1
|
Ghavi Hossein-Zadeh N. An overview of recent technological developments in bovine genomics. Vet Anim Sci 2024; 25:100382. [PMID: 39166173 PMCID: PMC11334705 DOI: 10.1016/j.vas.2024.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.
Collapse
Affiliation(s)
- Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
| |
Collapse
|
2
|
Ge S, Wang Y, Song M, Li X, Yu X, Wang H, Wang J, Zeng Q, Wang W. Type 2 Diabetes Mellitus: Integrative Analysis of Multiomics Data for Biomarker Discovery. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:514-523. [PMID: 30004843 DOI: 10.1089/omi.2018.0053] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Increased fasting plasma glucose (FPG) is an independent risk factor for type 2 diabetes mellitus (T2DM). The development of systems biology technologies for integration of multiomics data is crucial for predicting increased FPG levels. In this case-control study, immunoglobulin (Ig) G glycosylation profiling and genome-wide association analyses were performed on 511 participants, and among them 76 had increased FPG (aged 47.6 ± 6.14 years), and 435 had decreased or fluctuant FPG (aged 47.9 ± 6.08 years). We identified nine single nucleotide polymorphisms (SNPs) in five genes (RPL7AP27, SNX30, SLC39A12, BACE2, and IGFL2) that were significantly associated with increased FPG (odds ratios 1.937-2.393). Moreover, of the 24 glycan peaks (GPs), GPs 3, 8, and 11 presented positive trends with increased FPG levels, whereas GPs 4 and 14 presented negative trends. A significant improvement of predictive power was observed when adding 24 IgG GPs to 9 SNPs with the area under the curve increased from 0.75 to 0.81. This report shows that the combination of candidate SNPs with IgG glycomics offers biomarker potentials for T2DM. The substantial predictive power obtained from integrating genomics and glycomics biomarkers suggests the feasibility of applying such multiomics strategies to enable predictive, preventive, and personalized medicine for T2DM.
Collapse
Affiliation(s)
- Siqi Ge
- 1 Beijing Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University , Beijing, China .,2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| | - Youxin Wang
- 1 Beijing Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University , Beijing, China .,2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| | - Manshu Song
- 1 Beijing Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University , Beijing, China .,2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| | - Xingang Li
- 2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| | - Xinwei Yu
- 1 Beijing Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University , Beijing, China .,2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| | - Hao Wang
- 1 Beijing Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University , Beijing, China .,2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| | - Jing Wang
- 3 Department of Pathophysiology, Peking Union Medical College , China Academy of Medical Sciences, Beijing, China
| | - Qiang Zeng
- 4 Department of International Inpatient, Institute of Health Management , Chinese PLA General Hospital, Beijing, China
| | - Wei Wang
- 1 Beijing Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University , Beijing, China .,2 Department of Public Health, School of Medical and Health Sciences, Edith Cowan University , Perth, Australia
| |
Collapse
|
3
|
IP 3 receptor signaling and endothelial barrier function. Cell Mol Life Sci 2017; 74:4189-4207. [PMID: 28803370 DOI: 10.1007/s00018-017-2624-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022]
Abstract
The endothelium, a monolayer of endothelial cells lining vessel walls, maintains tissue-fluid homeostasis by restricting the passage of the plasma proteins and blood cells into the interstitium. The ion Ca2+, a ubiquitous secondary messenger, initiates signal transduction events in endothelial cells that is critical to control of vascular tone and endothelial permeability. The ion Ca2+ is stored inside the intracellular organelles and released into the cytosol in response to environmental cues. The inositol 1,4,5-trisphosphate (IP3) messenger facilitates Ca2+ release through IP3 receptors which are Ca2+-selective intracellular channels located within the membrane of the endoplasmic reticulum. Binding of IP3 to the IP3Rs initiates assembly of IP3R clusters, a key event responsible for amplification of Ca2+ signals in endothelial cells. This review discusses emerging concepts related to architecture and dynamics of IP3R clusters, and their specific role in propagation of Ca2+ signals in endothelial cells.
