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BackgroundThe selection of beef cattle for feed efficiency (FE) traits is very important not only for productive and economic efficiency but also for reduced environmental impact of livestock. Considering that FE is multifactorial and expensive to measure, the aim of this study was to identify biological functions and regulatory genes associated with this phenotype.ResultsEight genes were differentially expressed between high and low feed efficient animals (HFE and LFE, respectively). Co-expression analyses identified 34 gene modules of which 4 were strongly associated with FE traits. They were mainly enriched for inflammatory response or inflammation-related terms. We also identified 463 differentially co-expressed genes which were functionally enriched for immune response and lipid metabolism. A total of 8 key regulators of gene expression profiles affecting FE were found. The LFE animals had higher feed intake and increased subcutaneous and visceral fat deposition. In addition, LFE animals showed higher levels of serum cholesterol and liver injury biomarker GGT. Histopathology of the liver showed higher percentage of periportal inflammation with mononuclear infiltrate.ConclusionLiver transcriptomic network analysis coupled with other results demonstrated that LFE animals present altered lipid metabolism and increased hepatic periportal lesions associated with an inflammatory response composed mainly by mononuclear cells. We are now focusing to identify the causes of increased liver lesions in LFE animals.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2292-8) contains supplementary material, which is available to authorized users.

The current research was conducted to estimate the heritability coefficients and the genetic correlations for performance and carcass and body composition traits in a single sire broiler line. The performance traits analyzed were BW at 38 d, ultrasound records of pectoral muscle depth, feed intake, feed conversion ratio, and BW at 42 d. The carcass traits analyzed were eviscerated BW, breast weight, and leg weight, and the body composition traits analyzed were abdominal fat content, heart weight, gizzard weight, liver weight, and intestine weight. The number of observations varied between 4,120 and 29,040 for each trait. The (co)variance components, heritability, and genetic correlation estimates were obtained by restricted maximum likelihood. The numerator relationship matrix had 42,912 animals. Based on the heritability estimates obtained, the analyzed traits seemed to be able to respond to selection, at variable intensities. The genetic correlation estimates between a great number of performance traits, as well as between a great number of carcass traits, were suggestive of a close genetic relationship between these traits. The genetic correlation estimates between body composition traits were variable. A large genetic association between a great number of performance and carcass traits seemed to exist. The genetic correlation estimates between performance and body composition traits were variable, and important associations between carcass and body composition traits did not seem to exist.

Estimates of (co)variance components and genetic parameters were obtained for birth, 205-d, and 365-d weight for Nelore cattle in Brazil, using single and multiple-trait animal models. Data were from the Brazilian Zebu Breeders Association (ABCZ). Records of 27,549 calves sired by 587 bulls and raised on pasture in 57 herds were analyzed by restricted maximum likelihood fitting an animal model including direct and maternal genetic and permanent environmental effects. Single and multiple-trait analyses were carried out. Heritability estimates for direct effects were lower than previous values reported for the Nelore breed. The estimates for maternal genetic effects showed that the contribution of this component to the phenotypic variance of birth and weaning weight is not very high but is still present at yearling weight. Correlations between direct and maternal additive genetic effects were negative for all traits analyzed except for yearling weight in the single-trait analysis where the sign was positive but the magnitude was small (+.09). Genetic correlations between weaning and yearling weights were .74 (direct effect) and .84 (maternal effect). Permanent environmental and residual correlations among traits were also obtained.

To estimate the heritability for the probability that yearling heifers would become pregnant, we analyzed the records of 11,487 Nellore animals that participated in breeding seasons at three farms in the Brazilian states of São Paulo and Mato Grosso do Sul. All heifers were exposed to a bull at the age of about 14 mo. The probability of pregnancy was analyzed as a categorical trait, with a value of 1 (success) assigned to heifers that were diagnosed pregnant by rectal palpation about 60 d after the end of the breeding season of 90 d and a value of 0 (failure) assigned to those that were not pregnant at that time. The estimate of heritability, obtained by Method R, was 0.57 with standard error of 0.01. The EPD was predicted using a maximum a posteriori threshold method and was expressed as deviations from 50% probability. The range in EPD was -24.50 to 24.55%, with a mean of 0.78% and a SD of 7.46%. We conclude that EPD for probability of pregnancy can be used to select heifers with a higher probability of being fertile. However, it is mainly recommended for the selection of bulls for the production of precocious daughters because the accuracy of prediction is higher for bulls, depending on their number of daughters.

