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Susgun S, Yucesan E, Goncu B, Hasanoglu Sayin S, Kina UY, Ozgul C, Duzenli OF, Kocaturk O, Calik M, Ozbek U, Ugur Iseri SA. Two rare autosomal recessive neurological disorders identified by combined genetic approaches in a single consanguineous family with multiple offspring. Neurol Sci 2024; 45:2271-2277. [PMID: 38012464 DOI: 10.1007/s10072-023-07211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
INTRODUCTION Neurodevelopmental disorders (NDDs) refer to a broad range of diseases including developmental delay, intellectual disability, epilepsy, autism spectrum disorders, and attention-deficit/hyperactivity disorder caused by dysfunctions in tightly controlled brain development. The genetic backgrounds of NDDs are quite heterogeneous; to date, recessive or dominant variations in numerous genes have been implicated. Herein, we present a large consanguineous family from Turkiye, who has been suffering from NDDs with two distinct clinical presentations. METHODS AND RESULTS Combined in-depth genetic approaches led us to identify a homozygous frameshift variant in NALCN related to NDD and expansion of dodecamer repeat in CSTB related to Unverricht-Lundborg disease (ULD). Additionally, we sought to functionally analyze the NALCN variant in terms of mRNA expression level and current alteration. We have both detected a decrease in the level of premature stop codon-bearing mRNA possibly through nonsense-mediated mRNA decay mechanism and also an increased current in patch-clamp recordings for the expressed truncated protein. CONCLUSION In conclusion, increased consanguinity may lead to the revealing of distinct rare neurogenetic diseases in a single family. Exome sequencing is generally considered the first-tier diagnostic test in individuals with NDD. Yet we underline the fact that customized approaches other than exome sequencing may be used as in the case of ULD to aid diagnosis and better genetic counseling.
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Affiliation(s)
- Seda Susgun
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba Cad., 34093, Istanbul, Türkiye
- Graduate School of Health Sciences, Istanbul University, Istanbul, Türkiye
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Türkiye
| | - Emrah Yucesan
- Department of Neurogenetics, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Beyza Goncu
- Department of Medical Services and Techniques, Vocational School of Health Sciences, Bezmialem Vakif University, Istanbul, Türkiye
| | | | - Umit Yasar Kina
- Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Türkiye
| | - Cemil Ozgul
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
| | - Omer Faruk Duzenli
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba Cad., 34093, Istanbul, Türkiye
- Graduate School of Health Sciences, Istanbul University, Istanbul, Türkiye
| | - Ozcan Kocaturk
- Department of Neurology, Interventional Neurology, Balıkesir Atatürk City Hospital, Balıkesir, Türkiye
| | - Mustafa Calik
- Department of Pediatric Neurology, Faculty of Medicine, Harran University, Sanliurfa, Türkiye
| | - Ugur Ozbek
- IBG-Izmir Biomedicine and Genome Center, Izmir, Türkiye
| | - Sibel Aylin Ugur Iseri
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba Cad., 34093, Istanbul, Türkiye.
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Torrey EF. Did the human genome project affect research on Schizophrenia? Psychiatry Res 2024; 333:115691. [PMID: 38219345 DOI: 10.1016/j.psychres.2023.115691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
The Human Genome Project was undertaken primarily to discover genetic causes and better treatments for human diseases. Schizophrenia was targeted since three of the project`s principal architects had a personal interest and also because, based on family, adoption, and twin studies, schizophrenia was widely believed to be a genetic disorder. Extensive studies using linkage analysis, candidate genes, genome wide association studies [GWAS], copy number variants, exome sequencing and other approaches have failed to identify causal genes. Instead, they identified almost 300 single nucleotide polymorphisms [SNPs] associated with altered risks of developing schizophrenia as well as some rare variants associated with increased risk in a small number of individuals. Risk genes play a role in the clinical expression of most diseases but do not cause the disease in the absence of other factors. Increasingly, observers question whether schizophrenia is strictly a genetic disorder. Beginning in 1996 NIMH began shifting its research resources from clinical studies to basic research based on the promise of the Human Genome Project. Consequently, three decades later NIMH's genetics investment has yielded almost nothing clinically useful for individuals currently affected. It is time to review NIMH`s schizophrenia research portfolio.
