additive genetic variance in iron content was detected at 72 Mb on bovine chromosome 12. Most of the candidate genes present in the QTL regions for mineral content were involved in signal transduction, signaling pathways via integral (also called intrinsic) membrane proteins, transcription regulation or metal ion binding. CONCLUSIONS: This study identified QTL and candidate genes that affect the mineral content of skeletal muscle. Our findings provide the first step towards understanding the molecular basis of mineral balance in bovine muscle and can also serve as a basis for the study of mineral balance in other organisms.

Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle.

BACKGROUND: Meat from Bos taurus and Bos indicus breeds are an important source of nutrients for humans and intramuscular fat (IMF) influences its flavor, nutritional value and impacts human health. Human consumption of fat that contains high levels of monounsaturated fatty acids (MUFA) can reduce the concentration of undesirable cholesterol (LDL) in circulating blood. Different feeding practices and genetic variation within and between breeds influences the amount of IMF and fatty acid (FA) composition in meat. However, it is difficult and costly to determine fatty acid composition, which has precluded beef cattle breeding programs from selecting for a healthier fatty acid profile. In this study, we employed a high-density single nucleotide polymorphism (SNP) chip to genotype 386 Nellore steers, a Bos indicus breed and, a Bayesian approach to identify genomic regions and putative candidate genes that could be involved with deposition and composition of IMF. RESULTS: Twenty-three genomic regions (1-Mb SNP windows) associated with IMF deposition and FA composition that each explain ≥1% of the genetic variance were identified on chromosomes 2, 3, 6, 7, 8, 9, 10, 11, 12, 17, 26 and 27. Many of these regions were not previously detected in other breeds. The genes present in these regions were identified and some can help explain the genetic basis of deposition and composition of fat in cattle. CONCLUSIONS: The genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.

Identification of KCNJ11 as a functional candidate gene for bovine meat tenderness.

The potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) gene was investigated as a candidate for meat tenderness based on the effects reported on muscle for KCNJ11 gene knockout in rat models and its position in a quantitative trait locus (QTL) for meat tenderness in the bovine genome. Sequence variations in the KCNJ11 gene were described by sequencing six amplified fragments, covering almost the entire gene. We identified single nucleotide polymorphisms (SNP) and validated them by different approaches, taking advantage of simultaneous projects that are being developed with the same Nelore population. By sequencing the KCNJ11 in Nelore steers representing extreme phenotypes for Warner-Bratzler shear force (WBSF), it was possible to identify 22 SNPs. We validated two of the identified markers by genotyping the whole population (n = 460). Analysis of association between genotypes and WBSF values revealed a significant additive effect of a SNP at different meat aging times (P ≤ 0.05). In addition, an association between the expression levels of KCNJ11 and WBSF was found, with lower expression levels of KCNJ11 associated with more tender meat (P ≤ 0.05). The results showed that the KCNJ11 gene is a candidate mapped to a QTL for meat tenderness previously identified on BTA15 and may be useful to identify animals with genetic potential to produce tender meat. The effect of KCNJ11 observed on muscle is potentially due to changes in activity of KATP channels, which in turn influence the flow of potassium in the intracellular space, allowing establishment of the membrane potential necessary for muscle contraction.

The energy requirement for maintenance of Nellore crossbreds in tropical conditions during the finishing period.

This study determined the energy requirement for maintenance of purebred Nellore cattle and its crossbreds using data from a comparative slaughter trial in which animals were raised under the same plane of nutrition from birth through slaughter and born from a single commercial Nellore cowherd. A total of 79 castrated steers (361 ± 54 kg initial body weight [BW]) were used in a completely randomized design by age (22 mo ± 23 d of age) with four genetic groups (GG): Nellore (NL), ½ Angus × ½ Nellore (AN), ½ Canchim × ½ Nellore (CN), and ½ Simmental × ½ Nellore (SN). The experimental design provided ranges in metabolizable energy (ME) intake (MEI), BW, and average daily gain needed to develop regression equations to predict net energy for maintenance (NEm) requirements. Four steers of each GG were slaughtered to determine the initial body composition. The remaining 63 steers were assigned to different nutritional treatments (NT) by GG; ad libitum or limit-fed treatments (receiving 70% of the daily feed of the ad libitum treatment of the same GG). Full BW was recorded at birth, weaning, 12, 18, and 22 mo. In the feedlot, steers were fed for 101 d a diet containing (DM basis) 60% corn silage and 40% concentrate. No difference in age at weaning (P = 0.534) and slaughter (P = 0.179 and P = 0.896, for GG and NT, respectively) were observed. AN steers were heavier at weaning weight, yearling weight and had higher empty BW (EBW; P = 0.007, P = 0.014, and P < 0.001, respectively) in comparison to NL, CN, and SN. There were no interactions (P > 0.05) between GG and NT for any variable evaluated. When fed ad libitum, AN steers had higher daily MEI (Mcal/d; P < 0.001) in comparison to NL, CN, and SN. On a constant age basis, differences were observed on body composition (P < 0.05) between GG. The slope (P = 0.600) and intercept (P = 0.702) of the regression of log heat production on MEI were similar among GG. Evaluating at the same age and the same frame size, there were no differences in NEm requirement between Nellore and AN (P = 0.528), CN (P = 0.671), and SN (P = 0.706). The combined data indicated a NEm requirement of 86.8 kcal/d/kg0.75 EBW and a ME required for maintenance requirement had a common value of 137.53 kcal/d/kg0.75 EBW. The efficiency of energy utilization for maintenance and the efficiency of energy utilization for growth values were similar among GG (P > 0.05 and P > 0.05, respectively) and were on average 63.2% and 26.0%, respectively. However, although not statistically different, the NEm values from NL showed a decrease in NEm of 5.76% compared with AN steers.

