Figure - available via license: Creative Commons Attribution 2.0 Generic
Content may be subject to copyright.
Gonadotropin-releasing hormone (GnRH) signaling pathway containing genes that are represented in the Partial Correlation Information Theory (PCIT) network “growth at the onset of puberty”. DAVID analysis indicating a nominally significant enrichment of genes from the GnRH signaling pathway that are associated with key- or supportive phenotypes for growth at the onset of puberty. Pathway components that are encoded by genes included in the PCIT network are colored in orange. Purple dots highlight betacellulin (BTC) and diacylglycerol kinase eta (DGKH), which were identified as major hubs in the growth network (Table 3). Arrows indicate molecular interactions or relations, dotted arrows indicate indirect effects. Graph adapted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg-bin/show_pathway?hsa04912, accessed: 06/20/2013).
Source publication
Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two c...
Similar publications
p class="Pa7"> Objective: We studied multi-loci variants to identify the contribution of six candidate genes ( ADIPOQ, CDH13, LYPLAL1, MC4R, PPARG and PGC1A ) in the development of obesity and overweight.
Design: We genotyped 404 chromosomes with eleven SNPs in Mexican female adolescents, who were subdivided into two groups (obesity-overweight and...
Salt stress was applied to tomato commercial genotypes to study adverse effects on their phenotypic traits. Three were saline tolerant (San Miguel, Romelia and Llanero), two were mildly tolerant (Perfect peel HF1 and Heinz 1350) whereas the remaining were sensitive. Genotyping cultivars using 19 polymorphic SSRs out of 25 tested produced a total of...
The CYP2D6 enzyme exhibits large interindividual differences in metabolic activity. Patients are commonly assigned a CYP2D6 phenotype based on their CYP2D6 genotype, but there is a lack of consensus on how to translate genotypes into phenotypes, causing inconsistency in genotype-based dose recommendations. The aim of this study was to quantify and...
Mutation and recombination operators play a key role in determining the performance of Genetic and Evolutionary Algorithms (GEAs). Prior work has analyzed the effects of these operators on genotypic variation, often using locality metrics that measure the sensitivity and stability of genotype-phenotype representations to these operators. In this pa...
Despite the importance of climate‐adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we empl...
Citations
... These two genomic regions are 2.31 Mb apart (based on the ARS-UI_Ramb_ V2.0 reference genome). The NCAPG-LCORL locus is one of the most relevant loci associated with pleiotropic effects in livestock species, with associations reported for height, body weight, feed intake, gain, age at puberty, and meat and carcass traits [222][223][224][225][226][227]. ...
Background
Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS).
Results
In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits.
Conclusions
The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
... The GOT2 gene, which participates in amino acid metabolism, has been reported to be downregulated in the hypothalamus of pigs fed three different meals per day, compared to pigs fed ad libitum 60 . In turn, diacylglycerol kinase (DGKH) has been related to cattle growth, due to its role in the cell growth promoting Ras/Raf/MEK/ERK signalling pathway 61 . Accordingly, LRP5 has been reported to promote cell proliferation 62 . ...
Seaweeds, including the green Ulva lactuca, can potentially reduce competition between feed, food, and fuel. They can also contribute to the improved development of weaned piglets. However, their indigestible polysaccharides of the cell wall pose a challenge. This can be addressed through carbohydrase supplementation, such as the recombinant ulvan lyase. The objective of our study was to assess the muscle metabolism of weaned piglets fed with 7% U. lactuca and 0.01% ulvan lyase supplementation, using an integrated transcriptomics (RNA-seq) and proteomics (LC–MS) approach. Feeding piglets with seaweed and enzyme supplementation resulted in reduced macronutrient availability, leading to protein degradation through the proteasome (PSMD2), with resulting amino acids being utilized as an energy source (GOT2, IDH3B). Moreover, mineral element accumulation may have contributed to increased oxidative stress, evident from elevated levels of antioxidant proteins like catalase, as a response to maintaining tissue homeostasis. The upregulation of the gene AQP7, associated with the osmotic stress response, further supports these findings. Consequently, an increase in chaperone activity, including HSP90, was required to repair damaged proteins. Our results suggest that enzymatic supplementation may exacerbate the effects observed from feeding U. lactuca alone, potentially due to side effects of cell wall degradation during digestion.
... In a study by Philipp Widmann et al., 2013, they merged two ideas -analysis of metabolism and systems biology approaches; where they tried to separate molecular pathways, genes that control evolution variation or growth differentiation of the male cattle at the beginning of puberty without a previous practical hypothesis [78]. They explored characteristic gene relations of myostatin (GDF8), subunit G (NCAPG-Non-SMC Condensin I Complex Subunit G) and non-SMC condensing I complex etc., to understand briefly unnoticeable trouble on a molecular pathway on differential body bulkiness point of view. ...
