Effect of IGF1, GH, and PIT1 markers on the genetic parameters of growth and reproduction traits in Canchim cattle

Haplotype structure of MSTN, IGF1, and BMP2 genes in Tunisian goats (Capra hircus) and their association with morphometric traits

The aim of the present study was to evaluate variability and haplotype structure of twenty-eight single nucleotide polymorphisms (SNPs) at myostatin (MSTN), insulin-like growth factor 1 (IGF1), and bone morphogenetic protein 2 (BMP2) genes. Association between the polymorphic SNPs and morphometric traits was performed on a population of 263 Tunisian goats. The SNPs analyzed were all polymorphic (except one), and the three genes had different haplotype structures. Significant association of SNPs at MSTN with head length was highlighted in the Tunisian goats. The variability at IGF1 gene was associated with body length, ear length, tail length, and chest depth. For BMP2, significant association was revealed with chest depth. Significant association was also detected between linkage disequilibrium (LD) block 2 at IGF1 with body length. These findings might play a potential role in gene-assisted programs.

Determination of the relationship between Anatolian black cattle growth properties and myostatin, GHR and Pit-1 gene

The aim of this study is to determine the relationship between some growth and development characteristics in Anatolian Black cattle from birth to twelve months of age with the Pit-1, GHR and Myostatin genes. PCR-RFLP method was used to detect the polymorphism. Genotype and allele frequencies were found to be AA/AB/BB: 0.096/0.519/0.385 and A/B: 0.356/0.644; AA/AG/GG: 0.346/0.385/0.269 and A/G: 0.538/0.462 in the Pit-1 and GHR genes respectively. Myostatin gene was found to be also monomorphic in all genotypes. Although the chi-square χ² test in the Pit-1 gene showed an agreement to Hardy-Weinberg equilibrium (p > 0.05), in the GHR gene did not showed an agreement (p < 0.05). The results of the statistical analysis indicated an association between Pit-1 and GHR genes polymorphism and growth traits at different stage ages in Anatolian Black cattle. But Pit-1/HinfI gene and GHR/Alul polymorphisms were not found statistically significant in the specified periods, at all characters. On the other hand, since the MSTN/BstF5I gene was found to be monomorphic, no association analysis was performed between the measured values and this gene. In conclusion, mutation of these genes is difficult to suggest as a potential marker in a herd selection regarding the growth and development characteristics.

Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection

Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential for morphological shifts to arise via drift alone. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, most of which could be accounted for by drift, without the need to invoke selection. However, signatures of selection at genes previously identified as candidates for bill size and body shape differences in a range of bird species, also suggests a role for selective processes in driving morphological shifts within this population. Twenty-four SNPs in our RAD-Seq dataset were also found to be strongly associated with phenotypic variation. Hence, even under population founding extremes, when it is difficult to reject drift as the sole mechanism based on rate tests of phenotypic shifts, the additional role of divergent natural selection in novel environments can be revealed at the level of the genome.

Mutations in growth hormone gene affect stability of protein structure leading to reduced growth, reproduction, and milk production in crossbred cattle-an insight

The GH has a multifaceted role in growth, reproduction, and milk production. Nonsynonymous mutations identified as L153V were observed from GH1 (L) to GH2 (V) with higher genotypic frequency for GH1 being 0.87. GH2 (V) allele was identified as a rare allele and the population followed Hardy-Weinberg equilibrium. LL homozygote variant had significantly better growth, reproduction, and expected milk production at different ages in crossbred (CB) males. Reports are scanty explaining the molecular mechanism of how individuals with LV genotype were phenotypically inferior to that of wild-type LL. In the present study, it was explored that GH peptide with LV heterozygotes of GH gene, were observed to have reduced structural stability thermodynamically and thus functionally leads to reduced economic traits in CB animals. The fact was first time reported and confirmed through genomic analysis, bioinformatics, and later confirmed through immunohistochemistry. Differential expression analysis of the GH gene with respect to other genes in the hypothalamus-pituitary growth axis of CB cattle was also studied to have a complete insight of the GH gene.

Assessment of growth hormone gene polymorphism effects on reproductive traits in Holstein dairy cattle in Tunisia

Research to assess the effect of single genes on reproductive traits in bovine species is imperative to elucidate genes' functions and acquire a better perspective of quantitative traits. The present study was undertaken to characterize genetic diversity in the bovine growth hormone (GH) gene in a population of 410 Holstein dairy cows in Tunisia. The analyses were based on single nucleotide polymorphisms, and GH-AluI and GH-MspI detections and genotyping were carried out using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Data were analyzed using a mixed linear model with the MIXED procedure to reveal the possible effect of GH genotypes on reproductive traits. The frequency data of AluI(L//V) and MspI( + // - ) alleles were 87.04//12.96 and 70.06//29.94, respectively. The distribution of the frequency of GH genotypes for LL/LV/VV and ( - / - )//( + / - )//( + / + ) were 77.75//18.59//3.66 and 15.37//29.13//55.50, respectively. The results of the statistical analyses proved that GH-AluI showed a substantial favorable effect on exanimate traits except for the age at first calving; however, only a suggestive effect of GH-MspI on the calving interval (CI) and the days open (DI) was found. The homozygous LL genotype seemed to be advantageous with respect to the CI and the DI compared with LV and VV genotypes. Heterozygous MspI( + / - ) cows tended to have a longer CI and DI than MspI( + / + ) and MspI( - / - ) cows, but the difference was not statistically significant. A significant effect of different GH-AluI-MspI combined genotypes was found on the number of inseminations per conception, the CI and the DI, and the LL/- combined genotype seemed to be associated with better reproductive performance. Based on these results, the LL genotype of the GH locus can be considered to be a favorable genotype for reproductive traits in Holstein dairy cattle, although these findings need to be confirmed by further research before polymorphisms can be used in a marker-assisted selection program.

Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Morphs breed randomly with respect to bill size, and differ in diet and feeding performance relative to seed hardness. Previous breeding experiments are consistent with the polymorphism being controlled by a single genetic factor. Here, we use genome-wide pooled sequencing to explore the underlying genetic basis of bill morphology and identify a single candidate region. Targeted resequencing reveals extensive linkage disequilibrium across a 300 Kb region containing the insulin-like growth factor 1 (IGF1) gene, with a single 5-million-year-old haplotype associating with phenotypic dominance of the large-billed morph. We find no genetic similarities controlling bill size in the well-studied Darwin’s finches (Geospiza). Our results show how a single genetic factor may control bill size and provide a foundation for future studies to examine this phenomenon within and among avian species.

Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph.

Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle

The identification of biological processes related to the regulation of complex traits is a difficult task. Commonly, complex traits are regulated through a multitude of genes contributing each to a small part of the total genetic variance. Additionally, some loci can simultaneously regulate several complex traits, a phenomenon defined as pleiotropy. The lack of understanding on the biological processes responsible for the regulation of these traits results in the decrease of selection efficiency and the selection of undesirable hitchhiking effects. The identification of pleiotropic key-regulator genes can assist in developing important tools for investigating biological processes underlying complex traits. A multi-breed and multi-OMICs approach was applied to study the pleiotropic effects of key-regulator genes using three independent beef cattle populations evaluated for fertility traits. A pleiotropic map for 32 traits related to growth, feed efficiency, carcass and meat quality, and reproduction was used to identify genes shared among the different populations and breeds in pleiotropic regions. Furthermore, data-mining analyses were performed using the Cattle QTL database (CattleQTLdb) to identify the QTL category annotated in the regions around the genes shared among breeds. This approach allowed the identification of a main gene network (composed of 38 genes) shared among breeds. This gene network was significantly associated with thyroid activity, among other biological processes, and displayed a high regulatory potential. In addition, it was possible to identify genes with pleiotropic effects related to crucial biological processes that regulate economically relevant traits associated with fertility, production and health, such as MYC, PPARG, GSK3B, TG and IYD genes. These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with undesirable phenotypes, such as decreased fertility, poor feed efficiency and negative energetic balance.

Insulin-like growth factor-1 (IGF1) in systemic lupus erythematosus: relation to disease activity, organ damage and immunological findings

Background Insulin growth factor-1 (IGF1) activates cell proliferation pathways and inhibits apoptosis. IGF1 is involved in tumour growth and required for T-cell independent activation of B cells. Activated B cells and autoantibody production are a hallmark of systemic lupus erythematosus (SLE). To investigate the possible role of IGF1 in SLE, we studied IGF1 across clinical characteristics, immunological biomarkers, disease activity and organ damage in SLE patients. Method In a cross-sectional study, we collected clinical characteristics, medication, disease activity (SLEDAI-2K) and organ damage (SDI) for 94 SLE patients. Autoantibodies and cytokines were measured by ELISA, and levels of IGF1 and IGF binding protein 3 (IGFBP3) by chemiluminescence. Free IGF1 was estimated by the IGF1:IGFBP3 ratio. Healthy controls served as a comparator group. Results There was a significant age-related decline in IGF1, IGFBP3 and free IGF1 (IGF1:IGFBP3 ratio) that was similar in SLE patients and controls with very few outliers. Free IGF1 was inversely related to blood pressure (Rs -0.327, p < 0.01) and HbA1c (Rs -0.31, p < 0.01). Free IGF1 was higher in disease-modifying antirheumatic drug-treated patients ( p < 0.01), but there was no significant association between the IGF1 axis and autoantibody profiles, cytokine levels or SLEDAI-2K or SDI categories. IGF1 correlated inversely with BAFF level and B, natural killer and CD8 + cell counts. Conclusion Free IGF1 levels in SLE patients declined appropriately with age. IGF1 levels were not associated with disease activity, severity or autoantibody levels in SLE. Free IGF1 had positive metabolic effects in SLE and may play an indirect role in dampening the cellular immune response by downregulating B- and T-cell activity.

Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais—37.5% Zebu) and MA genetic group (MA: 65.6% Charolais—34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.