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Brugger M, Lutz M, Müller-Nurasyid M, Lichtner P, Slater EP, Matthäi E, Bartsch DK, Strauch K. Joint Linkage and Association Analysis Using GENEHUNTER-MODSCORE with an Application to Familial Pancreatic Cancer. Hum Hered 2024; 89:8-31. [PMID: 38198765 DOI: 10.1159/000535840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Joint linkage and association (JLA) analysis combines two disease gene mapping strategies: linkage information contained in families and association information contained in populations. Such a JLA analysis can increase mapping power, especially when the evidence for both linkage and association is low to moderate. Similarly, an association analysis based on haplotypes instead of single markers can increase mapping power when the association pattern is complex. METHODS In this paper, we present an extension to the GENEHUNTER-MODSCORE software package that enables a JLA analysis based on haplotypes and uses information from arbitrary pedigree types and unrelated individuals. Our new JLA method is an extension of the MOD score approach for linkage analysis, which allows the estimation of trait-model and linkage disequilibrium (LD) parameters, i.e., penetrance, disease-allele frequency, and haplotype frequencies. LD is modeled between alleles at a single diallelic disease locus and up to three diallelic test markers. Linkage information is contributed by additional multi-allelic flanking markers. We investigated the statistical properties of our JLA implementation using extensive simulations, and we compared our approach to another commonly used single-marker JLA test. To demonstrate the applicability of our new method in practice, we analyzed pedigree data from the German National Case Collection for Familial Pancreatic Cancer (FaPaCa). RESULTS Based on the simulated data, we demonstrated the validity of our JLA-MOD score analysis implementation and identified scenarios in which haplotype-based tests outperformed the single-marker test. The estimated trait-model and LD parameters were in good accordance with the simulated values. Our method outperformed another commonly used JLA single-marker test when the LD pattern was complex. The exploratory analysis of the FaPaCa families led to the identification of a promising genetic region on chromosome 22q13.33, which can serve as a starting point for future mutation analysis and molecular research in pancreatic cancer. CONCLUSION Our newly proposed JLA-MOD score method proves to be a valuable gene mapping and characterization tool, especially when either linkage or association information alone provide insufficient power to identify the disease-causing genetic variants.
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Affiliation(s)
- Markus Brugger
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Medical Information Processing, Biometry and Epidemiology - IBE, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Lutz
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Medical Information Processing, Biometry and Epidemiology - IBE, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Medical Information Processing, Biometry and Epidemiology - IBE, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Emily P Slater
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University, Marburg, Germany
| | - Elvira Matthäi
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University, Marburg, Germany
| | - Detlef K Bartsch
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University, Marburg, Germany
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Medical Information Processing, Biometry and Epidemiology - IBE, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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Myśków B, Milczarski P, Stojałowski S. Genetic Map Construction Using F 2 and RIL/DH Mapping Population. Methods Mol Biol 2024; 2787:153-168. [PMID: 38656488 DOI: 10.1007/978-1-0716-3778-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Genetic mapping is the determination of the position and relative genetic distance between genes or molecular markers in the chromosomes of a particular species. The construction of genetic maps uses data from the genotyping of the mapping population. Among the different mapping populations used, two are relatively common: the F2 and recombinant inbred lines (RILs) obtained as a result of the controlled crossing of genetically diverse parental forms (e.g., inbred lines). Also, the dihaploid (DH) population is often used in plants, but obtaining DHs in different crops, including rye, is very difficult or even impossible. Any molecular marker system can be used for genotyping. Polymorphic markers are used for linkage analysis, differentiating parental forms with segregation in the mapping population, consistent with the appropriate single-gene model. A genetic map is a great source of information on a species and can be an exquisite tool for analyzing important quantitative traits (QT).This chapter presents the procedure of genetic map construction with two different algorithms using the JoinMap5.0 program. First, the Materials section briefly informs about the mapping program, showing how to obtain a mapping population and prepare data for mapping. Finally, the Methods section describes the protocol for the mapping procedure itself.
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Affiliation(s)
- Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin (ZUT), Szczecin, Poland.
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin (ZUT), Szczecin, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin (ZUT), Szczecin, Poland
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Mellinger S, Stervander M, Lundberg M, Drews A, Westerdahl H. Improved haplotype resolution of highly duplicated MHC genes in a long-read genome assembly using MiSeq amplicons. PeerJ 2023; 11:e15480. [PMID: 37456901 PMCID: PMC10349553 DOI: 10.7717/peerj.15480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/08/2023] [Indexed: 07/18/2023] Open
Abstract
Long-read sequencing offers a great improvement in the assembly of complex genomic regions, such as the major histocompatibility complex (MHC) region, which can contain both tandemly duplicated MHC genes (paralogs) and high repeat content. The MHC genes have expanded in passerine birds, resulting in numerous MHC paralogs, with relatively high sequence similarity, making the assembly of the MHC region challenging even with long-read sequencing. In addition, MHC genes show rather high sequence divergence between alleles, making diploid-aware assemblers incorrectly classify haplotypes from the same locus as sequences originating from different genomic regions. Consequently, the number of MHC paralogs can easily be over- or underestimated in long-read assemblies. We therefore set out to verify the MHC diversity in an original and a haplotype-purged long-read assembly of one great reed warbler Acrocephalus arundinaceus individual (the focal individual) by using Illumina MiSeq amplicon sequencing. Single exons, representing MHC class I (MHC-I) and class IIB (MHC-IIB) alleles, were sequenced in the focal individual and mapped to the annotated MHC alleles in the original long-read genome assembly. Eighty-four percent of the annotated MHC-I alleles in the original long-read genome assembly were detected using 55% of the amplicon alleles and likewise, 78% of the annotated MHC-IIB alleles were detected using 61% of the amplicon alleles, indicating an incomplete annotation of MHC genes. In the haploid genome assembly, each MHC-IIB gene should be represented by one allele. The parental origin of the MHC-IIB amplicon alleles in the focal individual was determined by sequencing MHC-IIB in its parents. Two of five larger scaffolds, containing 6-19 MHC-IIB paralogs, had a maternal and paternal origin, respectively, as well as a high nucleotide similarity, which suggests that these scaffolds had been incorrectly assigned as belonging to different loci in the genome rather than as alternate haplotypes of the same locus. Therefore, the number of MHC-IIB paralogs was overestimated in the haploid genome assembly. Based on our findings we propose amplicon sequencing as a suitable complement to long-read sequencing for independent validation of the number of paralogs in general and for haplotype inference in multigene families in particular.
