Genetic variation in the pro-melanin-concentrating hormone gene affects carcass traits in Bos taurus cattle

A SNP within the PMCH gene as a molecular marker associated with fertility traits in Angus and Brangus beef heifers raised under a desert environment

Components of the GH/IGF1 endocrine axis regulate growth and reproductive traits in cattle. The pro-melanin-concentrating hormone (PMCH) gene located within chromosome 5 belongs to this axis. Objective herein was to evaluate PMCH single-nucleotide polymorphisms (SNPs) as molecular markers associated with age at first calving, calving interval, and age at second calving in Angus and Brangus beef heifers raised in desert conditions. Five SNPs within the PMCH gene were included in the study. Three of these SNPs had minor allele frequency > 10% and only one SNP did not deviate from Hardy-Weinberg equilibrium. A genotype to phenotype association analyses was performed using a mixed-effects model which included phenotype as the response variable, SNP genotype, breed, year of birth and age of dam as fixed terms, and sire as a random effect. Genotypes from the SNP rs135033882 were found to be associated (P < 0.05) with all evaluated fertility traits, and the term breed resulted as a significant source of variation only for age at second calving. The allele A was the favorable allele because it decreased the age at first calving 98.6 days, the calving interval 85.3 days, and the age at second calving 183.1 days, in Angus and Brangus heifers. In conclusion, we proposed a SNP within the PMCH gene as a potential candidate marker associated with reproductive performance in Angus and Brangus beef heifers raised in a desert climate.

Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle

Systems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (Illumina HiSeq 2500, 100 bp, pared-end). From the 17,354 expressed genes considering all tissues, 1,335 were prioritized by five selection categories (differentially expressed, harboring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB1 were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated with FE. Moreover, we indicated potential biomarkers of FE, which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed the main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.

Association of pro-melanin concentrating hormone genotype with beef carcass quality and yield

Beef cattle from 3 independent studies conducted in the Texas Panhandle (Exp. 1: n = 3,906 and Exp. 2: n = 4,000) and southern Idaho (Exp. 3; n = 542) were used to investigate the association of pro-melanin concentrating hormone (PMCH) genotype with beef carcass quality and yield attributes. Tissue samples were collected from each animal to determine which PMCH allele they expressed (Trial 1: AA, 62.60%; AT, 32.05%; and TT, 5.35%; Trial 2: AA, 64.33%; AT, 31.07%; and TT, 4.60%; Trial 3: AA, 65.87%; AT, 29.34%; and TT, 4.80%). Twenty-four hours after harvest, carcass attributes were evaluated for all carcasses and longissimus dorsi steak samples were allocated from a subset of carcasses in Exp. 2 (n = 352; AA, 49.43%; AT, 28.98%; and TT, 21.59%) and each carcass in Exp. 3. Warner-Bratzler shear force measurements were determined for each steak after aging for 7, 14, or 21 d postmortem. Carcasses from Exp. 1 and 2 expressing the AA genotype had greater (P < 0.01) 12th rib subcutaneous (s.c.) fat depth and marbling scores, concurrent with smaller (P < 0.01) LM area than carcasses of AT and TT genotypes. Subsequently, carcasses expressing the AA genotype were represented by a greater (P < 0.02) proportion achieving Prime and Premium Choice quality grades, and a lesser (P < 0.01) proportion grading Select or Standard. In all trials, carcasses of the AA genotype had greater (P < 0.04) calculated yield grades than carcasses of the TT genotype. Carcass composition was associated with PMCH genotype evident by calculated empty body fat differences (P < 0.04) between AA and TT cattle in Exp. 1 and 3, and differences (P < 0.01) among all 3 genotypes in Trial 2. Shear force data on 7-d postmortem aging tended (P = 0.06) to favor cattle of the AA genotype in Exp. 2. However, additional aging to 14 or 21 d minimized any tenderness differences. These data illustrate the potential relationship that may exist among PMCH genotypes and indicators of carcass composition.

Association analyses of a SNP in the promoter of IGF1 with fat deposition and carcass merit traits in hybrid, Angus and Charolais beef cattle

A SNP in the promoter region of insulin like growth factor-1 (IGF1) (c.-512C>T) was analysed for associations with 10 fat deposition and carcass merit traits in hybrid (n = 455), Angus (n = 204) and Charolais (n = 186) beef cattle populations. Significant associations of the SNP were found for ultrasound backfat thickness (P = 0.030), carcass average backfat (P = 0.015) and carcass lean meat yield (LMY) (P = 0.023) in the Angus beef population, with the 'CC' genotype showing higher fat depth and lower LMY than the 'TT' genotype. Analyses of transcription factor binding sites based on transcription element search system prediction revealed that the 'C' allele introduces a binding site for nuclear factor I, which has an adipose tissue-specific regulatory role and thus may contribute to the SNP effect on fat deposition in the population of pure Angus cattle, a breed with greater fat depth than the hybrid and Charolais breeds.

Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches

Background

Neuropeptides are cell to cell signalling molecules that regulate many critical biological processes including development, growth and reproduction. These peptides result from the complex processing of prohormone proteins, making their characterization both challenging and resource demanding. In fact, only 42 neuropeptide genes have been empirically confirmed in cattle. Neuropeptide research using high-throughput technologies such as microarray and mass spectrometry require accurate annotation of prohormone genes and products. However, the annotation and associated prediction efforts, when based solely on sequence homology to species with known neuropeptides, can be problematic.

Results

Complementary bioinformatic resources were integrated in the first survey of the cattle neuropeptide complement. Functional neuropeptide characterization was based on gene expression profiles from microarray experiments. Once a gene is identified, knowledge of the enzymatic processing allows determination of the final products. Prohormone cleavage sites were predicted using several complementary cleavage prediction models and validated against known cleavage sites in cattle and other species. Our bioinformatics approach identified 92 cattle prohormone genes, with 84 of these supported by expressed sequence tags. Notable findings included an absence of evidence for a cattle relaxin 1 gene and evidence for a cattle galanin-like peptide pseudogene. The prohormone processing predictions are likely accurate as the mammalian proprotein convertase enzymes, except for proprotein convertase subtilisin/kexin type 9, were also identified. Microarray analysis revealed the differential expression of 21 prohormone genes in the liver associated with nutritional status and 8 prohormone genes in the placentome of embryos generated using different reproductive techniques. The neuropeptide cleavage prediction models had an exceptional performance, correctly predicting cleavage in more than 86% of the prohormone sequence positions.

Conclusion

A substantial increase in the number of cattle prohormone genes identified and insights into the expression profiles of neuropeptide genes were obtained from the integration of bioinformatics tools and database resources and gene expression information. Approximately 20 prohormones with no empirical evidence were detected and the prohormone cleavage sites were predicted with high accuracy. Most prohormones were supported by expressed sequence tag data and many were differentially expressed across nutritional and reproductive conditions. The complete set of cattle prohormone sequences identified and the cleavage prediction approaches are available at .