Although several studies have shown that the maintenance energy expenditures vary with breeds, there has been no available data comparing the energy requirements of different genetic groups of beef cattle determined during the finishing phase when raised under the same plane of nutrition from birth through slaughter born from a single cowherd. This study evaluated the influence of purebred Nellore and its crosses with Simmental, Angus, and Canchim slaughtered at the same age and body composition on their net energy requirement for maintenance (NEm). Animals were reared in tropical conditions, receiving only free-choice minerals from birth through the beginning of the feedlot phase, potentially altering the intake, carcass composition, mature weight, and consequently, affecting the energy requirement for maintenance during the finishing period. The pooled data analysis for Nellore and its crosses resulted in common NEm requirement of 86.9 kcal/d/kg0.75 of empty body weight (EBW). However, although not statistically different, the NEm values from Nellore (NL) and Angus × Nellore (AN) were 85.5 and 90.8 kcal/d/kg0.75 EBW, respectively, showing a decrease in NEm of 5.76% for NL in comparison with AN steers.

Genome-wide association for growth traits in Canchim beef cattle.

Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.

Growth hormone 1 gene (GH1) polymorphisms as possible markers of the production potential of beef cattle using the Brazilian Canchim breed as a model

The growth hormone 1 gene (GH1) is a candidate gene for body weight and weight gain in cattle since it plays a fundamental role in growth regulation. We investigated the GH1 gene AluI and DdeI restriction enzyme polymorphisms, located 149 bp apart in the cattle genome, as possible markers of the production potential of Canchim crossbreed cattle, a 5/8 Charolais (Bos taurus) and 3/8 Nelore (Bos indicus) breed developed in Brazil, by evaluating the birth weight, weaning weight, yearling weight and plasma insulin-like growth factor-1 (IGF-1) concentration of 7 month to 10 months old Canchim calves (n = 204) of known genealogy and which had been genotyped for the AluI and DdeI markers. Our results showed significant effect (p < 0.05) between the homozygous DdeI+/DdeI+ polymorphism and the estimated breeding value for weaning weight (ESB-WW), while the AluI leucine homozygous (L/L) and leucine/valine (L/V) heterozygous polymorphisms showed no significant effect on the traits studied. The restriction sites of the two enzymes led to the formation of haplotypes which also exerted a significant effect (p < 0.05) on the ESB-WW, with the largest difference being 8.5 kg in favor of the homozygous L plus DdeI+/L plus DdeI+ genotype over the heterozygous L plus DdeI-/V plus DdeI+ genotype.

QTL affecting body weight in a candidate region of cattle chromosome 5

The objective of this work was to identify QTLs for liveweight in a candidate region of bovine chromosome 5. Half-sib families from two lines, one traditional and the other new, of Canchim beef cattle (5/8 Charolais + 3/8 Zebu) were genotyped for four microsatellite markers, including the microsatellite in the IGF-1 (insulin-like growth factor-1) promoter region. Significant differences in allele distribution between the two lines were found for three markers. Interval mapping analyses in this region indicated the presence of a QTL controlling birth weight (p < 0.05) and of a QTL influencing breeding value for yearling weight (p < 0.01) in the newer line of the breed. The previously identified interaction between the IGF-1 genotype and genetic group strengthens the hypothesis of a linked QTL rather than an IGF-1 effect on growth traits in the Canchim cattle