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Affiliation(s)
- Samantha Mellinger
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Martin Stervander
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
- Bird Group, Natural History Museum, Tring, Hertfordshire, United Kingdom
| | - Max Lundberg
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Anna Drews
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
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Norris RH, Baker OS, Burgess ER, Tarone A, Gerry A, Trout Fryxell RT, Hinkle NC, Olds C, Boxler D, Wise KL, Machtinger ET, Scott JG. Selection for, and characterization of, fluralaner resistance in the house fly, Musca domestica. Pestic Biochem Physiol 2023; 191:105355. [PMID: 36963950 DOI: 10.1016/j.pestbp.2023.105355] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
House flies, Musca domestica (L), are the mechanical vector of >100 human and animal pathogens, including those that are antibiotic-resistant. Given that house flies are associated closely with human and livestock activity, they present medical and veterinary health concerns. Although there are numerous strategies for control of house fly populations, chemical control has been favored in many facilities. Products with pyrethroid active ingredients have been used predominantly for >35 years in space sprays. As a result, strong selection for pyrethroid resistance has led to reduced control of many populations. Reliance on a limited number of insecticides for decades has created fly control problems necessitating the discovery and formulation of new control chemistries. Fluralaner is a relatively new insecticide and acaricide (first reported in 2010), belonging to the isoxazoline class. These insecticides target the glutamate- and gamma-aminobutyric acid-gated (GABA) chloride channels, which is a different mode of action from other insecticides used against house flies. Although is it not currently registered for house fly control in the United States, previous work has shown that fluralaner is highly toxic to house flies and that there was limited cross-resistance found in laboratory strains having high levels of resistance to other insecticides. Herein, we characterized the time and age dependency of fluralaner toxicity, detected cross-resistance in populations from across the United States, and selected a highly resistant (>11,000-fold) house fly strain. We found that the fluralaner LD50 of 18-24 h old flies was 2-fold higher than for 5-6 d old flies. This appears to be due to more rapid penetration of fluralaner into the 5-6 d old flies. Fluralaner resistance was inherited as an intermediate to incompletely dominant trait and was mapped to chromosomes 5 and 3. Resistance could be suppressed to 7-fold with piperonyl butoxide, suggesting that cytochrome P450 (CYP)-mediated detoxification was a major mechanism of resistance. Decreased penetration was also demonstrated as a mechanism of resistance. The utility of fluralaner for house fly control is discussed.
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Affiliation(s)
- Rachel H Norris
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY 14853, USA
| | - Oshneil S Baker
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
| | - Edwin R Burgess
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
| | - Aaron Tarone
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alec Gerry
- Department of Entomology, University of California, Riverside, CA 92507, USA
| | - Rebecca T Trout Fryxell
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Nancy C Hinkle
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Cassandra Olds
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - David Boxler
- West Central Research, Extension and Education Center, University of Nebraska-Lincoln, North Platte, NE 69101, USA
| | - Kenneth L Wise
- NYS Integrated Pest Management Program, Cornell AgriTech, Geneva, NY 14456, USA
| | - Erika T Machtinger
- Department of Entomology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Jeffrey G Scott
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY 14853, USA.
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Susgun S, Kesim Y, Khalilov D, Sirin NG, Gezegen H, Salman B, Yucesan E, Gokcay G, Korbeyli HK, Balci MC, Iseri SAU, Baykan B, Bebek N. Reanalysis of exome sequencing data reveals a treatable neurometabolic origin in two previously undiagnosed siblings with neurodevelopmental disorder. Neurol Sci 2023:10.1007/s10072-023-06699-8. [PMID: 36849695 DOI: 10.1007/s10072-023-06699-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
Neurodevelopmental disorders (NDDs) have broad heterogeneity both clinically and genetically. Inborn errors of metabolism can be one of the reasons of neurodevelopmental disruption causing specific NDDs. Although there is tremendous advance in molecular identification via next-generation sequencing (NGS), there are still many unsolved patients with NDD. Reanalysis of NGS data with different pipelines can at least partially accomplish this challenge. Herein, we report clinic and genetic components of an adult sib-pair with an undiagnosed NDD condition, which has been solved through reanalysis of whole-exome sequencing (WES). Parallel analysis of SNP-based genotyping and WES was performed to focus on variants only in loci with positive logarithm of the odds scores. WES data was analyzed through three different pipelines with two distinct bed files. Reanalysis of WES data led us to detect a homozygous FOLR1 variant (ENST00000393676.5:c.610C > T, p.(Arg204Ter), rs952165627) in the affected sib-pair. Surprisingly, the variant could not be detected in the first analysis as the variant region is not included in the first bed file which may frequently be used. Biochemical tests of CSF have confirmed the genetic analysis, CSF folic acid levels were detected low in sib-pair, and intravenous folinic acid treatment improved the disease course for the first 6 months of follow-up even at late diagnosis age. Although combined analysis of SNP-based genotyping and WES is a powerful tool to reveal the genetic components of heterogeneous diseases, reanalysis of genome data still should be considered in unsolved patients. Also, biochemical screening helps us to decipher undiagnosed NDD that may be a treatable neurometabolic condition.