This book explores the intricate world of livestock sciences and production through the lens of systems biology. Offering a comprehensive exploration of both fundamental and advanced aspects, it unearths the potential of systems biology in the realm of livestock. The book presents 13 edited chapters on cutting-edge knowledge about systems biology and omics technology, showcasing genomics, transcriptomics, proteomics, metabolomics, and more. It illuminates the role of systems biology in livestock and disease management. Readers will learn about power of technologies that merge computational biology, nanobiotechnology, artificial intelligence, and single-cell sequencing. Each chapter is written by scientific experts and includes references for further reading.
The book covers 4 key themes:
Introduction to Systems Biology in Livestock Science: Uncover the foundation of integrating systems biology with omics data for animal scientists. Multi-scale Modeling Techniques: Explore how multi-scale modeling is shaping the future of system biology. Livestock Viral Diseases: Gain insights into how systems biology is revolutionizing our understanding of livestock viral diseases. Single Cell RNA-Sequencing: Understand the potential of this advanced technique in studying livestock animals at a cellular level.
This book is a timely resource for students and researchers, offering a pathway to comprehend the crucial role systems biology plays in sustainable livestock production and management.
... Calcium homeostasis has important roles in controlling the fate of muscle tissue through multiple pathways, and calcium signaling has a vital regulatory function in duck breast muscle development [50,51]. Moreover, the MAPK and GnRH signaling pathways are associated with animal body weight and contribute to muscle growth [52,53]. According to the PPI analysis, many proteins encoded by the parental genes of the differentially expressed circular RNAs had interactions with other parental proteins. ...
Circular RNAs are widespread in various species and have important roles in myogenesis. However, the circular RNAs involved in breast muscle development in ducks have not yet been studied. Here, to identify circular RNAs during duck skeletal muscle development, three pectorales from Shan Ma ducks at E13 and E19, which represent undifferentiated and differentiated myoblasts, respectively, were collected and subjected to RNA sequencing. A total of 16,622 circular RNAs were identified, of which approximately 80% were exonic circular RNAs and 260 were markedly differentially expressed between E19 and E13. The parental genes of the differentially expressed circular RNAs were significantly enriched in muscle-related biological processes. Moreover, we found that the overexpression of circGAS2-2 promoted cell cycle progression and increased the proliferation viability of duck primary myoblasts; conversely, knockdown of circGAS2-2 retarded the cell cycle and reduced the proliferation viability of myoblasts. Taken together, our results demonstrate that circular RNAs are widespread and variously expressed during the development of duck skeletal muscle and that circGAS2-2 is involved in the regulation of myogenesis.
... PENK participates in numerous physiologic functions and encodes a preproprotein, which is proteolytically processed to make multiple protein products. This gene is responsible for the regulation of GnRH [163,164], as the GnRH signaling pathway is involved in the characterization of the different stages of growth until puberty in cattle [165]. ...
The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.
... Complex traits are regulated at different molecular levels, and considerable effort has been made to generate multi-level studies, integrating different omic data to understand the inherent biological meaning of livestock traits (Widmann et al., 2013;Suravajhala et al., 2016). However, omic data integration using a hierarchical analysis approach or considering just the common pathway enrichment may not reveal non-obvious relationships that exist among omic data (Misra et al., 2018). ...
Data integration using hierarchical analysis based on the central dogma or common pathway enrichment analysis may not reveal non-obvious relationships among omic data. Here, we applied factor analysis (FA) and Bayesian network (BN) modeling to integrate different omic data and complex traits by latent variables (production, carcass, and meat quality traits). A total of 14 latent variables were identified: five for phenotype, three for miRNA, four for protein, and two for mRNA data. Pearson correlation coefficients showed negative correlations between latent variables miRNA 1 (mirna1) and miRNA 2 (mirna2) (−0.47), ribeye area (REA) and protein 4 (prot4) (−0.33), REA and protein 2 (prot2) (−0.3), carcass and prot4 (−0.31), carcass and prot2 (−0.28), and backfat thickness (BFT) and miRNA 3 (mirna3) (−0.25). Positive correlations were observed among the four protein factors (0.45–0.83): between meat quality and fat content (0.71), fat content and carcass (0.74), fat content and REA (0.76), and REA and carcass (0.99). BN presented arcs from the carcass, meat quality, prot2, and prot4 latent variables to REA; from meat quality, REA, mirna2, and gene expression mRNA1 to fat content; from protein 1 (prot1) and mirna2 to protein 5 (prot5); and from prot5 and carcass to prot2. The relations of protein latent variables suggest new hypotheses about the impact of these proteins on REA. The network also showed relationships among miRNAs and nebulin proteins. REA seems to be the central node in the network, influencing carcass, prot2, prot4, mRNA1, and meat quality, suggesting that REA is a good indicator of meat quality. The connection among miRNA latent variables, BFT, and fat content relates to the influence of miRNAs on lipid metabolism. The relationship between mirna1 and prot5 composed of isoforms of nebulin needs further investigation. The FA identified latent variables, decreasing the dimensionality and complexity of the data. The BN was capable of generating interrelationships among latent variables from different types of data, allowing the integration of omics and complex traits and identifying conditional independencies. Our framework based on FA and BN is capable of generating new hypotheses for molecular research, by integrating different types of data and exploring non-obvious relationships.
