Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle

Metabolomics has been applied to measure the dynamic metabolic responses, to understand the systematic biological networks, to reveal the potential genetic architecture, etc., for human diseases and livestock traits. For example, the current published results include the detected relevant candidate metabolites, identified metabolic pathways, potential systematic networks, etc., for different cattle traits that can be applied for further metabolomic and integrated omics studies. Therefore, summarizing the applications of metabolomics for economic traits is required in cattle. We here provide a comprehensive review about metabolomic analysis and its integration with other omics in five aspects: (1) characterization of the metabolomic profile of cattle; (2) metabolomic applications in cattle; (3) integrated metabolomic analysis with other omics; (4) methods and tools in metabolomic analysis; and (5) further potentialities. The review aims to investigate the existing metabolomic studies by highlighting the results in cattle, integrated with other omics studies, to understand the metabolic mechanisms underlying the economic traits and to provide useful information for further research and practical breeding programs in cattle.

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Metabolic screening and metabolomics analysis in the Intellectual Developmental Disorders Mexico Study

Salud Pública de México ◽

10.21149/8668 ◽

2017 ◽

Vol 59 (4, jul-ago) ◽

pp. 423 ◽

Cited By ~ 5

Author(s):

Isabel Ibarra-González ◽

Rocío Rodríguez-Valentín ◽

Eduardo Lazcano-Ponce ◽

Marcela Vela-Amieva

Keyword(s):

Inborn Errors Of Metabolism ◽

Developmental Disorders ◽

Unknown Etiology ◽

Metabolomic Analysis ◽

Metabolomic Profile ◽

Inborn Errors ◽

Metabolic Screening ◽

Metabolomics Analysis ◽

Rule Out

Objective. Inborn errors of metabolism (IEM) are genetic conditions that are sometimes associated with intellectual developmental disorders (IDD). The aim of this study is to contribute to the metabolic characterization of IDD of unknown etiology in Mexico. Materials and methods. Metabolic screening using tandem mass spectrometry and fluorometry will be performed to rule out IEM. In addition,target metabolomic analysis will be done to characterize the metabolomic profile of patients with IDD. Conclusion. Identification of new metabolomic profiles associated withIDD of unknown etiology and comorbidities will contribute to the development of novel diagnostic and therapeutic schemes for the prevention and treatment of IDD in Mexico.

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Analysis of metabolic pathways in intrauterine growth restriction

Biomeditsinskaya Khimiya ◽

10.18097/pbmc20206602174 ◽

2020 ◽

Vol 66 (2) ◽

pp. 174-180

Author(s):

N.E. Kan ◽

Z.V. Khachatryan ◽

V.V. Chagovets ◽

N.L. Starodubtseva ◽

E.Yu. Amiraslanov ◽

...

Keyword(s):

Pregnant Women ◽

Biological Networks ◽

Metabolic Pathways ◽

Intrauterine Growth Restriction ◽

Growth Restriction ◽

Liquid Chromatography Mass Spectrometry ◽

Metabolomic Profile ◽

Intrauterine Growth ◽

Second Stage ◽

The Relationship

Objective was to analyze metabolic pathways based on a study of the metabolomic profile of pregnant women with intrauterine growth restriction. The metabolic profile of pregnant women with fetal growth restriction has been analyzed using liquid chromatography-mass spectrometry. At the second stage pathways were identified using SMPDB and MetaboAnalyst databases to clarify the relationship between metabolites. Biological networks allow to determine the effect of proteins on the metabolic pathways involved in pathogenesis of IUGR and determine the epigenetic mechanisms of its formation.

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A Novel 13 bp Deletion within the NR6A1 Gene Is Significantly Associated with Growth Traits in Donkeys

Animals ◽

10.3390/ani9090681 ◽

2019 ◽

Vol 9 (9) ◽

pp. 681 ◽

Cited By ~ 3

Author(s):

Xiya Fang ◽

Zhenyu Lai ◽

Jie Liu ◽

Chunlan Zhang ◽

Shipeng Li ◽

...

Keyword(s):

Nuclear Receptor ◽

Growth Traits ◽

Polyacrylamide Gel Electrophoresis ◽

Embryonic Stem ◽

The Body ◽

Economic Traits ◽

Breeding Programs ◽

Intron 1 ◽

Group A ◽

Nuclear Receptor Family

Nuclear receptor subfamily 6, group A, member 1 (NR6A1), as an important member of the nuclear receptor family, plays an important role in regulating growth, metabolism, and differentiation of embryonic stem cells. For this reason, the NR6A1 gene is considered to be a promising candidate for economic traits and was found to be associated with body size traits in many livestock. However, no studies have been conducted on NR6A1 in donkeys so far. Thus, in this research, we focused on donkeys and identified a 13 bp deletion in intron-1 of the NR6A1 gene among 408 individuals from Guanzhong and Dezhou donkeys using polyacrylamide gel electrophoresis. Three genotypes were identified, namely II, ID, and DD. The association analysis indicated that the body lengths and body heights5f genotype II individuals were significantly different to those of genotype ID in Dezhou donkeys. Conclusively, the 13 bp deletion was associated with growth traits in both Guanzhong donkeys and Dezhou donkeys, indicating that the NR6A1 gene could be a possible candidate gene in marker-assisted selection for donkey breeding programs.