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Affiliation(s)
- Seda Susgun
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Yesim Kesim
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brooks University, Oxford, UK
| | - Dovlat Khalilov
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Nermin Gorkem Sirin
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Hasim Gezegen
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Baris Salman
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Emrah Yucesan
- Department of Neurogenetics, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gulden Gokcay
- Department of Pediatrics, Division of Pediatric Nutrition and Metabolism, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Huseyin Kutay Korbeyli
- Department of Pediatrics, Division of Pediatric Nutrition and Metabolism, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mehmet Cihan Balci
- Department of Pediatrics, Division of Pediatric Nutrition and Metabolism, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sibel Aylin Ugur Iseri
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
| | - Betul Baykan
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Nerses Bebek
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Qureshi MH, Ozlu N, Bayraktar H. Adaptive tracking algorithm for trajectory analysis of cells and layer-by-layer assessment of motility dynamics. Comput Biol Med 2022; 150:106193. [PMID: 37859286 DOI: 10.1016/j.compbiomed.2022.106193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/26/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2022]
Abstract
Tracking biological objects such as cells or subcellular components imaged with time-lapse microscopy enables us to understand the molecular principles about the dynamics of cell behaviors. However, automatic object detection, segmentation and extracting trajectories remain as a rate-limiting step due to intrinsic challenges of video processing. This paper presents an adaptive tracking algorithm (Adtari) that automatically finds the optimum search radius and cell linkages to determine trajectories in consecutive frames. A critical assumption in most tracking studies is that displacement remains unchanged throughout the movie and cells in a few frames are usually analyzed to determine its magnitude. Tracking errors and inaccurate association of cells may occur if the user does not correctly evaluate the value or prior knowledge is not present on cell movement. The key novelty of our method is that minimum intercellular distance and maximum displacement of cells between frames are dynamically computed and used to determine the threshold distance. Since the space between cells is highly variable in a given frame, our software recursively alters the magnitude to determine all plausible matches in the trajectory analysis. Our method therefore eliminates a major preprocessing step where a constant distance was used to determine the neighbor cells in tracking methods. Cells having multiple overlaps and splitting events were further evaluated by using the shape attributes including perimeter, area, ellipticity and distance. The features were applied to determine the closest matches by minimizing the difference in their magnitudes. Finally, reporting section of our software were used to generate instant maps by overlaying cell features and trajectories. Adtari was validated by using videos with variable signal-to-noise, contrast ratio and cell density. We compared the adaptive tracking with constant distance and other methods to evaluate performance and its efficiency. Our algorithm yields reduced mismatch ratio, increased ratio of whole cell track, higher frame tracking efficiency and allows layer-by-layer assessment of motility to characterize single-cells. Adaptive tracking provides a reliable, accurate, time efficient and user-friendly open source software that is well suited for analysis of 2D fluorescence microscopy video datasets.
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Affiliation(s)
- Mohammad Haroon Qureshi
- Department of Molecular Biology and Genetics, Koç University, Rumelifeneri Yolu, Sariyer, 34450, Istanbul, Turkey; Center for Translational Research, Koç University, Rumelifeneri Yolu, Sariyer, 34450, Istanbul, Turkey
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koç University, Rumelifeneri Yolu, Sariyer, 34450, Istanbul, Turkey
| | - Halil Bayraktar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Sariyer, 34467, Istanbul, Turkey.
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Wijesiriwardhana P, Musolf AM, Bailey-Wilson JE, Wetthasinghe TK, Dissanayake VHW. Genome-wide linkage search for cancer susceptibility loci in a cohort of non BRCA1/2 families in Sri Lanka. BMC Res Notes 2022; 15:190. [PMID: 35655316 DOI: 10.1186/s13104-022-06081-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Objective Although linkage studies have been utilized for the identification of variants associated with cancer in the world, little is known about their role in non BRCA1/2 individuals in the Sri Lankans. Hence we performed linkage analysis to identify susceptibility loci related to the inherited risk of cancer in a cohort of Sri Lankans affected with hereditary breast cancer. The Illumina global screening array having 654,027 single nucleotide polymorphism markers was performed in four families, in which at least three individuals within third degree relatives were affected by breast cancer. Two-point parametric linkage analysis was conducted assuming disease allele frequency of 1%. Penetrance was set at 90% for carriers with a 10% phenocopy rate. Results Thirty-one variants exhibited genome-wide suggestive HLODs. The top overall HLOD score was at rs1856277, an intronic variant in MYO16 on chromosome 13. The two most informative families also suggested several candidate linked loci in genes, including ERAP1, RPRM, WWOX, CDH1, EXOC1, HUS1B, STIM1 and TUSC1. This study provides the first step in identifying germline variants that may be involved in risk of cancer in cancer-aggregated non-BRCA1/2 families from the understudied Sri Lankan population. Several candidate linked regions showed suggestive evidence of linkage to cancer risk. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06081-5.