... BCL11B (BAF chromatin remodeling complex subunit BCL11B) is a member of the NF-kappaB signaling pathway, which also plays an essential role in myogenesis, influencing muscle hypertrophy (Peterson et al., 2011). LRRK1 (leucine-rich repeat kinase 1) is involved in the trafficking of epidermal growth factor receptor (EGFR), which stimulates the growth process in various tissues (Widmann et al., 2013). Variants in LRRK1 were associated with height (Tachmazidou et al., 2017) and body weight (Galván-Femenía et al., 2018) in humans. ...
Primal cuts and dressing percentage are complex traits to record on a large scale, and information from molecular markers can improve the selection schemes for these traits. Thus, 490 Santa Ines lambs were genotyped for 50K SNP chip to perform a genomic study for dressing percentage as well as shoulder, loin, rib, and leg yields. Variance components were estimated through a univariate animal model with a genomic relationship matrix. Weighted single-step association analyses were carried out to estimate the variance percentage explained by adjacent SNPs in genome windows (GW) of 1.0 Mbp. The estimates of heritability were 0.32 ± 0.14 (carcass), 0.28 ± 0.11 (loin), 0.41 ± 0.13 (rib), 0.32 ± 0.13 (shoulder), and 0.46 ± 0.13 (leg). The number of GW explaining more than 1% of additive genetic variance (VA) and the total percentages of VA explained for dressing percentage, loin, rib, shoulder, and leg yields were, respectively, eight (12.5%), ten (19.2%), nine (20.1%), ten (18.8%), and seven (13.1%). Inside the GW, 355 protein-coding genes were found, 31 of them (FAIM, MRAS, PIK3CB, NHLH2, CASQ2, NAALADL2, ATPL1, GLIS3, TMOD1, CNTN1, LRRK2, HMGA2, MSRB3, ANKS1B, IR29A, LCORL, NCAPG, DTHD1, ARAP2, SYNE2, SPTB, KHDRBS3, CLVS1, NKAIN3, UBL3, SLC7A1, GSKIP, BDKRB2, SETD3, BCL11B and LRRK1) can be considered as candidate genes for carcass traits due their biological functions. Moreover, other sixteen genes take part in the neuroactive ligand-receptor interaction pathway, and this pathway was significant in functional annotation analysis of the genes mapped for primal cuts. These results revealed novel insights regarding the genetic control for primal cuts in sheep and are a novel source of information for future genomic studies related to carcass yield in livestock.
... Some genes, including DGKH, DLEU7, FOXO1, KPNA3, CAB39L, KCNIP4, SLIT2, which were found to be associated with growth traits in farm animals, were considered as important candidate genes for growth traits in broilers. DGKH was identified as a candidate gene affecting divergent growth in cattle (38), and this gene could regulate the growth of cattle by regulating the secretion of growth-related hormones (39). KPNA3 was found to be associated with chicken growth traits in a previous GWAS (10,40). ...
Rapid growth is one of the most important economic traits in broiler breeding programs. Identifying markers and genes for growth traits may not only benefit marker-assisted selection (MAS)/genomic selection (GS) but also provide important information for understanding the genetic architecture of growth traits in broilers. In the present study, an F2 resource population derived from a cross between the broiler and Baier yellow chicken (a Chinese local breed) was used and body weights from 1 to 12 weeks of age [body weight (BW) 1–BW12)] were measured. A total of 519 F2 birds were genome re-sequenced, and a combination of genome-wide association study (GWAS) and selective sweep analysis was carried out to characterize the genetic architecture affecting chicken body weight comprehensively. As a result, 1,539 SNPs with significant effects on body weights at different weeks of age were identified using a genome-wide efficient mixed-model association (GEMMA) package. These SNPs were distributed on chromosomes 1 and 4. Besides, windows under selection identified for BW1–BW12 varied from 1,581 to 2,265. A total of 42 genes were also identified with significant effects on BW1–BW12 based on both GWAS and selective sweep analysis. Among these genes, diacylglycerol kinase eta (DGKH), deleted in lymphocytic leukemia (DLEU7), forkhead box O17 (FOXO1), karyopherin subunit alpha 3 (KPNA3), calcium binding protein 39 like (CAB39L), potassium voltage-gated channel interacting protein 4 (KCNIP4), and slit guidance ligand 2 (SLIT2) were considered as important genes for broiler growth based on their basic functions. The results of this study may supply important information for understanding the genetic architecture of growth traits in broilers.