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A New Breeding Strategy towards Introgression and Characterization of Stay-Green QTL for Drought Tolerance in Sorghum

Agriculture ◽

10.3390/agriculture11070598 ◽

2021 ◽

Vol 11 (7) ◽

pp. 598

Author(s):

Nasrein Mohamed Kamal ◽

Yasir Serag Alnor Gorafi ◽

Hanan Abdeltwab ◽

Ishtiag Abdalla ◽

Hisashi Tsujimoto ◽

...

Keyword(s):

Phenotypic Expression ◽

Phenotypic Selection ◽

Breeding Strategy ◽

Stay Green ◽

Breeding Programs ◽

The Public ◽

Drought Tolerant ◽

Selection Step ◽

The Cost

Several marker-assisted selection (MAS) or backcrossing (MAB) approaches exist for polygenic trait improvement. However, the implementation of MAB remains a challenge in many breeding programs, especially in the public sector. In MAB introgression programs, which usually do not include phenotypic selection, undesired donor traits may unexpectedly turn up regardless of how expensive and theoretically powerful a backcross scheme may be. Therefore, combining genotyping and phenotyping during selection will improve understanding of QTL interactions with the environment, especially for minor alleles that maximize the phenotypic expression of the traits. Here, we describe the introgression of stay-green QTL (Stg1–Stg4) from B35 into two sorghum backgrounds through an MAB that combines genotypic and phenotypic (C-MAB) selection during early backcross cycles. The background selection step is excluded. Since it is necessary to decrease further the cost associated with molecular marker assays, the costs of C-MAB were estimated. Lines with stay-green trait and good performance were identified at an early backcross generation, backcross two (BC2). Developed BC2F4 lines were evaluated under irrigated and drought as well as three rainfed environments varied in drought timing and severity. Under drought conditions, the mean grain yield of the most C-MAB-introgression lines was consistently higher than that of the recurrent parents. This study is one of the real applications of the successful use of C-MAB for the development of drought-tolerant sorghum lines for drought-prone areas.

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Comprehensive Plasma Metabolomic Profile of Patients with Advanced Neuroendocrine Tumors (NETs). Diagnostic and Biological Relevance

Cancers ◽

10.3390/cancers13112634 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2634

Author(s):

Beatriz Soldevilla ◽

Angeles López-López ◽

Alberto Lens-Pardo ◽

Carlos Carretero-Puche ◽

Angeles Lopez-Gonzalvez ◽

...

Keyword(s):

Metabolic Pathways ◽

Metabolic Networks ◽

Tca Cycle ◽

Metabolomic Profile ◽

Diagnostic Potential ◽

The Tca Cycle ◽

Novel Biomarkers ◽

Potential Methods ◽

Clinical Potential ◽

First Time

Purpose: High-throughput “-omic” technologies have enabled the detailed analysis of metabolic networks in several cancers, but NETs have not been explored to date. We aim to assess the metabolomic profile of NET patients to understand metabolic deregulation in these tumors and identify novel biomarkers with clinical potential. Methods: Plasma samples from 77 NETs and 68 controls were profiled by GC−MS, CE−MS and LC−MS untargeted metabolomics. OPLS-DA was performed to evaluate metabolomic differences. Related pathways were explored using Metaboanalyst 4.0. Finally, ROC and OPLS-DA analyses were performed to select metabolites with biomarker potential. Results: We identified 155 differential compounds between NETs and controls. We have detected an increase of bile acids, sugars, oxidized lipids and oxidized products from arachidonic acid and a decrease of carnitine levels in NETs. MPA/MSEA identified 32 enriched metabolic pathways in NETs related with the TCA cycle and amino acid metabolism. Finally, OPLS-DA and ROC analysis revealed 48 metabolites with diagnostic potential. Conclusions: This study provides, for the first time, a comprehensive metabolic profile of NET patients and identifies a distinctive metabolic signature in plasma of potential clinical use. A reduced set of metabolites of high diagnostic accuracy has been identified. Additionally, new enriched metabolic pathways annotated may open innovative avenues of clinical research.

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Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests

Genes ◽

10.3390/genes12050702 ◽

2021 ◽

Vol 12 (5) ◽

pp. 702

Author(s):

Simon Jansen ◽

Ulrich Baulain ◽

Christin Habig ◽

Faisal Ramzan ◽

Jens Schauer ◽

...