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Li T, Li Q, Wang J, Yang Z, Tang Y, Su Y, Zhang J, Qiu X, Pu X, Pan Z, Zhang H, Liang J, Liu Z, Li J, Yan W, Yu M, Long H, Wei Y, Deng G. High-resolution detection of quantitative trait loci for seven important yield-related traits in wheat (Triticum aestivum L.) using a high-density SLAF-seq genetic map. BMC Genom Data 2022; 23:37. [PMID: 35562674 PMCID: PMC9107147 DOI: 10.1186/s12863-022-01050-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat (Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments. RESULTS A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. CONCLUSIONS Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.
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Affiliation(s)
- Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Wuyun Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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11
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Cheng B, Gao X, Cao N, Ding Y, Chen T, Zhou Q, Gao Y, Xin Z, Zhang L. QTL mapping for adult plant resistance to wheat stripe rust in M96-5 × Guixie 3 wheat population. J Appl Genet 2022. [PMID: 35338429 DOI: 10.1007/s13353-022-00686-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/11/2021] [Accepted: 05/15/2021] [Indexed: 11/02/2022]
Abstract
Development of cultivars with multiple resistances has proven to be an effective way to prevent diseases in wheat breeding. The Guixie 3 variety (GX3) has shown excellent performance in resistance to stripe rust in field for many years. The purpose of this study was to detect quantitative trait loci (QTL) associated with resistance to stripe rust in the adult plant stage and determine closely linked molecular markers. A population of recombinant inbred lines (n = 228) was derived from a cross between the susceptible landrace Mian 96-5 (M96-5) and GX3 variety and evaluated in multiple field studies, and QTL analysis enabled to elucidate genetic architecture of wheat resistance to stripe rust. A total of 19 QTL for stripe rust resistance were mapped on 12 chromosomes using phenotypic data from multiple field tests over the course of 6 years. These chromosomes included 1B (2), 1D (2), 2A (2), 2B (2), 2D (1), 4B (2), 4D (1), 5A (3), 5B (1), 6A (1), 6B (1), and 7B (1). Two stable QTL on chromosomes 2AS (Qyr.gaas.2A) and 6AL (Qyr.gaas.6A) were detected in six and five different environments, respectively; in both QTL, positive allele was contributed by GX3 variety. Qyr.gaas.2A was found to be crucial for increasing adult plant resistance, which may explain the large phenotypic variation of 45.52%. Our results provide theoretical and molecular insight for wheat breeding and suggest the cloning of genes associated with the GX3 variety may be beneficial in future studies.
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12
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Susgun S, Kasan K, Yucesan E. Gene Hunting Approaches through the Combination of Linkage Analysis with Whole-Exome Sequencing in Mendelian Diseases: From Darwin to the Present Day. Public Health Genomics 2022; 24:207-217. [PMID: 34237751 DOI: 10.1159/000517102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the context of medical genetics, gene hunting is the process of identifying and functionally characterizing genes or genetic variations that contribute to disease phenotypes. In this review, we would like to summarize gene hunting process in terms of historical aspects from Darwin to now. For this purpose, different approaches and recent developments will be detailed. SUMMARY Linkage analysis and association studies are the most common methods in use for explaining the genetic background of hereditary diseases and disorders. Although linkage analysis is a relatively old approach, it is still a powerful method to detect disease-causing rare variants using family-based data, particularly for consanguineous marriages. As is known that, consanguineous marriages or endogamy poses a social problem in developing countries, however, this same condition also provides a unique opportunity for scientists to identify and characterize pathogenic variants. The rapid advancements in sequencing technologies and their parallel implementation together with linkage analyses now allow us to identify the candidate variants related to diseases in a relatively short time. Furthermore, we can now go one step further and functionally characterize the causative variant through in vitro and in vivo studies and unveil the variant-phenotype relationships on a molecular level more robustly. Key Messages: Herein, we suggest that the combined analysis of linkage and exome analysis is a powerful and precise tool to diagnose clinically rare and recessively inherited conditions.
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Affiliation(s)
- Seda Susgun
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey.,Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Koray Kasan
- Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Emrah Yucesan
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
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13
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Yang IJ, Tu YA, Pan SP, Huang TC, Chen CL, Lin MW, Tsai YY, Yao YL, Su YN, Chen SU. First report of a successful pregnancy by preimplantation genetic testing for Beckwith-Wiedemann syndrome. Taiwan J Obstet Gynecol 2022; 61:174-179. [PMID: 35181034 DOI: 10.1016/j.tjog.2021.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE Beckwith-Wiedemann syndrome (BWS) is a rare imprinting gene disorder. Maternal CDKN1C mutation comprises 5% of etiologies of BWS. There is no successful report of preventing BWS by preimplantation genetic testing for monogenic disease (PGT-M) in the literature. Is PGT-M applicable for preventing BWS ? CASE REPORT This 39-year-old woman conceived naturally and delivered a boy who was diagnosed of BWS. The genetic testing of her son revealed CDKN1C gene mutation, and of the mother showed a carrier of the same mutation. She underwent controlled ovarian stimulation, oocyte pickup, and intracytoplasmic sperm injection. Trophectoderm biopsies were performed and samples were checked for PGT. Two wild-type and euploid embryos were thawed and transferred. One intrauterine pregnancy was achieved. The patient delivered a healthy female baby at 37 weeks of gestation. CONCLUSION In this case, we first report a successful pregnancy with a wild-type CDKN1C gene baby achieved by PGT-M.
