R. R. Tullio

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

BackgroundMeat 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.ResultsTwenty-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.ConclusionsThe 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.

Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes

BackgroundEfficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock remains poorly understood. Recent developments in molecular genetics, such as platforms for genome-wide genotyping and sequencing, provide an opportunity to identify genes and pathways that influence production traits. It is known that transcriptional networks influence feed efficiency-related traits such as growth and energy balance. This study sought to identify differentially expressed genes in animals genetically divergent for Residual Feed Intake (RFI), using RNA sequencing methodology (RNA-seq) to obtain information from genome-wide expression profiles in the liver tissues of Nelore cattle.ResultsDifferential gene expression analysis between high Residual Feed Intake (HRFI, inefficient) and low Residual Feed Intake (LRFI, efficient) groups was performed to provide insights into the molecular mechanisms that underlie feed efficiency-related traits in beef cattle. A total of 112 annotated genes were identified as being differentially expressed between animals with divergent RFI phenotypes. These genes are involved in ion transport and metal ion binding; act as membrane or transmembrane proteins; and belong to gene clusters that are likely related to the transport and catalysis of molecules through the cell membrane and essential mechanisms of nutrient absorption. Genes with functions in cellular signaling, growth and proliferation, cell death and survival were also differentially expressed. Among the over-represented pathways were drug or xenobiotic metabolism, complement and coagulation cascades, NRF2-mediated oxidative stress, melatonin degradation and glutathione metabolism.ConclusionsOur data provide new insights and perspectives on the genetic basis of feed efficiency in cattle. Some previously identified mechanisms were supported and new pathways controlling feed efficiency in Nelore cattle were discovered. We potentially identified genes and pathways that play key roles in hepatic metabolic adaptations to oxidative stress such as those involved in antioxidant mechanisms. These results improve our understanding of the metabolic mechanisms underlying feed efficiency in beef cattle and will help develop strategies for selection towards the desired phenotype.

Características da carcaça e da carne de bovinos sob diferentes dietas, em confinamento

The carcass and meat qualitative characteristics of 10 young bulls, 10 castrated males, and 10 females of Canchim breed finished in feedlot were evaluated. Animals were fed: 1 - corn silage and concentrate containing soybean meal, corn and citrus pulp (CS), and 2 - sugar cane and concentrate containing soybean meal, corn, sunflower grains, and citrus pulp (SC). The data were analized by completely randomized design in a factorial 3x2 arrangement (three sexual conditions x two diets), and the experimental period lasted 105 days. No interactions were observed and the young bulls presented higher (P<0.05) hot carcass weights and loin area, higher hindquarter and lower forequarter yields in relation to the castrated males and females. The samples of loin did not show differences among treatments in relation to shear force, pH, total losses due dripping on capacity of water retention, and meat color. The castrated males and females presented better texture of meat. The CS and SC diets can be used in finishing cattle under confinement.

Composição química e perfil de ácidos graxos da carne de bovinos de diferentes condições sexuais recebendo silagem de milho e concentrado ou cana-de-açúcar e concentrado contendo grãos de girassol

O objetivo neste trabalho foi avaliar as caracteristicas quimicas e a composicao em acidos graxos do contrafile (musculo Longissimus) de tourinhos, novilhos e novilhas da raca Canchim. Os animais foram terminados em confinamento com duas dietas experimentais, uma com silagem de milho e concentrado e outra com cana-de-acucar e concentrado contendo graos de girassol. Os teores de umidade, proteina e minerais no musculo nao diferiram entre as dietas e as condicoes sexuais dos animais. A carne de novilhos terminados com a dieta com graos de girassol apresentou maior teor de lipidios (3,31%) em comparacao a dos animais de outras categorias. Os animais que receberam a dieta com graos de girassol apresentaram maiores concentracoes de acido linoleico conjugado (18:2 cis9, trans-11) (0,73%) e acidos graxos poliinsaturados (8,12%) no musculo, e tambem relacoes mais elevadas de acidos graxos insaturados:saturados (0,93) e acidos graxos poliinsaturados:saturados (0,16) em comparacao aqueles que receberam a dieta convencional, a base de silagem de milho (0,34%; 6,31%; 0,86; e 0,11, respectivamente). A composicao em acidos graxos da carne de bovinos pode ser melhorada com a utilizacao de cana-de-acucar e graos de girassol na dieta dos animais terminados em confinamento.The objective in this work was to evaluate the chemical characteristics and the fatty acids composition of beef loin (Longissimus muscle) of young bulls, steers and heifers of Canchim breed. The animals were finished in feedlot system and fed two experimental diets, one with corn silage and concentrate (SIL) and the other with sugar cane, as exclusive roughage, and concentrate containing sunflower grains (CNA). Differences were not detected in relation to moisture, protein and mineral contents between diets or sexual categories. The meat from steers that received the CNA diet had higher lipid content (3.31%) in relation to meat from young bulls and heifers receiving the same diet. The meat from animals that received the CNA diet had higher concentrations of conjugated linoleic acid (18:2 cis-9, trans-11) and polyunsaturated fatty acids, and showed higher unsaturated fatty acids:saturated fatty acids and polyunsaturated fatty acids:saturated fatty acids ratios than those of animals fed with SIL diet; respectively 0.73 and 0.34%; 8.12 and 6.31%; 0.93 and 0.86; 0.16 and 0.11. The fatty acids composition in meat from beef cattle can be improved with the utilization of sugar cane and sunflower grains in the finishing diet.