... It is well-known that growth is a complex process controlled by many genes, environmental factors, and epigenetic and pleiotropic mechanisms [17]. Data presented herein support this assertion but begin to help us unravel the biology driving improved performance in growing cattle over a wide range of production scenarios. ...
... This possibility is supported by the fact that we observed higher amounts of amino acids in the muscle of faster-growing cattle. Along this same line of reasoning, Widmann et al. [17] showed that growth-related changes in metabolisms at the onset of puberty in heifers elicited a torrent of processes in cells and showed that arginine metabolism is highly correlated with several key cellular pathways in these processes. Therefore, it is unsurprising that arginine biosynthesis is one of the most important pathways observed in enrichment analyses differentiating growth rate in cattle in our study. ...
The present study explored changes in the meat metabolome of animals subjected to different finishing systems and growth rates. Thirty-six Angus × Nellore crossbred steers were used in a completely randomized design with four treatments: (1) feedlot system with high average daily gain (ADG; FH); (2) feedlot system with low ADG (FL); (3) pasture system with high ADG (PH); and (4) pasture system with low ADG (PL). After harvest and chilling, Longissimus thoracis (LT) muscle samples were taken for metabolite profile analysis using nuclear magnetic resonance. Spectrum was analyzed using chenomx software, and multi- and mega-variate data analyses were performed. The PLS-DA showed clear separation between FH and PL groups and overlap among treatments with different finishing systems but similar for matching ADG (FL and PH) treatments. Using a VIP cut-off of around 1.0, ATP and fumarate were shown to be greater in meat from PL cattle, while succinate, leucine, AMP, glutamate, carnosine, inosine, methionine, G1P, and choline were greater in meat from FH. Comparing FL and PH treatments, glutamine, carnosine, urea, NAD+, malonate, lactate, isoleucine, and alanine were greater in the meat of PH cattle, while G6P and betaine were elevated in that of FL cattle. Relevant pathways were also identified by differences in growth rate (FH versus PL) and finishing system were also noted. Growth rate caused a clear difference in meat metabolism that was highlighted by energy metabolism and associated pathways, while the feeding system tended to alter protein and lipid metabolism.
... The key tissues are known given the reproductive cycle is regulated by activation across the brain, pituitary, gonadal (BPG) axis in organisms spanning from mammals to teleost fish. Further, upon maturation these tissues undergo known and often profound transcriptomic remodeling providing a large dynamic range to increase the likelihood of identifying regulatory networks [9][10][11][12]. An energy-intensive process such as sexual maturation involves the liver as energy homeostasis is linked to fertility (Mircea et al. [13]; Montagner et al. [14]). ...
Background
Despite sexual development being ubiquitous to vertebrates, the molecular mechanisms underpinning this fundamental transition remain largely undocumented in many organisms. We designed a time course experiment that successfully sampled the period when Atlantic salmon commence their trajectory towards sexual maturation.
Results
Through deep RNA sequencing, we discovered key genes and pathways associated with maturation in the pituitary-ovarian axis. Analyzing DNA methylomes revealed a bias towards hypermethylation in ovary that implicated maturation-related genes. Co-analysis of DNA methylome and gene expression changes revealed chromatin remodeling genes and key transcription factors were both significantly hypermethylated and upregulated in the ovary during the onset of maturation. We also observed changes in chromatin state landscapes that were strongly correlated with fundamental remodeling of gene expression in liver. Finally, a multiomic integrated analysis revealed regulatory networks and identified hub genes including TRIM25 gene (encoding the estrogen-responsive finger protein) as a putative key regulator in the pituitary that underwent a 60-fold change in connectivity during the transition to maturation.
Conclusion
The study successfully documented transcriptome and epigenome changes that involved key genes and pathways acting in the pituitary – ovarian axis. Using a Systems Biology approach, we identified hub genes and their associated networks deemed crucial for onset of maturation. The results provide a comprehensive view of the spatiotemporal changes involved in a complex trait and opens the door to future efforts aiming to manipulate puberty in an economically important aquaculture species.