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Affiliation(s)
- Ih-Jane Yang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-An Tu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Song-Po Pan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ting-Chi Huang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Ling Chen
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Wei Lin
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Yi Tsai
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Yao
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Ning Su
- Sofiva Genomics Co, Ltd., Taipei, Taiwan; Dianthus Maternal Fetal Medicine Clinic, Taipei, Taiwan
| | - Shee-Uan Chen
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan.
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14
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Badhan A, Low KE, Jones DR, Xing X, Milani MRM, Polo RO, Klassen L, Venketachalam S, Hahn MG, Abbott DW, McAllister TA. Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses. Comput Struct Biotechnol J 2022; 20:148-164. [PMID: 34976318 PMCID: PMC8702857 DOI: 10.1016/j.csbj.2021.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.
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Key Words
- AB, arabinan
- ADF, acid detergent fibre
- AG, arabinogalactan
- AGP, arabinogalactan protein
- AIR, alcohol insoluble residue
- AO, ammonium oxalate
- AX, arabinoxylan
- BS, barley straw
- CAZyme, carbohydrate active enzyme
- CAZymes
- CE, carbohydrate esterase
- CH, chlorite
- DE, differentially expressed
- Dietary polysaccharides
- Differential gene expression
- ELISA, enzyme-linked immunosorbent assay
- FID, flame ionization detection GC, gas chromatography
- GH, glycosyl hydrolase
- Glycome profiling
- Glycoside hydrolase
- HG, homogalacturonan
- HPAEC-PAD, high performance anion exchange chromatography coupled with pulsed amperometric detection
- HX, heteroxylan
- Linkage analysis
- MS, mass spectrometry
- NDF, neutral detergent fibre
- Nutrient utilization
- PC, post-chlorite
- PL, polysaccharide lyase
- RG, rhamnogalacturonan
- Rumen microbiome
- SC, sodium carbonate
- TTIR, total tract indigestible residue
- Transcriptome
- XG, xyloglucan
- mAbs, monoclonal antibodies
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Affiliation(s)
- Ajay Badhan
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Kristin E Low
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Xiaohui Xing
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Mohammad Raza Marami Milani
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Rodrigo Ortega Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Leeann Klassen
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Sivasankari Venketachalam
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
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15
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Kimura S. Secular change of interdependencies in the clusters of the Japanese motor vehicle industry: a case study in the Tokai region. SN Bus Econ 2022; 2:174. [PMID: 36275918 PMCID: PMC9579610 DOI: 10.1007/s43546-022-00348-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/02/2022] [Indexed: 11/07/2022]
Abstract
The Tokai region, including the prefectures of Aichi, Shizuoka, Mie, Gifu, and Shiga, in the center of Japan’s largest island, Honshu, houses clusters of the motor vehicle industry (MVI) and accounts for more than 50% of the domestic value from the MVI’s manufactured goods shipments. The subcontracted factories in the MVI tend to locate their main hub close to the assembly factories, creating large supply-chain structures with wide transactions. Since the 1990s, new automotive assembly factories and subcontracted factories have been built outside Aichi, in the Kyushu and Tohoku regions. This may have had an influence on local industries and economy. This study applies the hypothetical extraction method to the Tokai region using the Chubu-region multi-regional input–output tables to understand the secular changes of interdependencies in the MVI as each prefecture in the Tokai region has automotive assembly factories. The study shows that the Aichi MVI has strengthened its ties with industries in other prefectures in the Tokai region and elsewhere because the rate of growth for Aichi dropped from 2005 to 2010. Still, other prefecture rates rose, thus expanding its supply-chain structure throughout Japan more than before. In addition, the study shows that the Shizuoka MVI has increased business relationships not only within its region but also with Aichi. These results highlight that the industrial linkage between the Aichi MVI and the Shizuoka MVI has deepened. However, the results show that the supply-chain structures of the Mie, Gifu, and Shiga MVI have remained inside of their respective regions.
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Affiliation(s)
- Shinichiro Kimura
- Chubu Region Institute for Social and Economic Research, 3F Hisaya Park Building, 4-14-2 Sakae, Naka-ku, Nagoya, Aichi 460-0008 Japan
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16
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Lup SD, Wilson-Sánchez D, Micol JL. Mapping-by-Sequencing of Point and Insertional Mutations with Easymap. Methods Mol Biol 2022; 2484:343-361. [PMID: 35461462 DOI: 10.1007/978-1-0716-2253-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Random mutagenesis followed by screening for phenotypes of interest is a widely used strategy for genetic dissection of biological pathways; however, identifying the causal gene traditionally required time-consuming mapping approaches based on iterative linkage analysis. Mapping-by-sequencing accelerates this process, efficiently linking the phenotype of a mutant to a narrow candidate genomic region, using next-generation sequencing (NGS) data from a mapping population segregating for the mutant phenotype. To enable researchers at any bioinformatics skill level to conduct mapping-by-sequencing, we developed the Easymap mapping software. In this protocol we break down the steps involved in mapping-by-sequencing. First, we describe different ways of obtaining a mapping population and the steps used to generate NGS data. Next, we show how to analyze the NGS data using Easymap and how to obtain a list of candidate mutations, along with comprehensive information for assessing the potential causality of each candidate. Thus, this protocol enables the user to conduct mapping-by-sequencing using Easymap, facilitating the identification of causal loci for a mutant phenotype of interest.