Avaliação econômica e desempenho de machos e fêmeas Canchim em confinamento alimentados com dietas à base de silagem de milho e concentrado ou cana-de-açúcar e concentrado contendo grãos de girassol

The objective of this experiment was to evaluate the effects of diets with corn silage or with sugar cane + sunflower seed and influence of sexual categories of fedlot young cattle on the performance and economic results of this production system. Thirty animals of Canchim breed (10 young bulls, 10 castrated males and 10 females) averagfing 15 months old and 289 kg BW were housed in individual stalls, for 105 days and weighted in the beginning of the experiment and every 35 days. At the end of the feedlot, all the animals were slaughtered in commercial frigorific and measures of carcass characteristics were made. Young bulls showed higher nutrient intakes as compared to females, in absolute values and in relation LW values. The castrated males presented intermediary values, not differing from young bulls and females. Young bulls presented higher daily weight gain and muscular development, represented by the largest rib eye area. They were also more efficient as for feed conversion and carcass yield. No effect was observed for diets on the ingestion of nutrients, except for EE, that was higher for the diet with sugarcane + sunflower seed, with more of this nutrient. Diets also did not influence performance of the animals. Diet with corn silage showed more economically viable to raised young cattle in fed lot finishing. Young bulls were the animals more adequate for the exploration of young cattle in feedlot, independently of diet.

Identification of genomic regions associated with feed efficiency in Nelore cattle

BackgroundFeed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology.ResultsThirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7.ConclusionsSome genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.

Heat shock and structural proteins associated with meat tenderness in Nellore beef cattle, a Bos indicus breed.

Nellore beef cattle, a Bos indicus (Zebu) breed, is well adapted to tropical conditions and has allowed Brazil to become one of the largest producers of red meat. Nevertheless, B. indicus breeds are reported to have less tender meat than Bos taurus. This study was designed to identify genes associated with meat tenderness and thus provides important information for breeding programs. A group of 138 animals was evaluated for longissimus thoracis muscle shear force (SF). Animals with the highest and lowest SF values (six animals each) were then selected for protein abundance studies. Samples were subjected to two-dimensional gel electrophoresis (2-DE) followed by peptide sequencing through mass spectrometry (MS) to identify differentially expressed proteins associated with SF values. Seventeen differentially expressed spots were observed (p<0.05) between the two groups. The 13 proteins identified included structural proteins (alpha actin-1, MLC1, MLC3, MLC2F and tropomyosin), related to cell organization (HSPB1 and HSP70), metabolism (beta-LG, ACBD6 and Complex III subunit I) and some uncharacterized proteins. Results confirm the existence of differentially expressed proteins associated with SF, which can lead to a better understanding of mechanisms involved in meat tenderness.

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

BackgroundMeat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal’s life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.ResultsThe set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.ConclusionsThese results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.

Calcium and potassium content in beef: Influences on tenderness and associations with molecular markers in Nellore cattle

Calcium (Ca) and potassium (K) are essential nutrients in animal nutrition. Furthermore, the Ca content can influence meat tenderness because it is needed by the proteolytic system of calpains and calpastatins, major factors in postmortem tenderization of skeletal muscles. K content, which is needed for muscle contraction, can also affect meat tenderness. This study showed that K positively affects the Warner-Bratzler shear force (WBSF), measured at 14days of meat aging, which means that higher levels of K are related to lower meat tenderness. Additionally, a significant effect (P≤0.015) of a SNP in the calcium-activated neutral protease 1 (CAPN1) gene on Ca content was observed. Metal content in beef can affect not only nutritional values but also meat quality traits. Part of this effect may be related to variation in specific genes.

Composição corporal e exigências líquidas de proteína e energia de bovinos de quatro grupos genéticos terminados em confinamento

The body composition and protein and energy requirements for growth of steers of four genetic groups finished in feedlot were evaluated in this experiment. comparative slaughter method was used in a completely randomly experimental design, with four treatments: Nellore (NE), ½ Aberdeen Angus + ½ Nellore (AN), ½ Canchim + ½ Nellore (CN) e ½ Simmental + ½ Nellore (SN). Forty-seven steers averaging 310 kg initial shrunk body weight (SBW) and 22 months were fed during 101 days in a feedlot. Diet on feedlot had the following composition: crude protein, 13.34%; rumen degradable protein, 9.35%; and total digestible nutrients, 71.81% (estimated value). Composition of the 9th-10th-11th ribs was used to calculate empty body composition. No significant differences were found between AN (428 kg) and SN (410 kg) in final empty body weight (EBW), and similarly among CN, NE and SN (389, 390 and 410 kg, respectively), but EBW of AN steers was greater than that of CN and NE cattle. AN steers had higher amount of fat percentage on rib cut. However, less proportion of muscle was observed in the AN group and less bone percentage at the rib cut of the Nelore breed. AN and SN groups had the largest concentration of ether extract and the smallest amount of water percentage on the empty body at slaughter. Steers of AN, NE and SN groups were similar in rate of energy deposition (6.06, 5.20 and 5.80 Mcal/day, respectively). There was no difference among AN and CN cattle on ether extract in empty body weight gain. Simmental × Nelore demonstrated the greatest requirements of protein (0.164 kg/kg of EWG), and AN and CN cattle (0.140 and 0.142 kg/kg of EWG, respectively), the smallest. Angus × Nelore animals required the greatest net energy for gain (4.685 Mcal/kg of EWG).