Keyword(s):

Random Forests ◽

Metabolic Pathways ◽

Genetic Architecture ◽

Laying Hens ◽

Enrichment Analysis ◽

Nucleotide Polymorphisms ◽

Mineral Density ◽

Single Nucleotide ◽

Economic Problems ◽

Close Proximity

Skeletal disorders, including fractures and osteoporosis, in laying hens cause major welfare and economic problems. Although genetics have been shown to play a key role in bone integrity, little is yet known about the underlying genetic architecture of the traits. This study aimed to identify genes associated with bone breaking strength and bone mineral density of the tibiotarsus and the humerus in laying hens. Potentially informative single nucleotide polymorphisms (SNP) were identified using Random Forests classification. We then searched for genes known to be related to bone stability in close proximity to the SNPs and identified 16 potential candidates. Some of them had human orthologues. Based on our findings, we can support the assumption that multiple genes determine bone strength, with each of them having a rather small effect, as illustrated by our SNP effect estimates. Furthermore, the enrichment analysis showed that some of these candidates are involved in metabolic pathways critical for bone integrity. In conclusion, the identified candidates represent genes that may play a role in the bone integrity of chickens. Although further studies are needed to determine causality, the genes reported here are promising in terms of alleviating bone disorders in laying hens.

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Genetic diversity of table grape based on morphoagronomic traits

Scientia Agricola ◽

10.1590/s0103-90162011000100007 ◽

2011 ◽

Vol 68 (1) ◽

pp. 42-49 ◽

Cited By ~ 14

Author(s):

Patrícia Coelho de Souza Leão ◽

Cosme Damião Cruz ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Clustering Analysis ◽

Germplasm Collection ◽

Table Grape ◽

Cluster Method ◽

Breeding Programs ◽

Method Analysis ◽

Vitis Spp ◽

Grape Cultivars

The conservation and characterization of grape (Vitis spp) genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits), and 9 clusters (taking into consideration multicategorical traits). There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.

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Preliminary comparative deep metabolomic analysis of spermatozoa from zebu and crossbred cattle suggests associations between metabolites, sperm quality and fertility

Reproduction Fertility and Development ◽

10.1071/rd20304 ◽

2021 ◽

Vol 33 (6) ◽

pp. 427

Author(s):

Mohua DasGupta ◽

Arumugam Kumaresan ◽

Kaustubh Kishor Saraf ◽

Gayathree Karthikkeyan ◽

T. S. Keshava Prasad ◽

...

Keyword(s):

Mass Spectrometry ◽

Semen Quality ◽

Sperm Quality ◽

Tandem Mass ◽

Metabolomic Analysis ◽

Metabolomic Profile ◽

Crossbred Cattle ◽

Acetyl Coenzyme A ◽

Chromatography Tandem Mass Spectrometry ◽

Liquid Chromatography Tandem Mass

Poor semen quality and infertility/subfertility are more frequent in crossbred than zebu bulls. Using a high-throughput liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based approach, we established the preliminary metabolomic profile of crossbred and zebu bull spermatozoa (n=3 bulls each) and identified changes in sperm metabolomics between the two groups. In all, 1732 and 1240 metabolites were detected in zebu and crossbred bull spermatozoa respectively. After excluding exogenous metabolites, 115 and 87 metabolites were found to be unique to zebu and crossbred bull spermatozoa respectively whereas 71 metabolites were common to both. In the normalised data, 49 metabolites were found to be differentially expressed between zebu and crossbred bull spermatozoa. The significantly enriched (P<0.05) pathways in spermatozoa were taurine and hypotaurine metabolism (observed metabolites taurine and hypotaurine) in zebu and glycerophospholipid metabolism (observed metabolites phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine) in crossbred bulls. The abundance of nitroprusside (variable importance in projection (VIP) score >1.5) was downregulated, whereas that of l-cysteine, acetyl coenzyme A and 2′-deoxyribonucleoside 5′-diphosphate (VIP scores >1.0) was upregulated in crossbred bull spermatozoa. In conclusion, this study established the metabolomic profile of zebu and crossbred bull spermatozoa and suggests that aberrations in taurine, hypotaurine and glycerophospholipid metabolism may be associated with the higher incidence of infertility/subfertility in crossbred bulls.

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Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

مجلة جامعة فلسطين التقنية للأبحاث ◽

10.53671/pturj.v3i1.34 ◽

2015 ◽

Vol 3 (1) ◽

pp. 1-11

Author(s):

Rezq Basheer-Salimia

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Germplasm Conservation ◽

Genetic Distances ◽

Vitis Vinifera L ◽

Similarity Matrix ◽

Breeding Programs ◽

Local Varieties ◽

Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

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