RESUMO -Dados de perímetro escrotal e de características reprodutivas medidas na fêmea foram analisados com o objetivo de estimar o coeficiente de herdabilidade de cada característica e a correlação genética entre as características. Os dados foram obtidos em 11 fazendas pertencentes a uma mesma empresa, situadas nos Estados de São Paulo, Mato Grosso do Sul e Goiás. Os componentes de variância foram estimados por máxima verossimilhança restrita utilizando modelo animal bi-característica. Para as características com medidas repetidas, foram utilizados dois modelos matemáticos: um incluindo ambiente permanente da vaca e outro não. As análises nas quais o modelo não incluía o ambiente permanente da vaca mostraram as seguintes herdabilidades 0,51; 0,12; 0,17; 0,06; e 0,13 para perímetro escrotal (PE), idade ao primeiro parto (IPP), dias para o parto (DPP), intervalo de partos (IP) e duração da gestação (DG), respectivamente. Nestas análises, as correlações genéticas foram: -0,22 (PE x IPP), -0,04 (PE x DPP), 0,10 (PE x IP) e -0,04 (PE x DG). Quando o ambiente permanente foi incluído no modelo, as herdabilidades de DPP (0,07) e DG (0,06) foram menores, indicando que modelos sem ambiente permanente podem superestimar a variância genética aditiva dessas duas características. Os parâmetros da característica IP não foram, entretanto, alterados pela inclusão do ambiente permanente no modelo. O PE apresentou correlações genéticas favoráveis com IPP, DPP e DG, mas estas foram geralmente de baixa magnitude. Estes resultados permitem a utilização do perímetro escrotal como critério de seleção para melhorar a eficiência reprodutiva das fêmeas.Palavras-chave: características reprodutivas, correlação genética, modelo animal, perímetro escrotal Genetic Correlation Between Scrotal Circumference and Some Reproductive Traits in Nellore CattleABSTRACT -Data of scrotal circumference and female reproductive traits were analyzed to estimate heritabilities and genetic correlations. Data were obtained from 11 farms by the same company, located in the States of São Paulo, Mato Grosso do Sul and Goiás. Variance components were estimated by restricted maximum likelihood using two-trait animal models. For traits with repeated measures, two mathematical models were used: including or not the permanent environment of the cow. Analyses that not included the permanent environment of the cow showed the following heritabilities 0.51, 0.12, 0.17, 0.06 and 0.13 for scrotal circumference (SC), age at first calving (AFC), days to calving (DC), calving interval (CI) and gestation length (GL), respectively. In these analyses, the genetic correlations were: -0.22 (SC x AFC), -0.04 (SC x DC), 0.10 (SC x CI) and -0.04 (SC x GL). When permanent environment of the cow were included in the model, heritabilities of DC (0.07) and GL (0.06) were smaller, indicating that models without permanent environment of the cow can overestimate the additive genetic variance of these two traits. However, the CI parameters did not change with the inclusion of permanent enviro...

ABSTRACTranged from .01 to .14 for NBA, from .18 to .22 for LW, from .23 to .34 for ADG, and from .40 to .50 for BF. Maternal genetic variance was from 2.4 to 3.8% of phenotypic variance in NBA, from 1.2 to 3.6% in LW, from .5 to 1.5% in ADG, and from 1.9 to 3.4% in BF.The correlation between o and m was -.07 for NBA, -.25 for LW, -.34 for ADG, and -.26 for BF. Permanent environmental effects explained from 16 to 17% of total phenotypic variation for NBA and from 1.6 to 5.3% for LW. Approximately 7% of the variation in ADG and 5% in BF was due to litter environmental effects. Genetic trends were .012 pigsiyr for NBA, .25 kg/yr for LW, 5.91 g/yr for ADG, and -.063 mmlyr for BF.

BackgroundApart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed).ResultsWe have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits.ConclusionThis study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2461-4) contains supplementary material, which is available to authorized users.