Collapse
|
4
|
Tayo BO, Tong L, Cooper RS. Association of polymorphisms in the aldosterone-regulated sodium reabsorption pathway with blood pressure among Hispanics. BMC Proc 2016; 10:343-348. [PMID: 27980660 PMCID: PMC5133472 DOI: 10.1186/s12919-016-0054-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Whereas genome-wide association study (GWAS) has proven to be an important tool for discovery of variants influencing many human diseases and traits, unfortunately its performance has not been much of all-around success for some complex conditions, for example, hypertension. Because some of the existing effective pharmacotherapeutic agents act by targeting known biological pathways, pathway-based analytical approaches could lead to more success in discovery of disease-associated variants. The objective of the present study was to identify functional variants associated with blood pressure in the aldosterone-regulated sodium reabsorption pathway using the simulated and real blood pressure phenotypes provided for Genetic Analysis Workshop 19. METHODS The present analysis included 1942 samples with exome sequencing data and for whom blood pressure phenotypes were available. Because only odd-numbered autosomes were available, we restricted analysis to 127 quality-controlled single-nucleotide polymorphisms from the aldosterone-regulated sodium reabsorption pathway. We performed pathway-based association analysis using appropriate regression models for single variant, haplotype and epistasis association analyses. To account for multiple comparisons, statistical significance was empirically derived by permutation procedure and Bonferroni correction. RESULTS The topmost pathway-based association signals were observed in PRKCA gene for diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) in both real and simulated data. The associations remained significant (P <0.05) after multiple testing corrections for the number of genes. Similarly, the pathway-based 2-locus epistasis analysis indicated significant interactions between INSR and PRKCG for SBP and MAP; INS and PIK3R2 for DBP; PIK3CD and ATP1B2 for hypertension in the real data set. We also observed significant within-gene interactions in INSR for SBP, DBP, and hypertension in the simulated data set. CONCLUSION The findings from this study show that pathway-based analytical approach targeting known biological pathways can be useful in identification of disease-associated variants that are otherwise undetectable by GWAS. The approach takes advantage of the assumption of nonindependence of variants within and across pathway genes which leads to reduced penalty of multiple testing and thus less-stringent statistical significance threshold.
Collapse
Affiliation(s)
- Bamidele O. Tayo
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153 USA
| | - Liping Tong
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153 USA
| | - Richard S. Cooper
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153 USA
| |
Collapse
|
5
|
Maintenance of normal blood pressure is dependent on IP3R1-mediated regulation of eNOS. Proc Natl Acad Sci U S A 2016; 113:8532-7. [PMID: 27402766 DOI: 10.1073/pnas.1608859113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Endothelial cells (ECs) are critical mediators of blood pressure (BP) regulation, primarily via the generation and release of vasorelaxants, including nitric oxide (NO). NO is produced in ECs by endothelial NO synthase (eNOS), which is activated by both calcium (Ca(2+))-dependent and independent pathways. Here, we report that intracellular Ca(2+) release from the endoplasmic reticulum (ER) via inositol 1,4,5-trisphosphate receptor (IP3R) is required for Ca(2+)-dependent eNOS activation. EC-specific type 1 1,4,5-trisphosphate receptor knockout (IP3R1(-/-)) mice are hypertensive and display blunted vasodilation in response to acetylcholine (ACh). Moreover, eNOS activity is reduced in both isolated IP3R1-deficient murine ECs and human ECs following IP3R1 knockdown. IP3R1 is upstream of calcineurin, a Ca(2+)/calmodulin-activated serine/threonine protein phosphatase. We show here that the calcineurin/nuclear factor of activated T cells (NFAT) pathway is less active and eNOS levels are decreased in IP3R1-deficient ECs. Furthermore, the calcineurin inhibitor cyclosporin A, whose use has been associated with the development of hypertension, reduces eNOS activity and vasodilation following ACh stimulation. Our results demonstrate that IP3R1 plays a crucial role in the EC-mediated vasorelaxation and the maintenance of normal BP.
Collapse
|
6
|
Aslibekyan S, Almeida M, Tintle N. Pathway analysis approaches for rare and common variants: insights from Genetic Analysis Workshop 18. Genet Epidemiol 2014; 38 Suppl 1:S86-91. [PMID: 25112195 DOI: 10.1002/gepi.21831] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pathway analysis, broadly defined as a group of methods incorporating a priori biological information from public databases, has emerged as a promising approach for analyzing high-dimensional genomic data. As part of Genetic Analysis Workshop 18, seven research groups applied pathway analysis techniques to whole-genome sequence data from the San Antonio Family Study. Overall, the groups found that the potential of pathway analysis to improve detection of causal variants by lowering the multiple-testing burden and incorporating biologic insight remains largely unrealized. Specifically, there is a lack of best practices at each stage of the pathway approach: annotation, analysis, interpretation, and follow-up. Annotation of genetic variants is inconsistent across databases, incomplete, and biased toward known genes. At the analysis stage insufficient statistical power remains a major challenge. Analyses combining rare and common variants may have an inflated type I error rate and may not improve detection of causal genes. Inclusion of known causal genes may not improve statistical power, although the fraction of explained phenotypic variance may be a more appropriate metric. Interpretation of findings is further complicated by evidence in support of interactions between pathways and by the lack of consensus on how to best incorporate functional information. Finally, all presented approaches warranted follow-up studies, both to reduce the likelihood of false-positive findings and to identify specific causal variants within a given pathway. Despite the initial promise of pathway analysis for modeling biological complexity of disease phenotypes, many methodological challenges currently remain to be addressed.
Collapse
Affiliation(s)
- Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | | | | |
Collapse
|