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Affiliation(s)
- Samuel Daniel Lup
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - David Wilson-Sánchez
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain.
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17
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Wang Y, Chen X, Jiang T, Gu Y, Zhang X, Yuan W, Zhao A, Li R, Wang Z, Hu Z, Liu H. Expanding the phenotypic spectrum of mutations in LRP2: a novel candidate gene of non-syndromic familial comitant strabismus. J Transl Med 2021; 19:495. [PMID: 34872573 PMCID: PMC8647414 DOI: 10.1186/s12967-021-03155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Background Comitant strabismus (CS) is a heterogeneous disorder that is a major contributing factor to unilateral childhood-onset visual impairment. Studies have confirmed that genetic factors play an important role in the development of CS. The aim of this study was to identify the genetic cause of non-syndromic familial CS. Methods Fourteen unrelated CS families were recruited for the study. Twelve affected and 2 unaffected individuals from a large four-generation family (CS08) were selected to perform whole genome-wide linkage analysis. Parallel whole-exome sequencing (WES) was conducted in the same family (9 patients and 1 unaffected member) and 31 additional CS cases from 13 other unrelated families. Sanger sequencing was used to determine whether any of the remaining variants co-segregated with the disease phenotype in the corresponding family. Results Based on linkage analysis, CS in family CS08 mapped to a novel region of 34.17 centimorgan (cM) on chromosome 2q22.3-2q32.1 between markers D2S151 and D2S364, with a maximum log odds (LOD) score of 3.54 (theta = 0) at D2S142. Parallel WES identified a heterozygous variant, LRP2 c.335 A > G (p.Q112R), located in such a linkage interval that completely co-segregated with the disease in the family. Furthermore, another novel heterozygous variant (c.7274A > G, p.D2425G) in LRP2 that co-segregated was detected in 2 additional affected individuals from another unrelated family by WES. Both variants are predicted to be damaging by PolyPhen-2, SIFT and MutationTaster, and were absent in 100 ethnically matched normal controls. Conclusion LRP2 is a novel candidate genetic cause of non-syndromic familial CS. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03155-z.
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Affiliation(s)
- Yue Wang
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Xuejuan Chen
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Tao Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Yayun Gu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Xiaohan Zhang
- Department of Ophthalmology, Wuxi Children's Hospital, Wuxi, China
| | - Wenwen Yuan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Andi Zhao
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China
| | - Rui Li
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China
| | - Zijin Wang
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China.
| | - Hu Liu
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China.
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18
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Wei W, Wang P, Li S, Fan G, Zhao F, Zhang X, Shi G, Feng X, Song G, Wang X, Wang F, Wang D, Zhang W, Qiu F, Zhang Y, Li X, Pei J, Zhou X, Zhao Z. Rapid identification of candidate genes controlling male-sterility in Foxtail millet ( Setaria italica). Mol Breed 2021; 41:73. [PMID: 37309520 PMCID: PMC10236058 DOI: 10.1007/s11032-021-01269-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Photo-(thermo-) sensitive genic male-sterile line is the key component of two-line hybridization system in foxtail millet (Setaria italica), but the genetic basis of male sterility in most male-sterile lines is still unclear. In the present study, a large F2 population was developed derived from a cross between the photo-(thermo-) sensitive male-sterile line A2 and the fertile-line 1484-5. Thirty plants with extreme high and extreme low fertility were selected from the population to construct a sterile DNA pool and a fertile DNA pool, respectively. Sequencing both DNA pools and data analysis revealed that two QTLs conferred male-sterility, qSiMS6.1 with a major effect and qSiMS6.2 with a minor effect, on chromosome 6. Both QTLs exhibited complete dominance. The major QTL, qSiMS6.1, was delimited to a 186-kb interval between the markers SiM20 and SiM9 by the joint analysis of QTL-seq and QTL mapping with SSR and structure variation markers. Millet_GLEAN_10020454 in this region is the most likely candidate gene for qSiMS6.1 since it is predicted to encode a male-sterile 5 like protein. These results lay a solid foundation for qSiMS6.1 cloning and provided gene resources for breeding new male-sterile lines. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01269-2.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Fengcang Qiu
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
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Strzelec K, Dziedzic A, Łazarz-Bartyzel K, Grabiec AM, Gutmajster E, Kaczmarzyk T, Plakwicz P, Gawron K. Clinics and genetic background of hereditary gingival fibromatosis. Orphanet J Rare Dis 2021; 16:492. [PMID: 34819125 PMCID: PMC8611899 DOI: 10.1186/s13023-021-02104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 11/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hereditary gingival fibromatosis (HGF) is a rare condition characterized by slowly progressive overgrowth of the gingiva. The severity of overgrowth may differ from mild causing phonetic and masticatory issues, to severe resulting in diastemas or malposition of teeth. Both, autosomal-dominant and autosomal-recessive forms of HGF are described. The aim of this review is a clinical overview, as well as a summary and discussion of the involvement of candidate chromosomal regions, pathogenic variants of genes, and candidate genes in the pathogenesis of HGF. The loci related to non-syndromic HGF have been identified on chromosome 2 (GINGF, GINGF3), chromosome 5 (GINGF2), chromosome 11 (GINGF4), and 4 (GINGF5). Of these loci, pathogenic variants of the SOS-1 and REST genes inducing HGF have been identified in the GINGF and the GINGF5, respectively. Furthermore, among the top 10 clusters of genes ranked by enrichment score, ATP binding, and fibronectin encoding genes were proposed as related to HGF. CONCLUSION The analysis of clinical reports as well as translational genetic studies published since the late'90s indicate the clinical and genetic heterogeneity of non-syndromic HGF and point out the importance of genetic studies and bioinformatics of more numerous unrelated families to identify novel pathogenic variants potentially inducing HGF. This strategy will help to unravel the molecular mechanisms as well as uncover specific targets for novel and less invasive therapies of this rare, orphan condition.
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Affiliation(s)
- Karolina Strzelec
- Department of Molecular Biology and Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medykow 18, 40-752, Katowice, Poland
| | - Agata Dziedzic
- Department of Molecular Biology and Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medykow 18, 40-752, Katowice, Poland
| | - Katarzyna Łazarz-Bartyzel
- Department of Periodontology and Oral Medicine, Medical College, Jagiellonian University, Kraków, Poland
| | - Aleksander M Grabiec
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Ewa Gutmajster
- Department of Molecular Biology and Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medykow 18, 40-752, Katowice, Poland
| | - Tomasz Kaczmarzyk
- Department of Periodontology and Oral Medicine, Medical College, Jagiellonian University, Kraków, Poland.,Department of Oral Surgery, Medical College, Jagiellonian University, Kraków, Poland
| | - Paweł Plakwicz
- Department of Periodontology and Oral Diseases, Faculty of Dentistry, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Gawron
- Department of Molecular Biology and Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medykow 18, 40-752, Katowice, Poland.
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20
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Lan H, Nunes C, Lopes GR, Wang K, Zhao L, Coimbra MA, Hu Z. In vitro immunomodulatory activity of water-soluble glucans from fresh and dried Longan (Dimocarpus longan Lour.). Carbohydr Polym 2021; 266:118106. [PMID: 34044924 DOI: 10.1016/j.carbpol.2021.118106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022]
Abstract
Longan (Dimocarpus longan Lour.) is a seasonal tropical fruit used by Chinese medicine in both fresh and dried pulp forms. Their polysaccharides have been reported to have biological activity. However, their composition and immune activity have not yet been disclosed. To fulfil this aim, hot water-soluble polysaccharides of fresh and dried longan pulp were fractionated according to their molecular weight by ultrafiltration (10, 50, 100 kDa cut off). The main polysaccharides recovered were 1,6-linked glucans branched at O-3 (4-8%), O-2 (1%), O-2,4 (0.1%), and O-3,4 (0.1%). The drying process promotes the solubility of the polysaccharides. These glucans from fresh and dried longan pulp have immunomodulatory activity, shown by in vitro phagocytosis, NO, TNF-α, and IL-6 macrophages production assays. They showed also to inhibit the inflammatory response induced by LPS. The immunological activity of these glucans seems to have different responses dependent on their molecular weight, related to the immune regulatory pathways.
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Affiliation(s)
- Haibo Lan
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Cláudia Nunes
- CICECO - Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal; LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Guido R Lopes
- CICECO - Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal; LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Kai Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lei Zhao
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Manuel A Coimbra
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Zhuoyan Hu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China.
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21
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Black I, Heiss C, Carlson RW, Azadi P. Linkage Analysis of Oligosaccharides and Polysaccharides: A Tutorial. Methods Mol Biol 2021; 2271:249-271. [PMID: 33908013 DOI: 10.1007/978-1-0716-1241-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Polysaccharides and oligosaccharides are a diverse group of natural polymers with important biological functions. The diversity of carbohydrate polymers is vast, ranging from small oligosaccharides of defined composition decorating proteins, to large, complex heteropolymers comprising integral cell wall components of plants, fungi and bacteria. An important step in the elucidation of unknown carbohydrate structures in a sample is the assessment of the various linkages present. This is accomplished by performing linkage analysis of the sample. The analysis proceeds as a successive series of chemical steps in which unlinked carbohydrate hydroxyls are marked with methyl groups, the sample is hydrolyzed into monosaccharides and reduced to alditols, and finally free hydroxyls are acetylated. Gas chromatography-mass spectrometry (GC-MS) analysis is employed to analyze the resultant partially methylated alditol acetates (PMAAs). The following paper reviews the major literature pertaining to the specific protocol for linkage analysis of carbohydrates outlined herein. The review details additional steps necessary for the completion of uronic acid linkage analysis, as well as analysis of chitin containing polymers. It also gives chromatographic examples of common erroneous results which the first time practitioner will want to be aware of. Our hope is that this protocol will serve as a definitive guide, allowing novice researchers to perform linkage analysis of carbohydrates in their own lab.
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Affiliation(s)
- Ian Black
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Russell W Carlson
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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22
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Teerlink CC, Stevens J, Hernandez R, Facelli JC, Cannon-Albright LA. An intronic variant in the CELF4 gene is associated with risk for colorectal cancer. Cancer Epidemiol 2021; 72:101941. [PMID: 33930674 DOI: 10.1016/j.canep.2021.101941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/17/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Germline predisposition variants associated with colorectal cancer (CRC) have been identified but all are not yet identified. We sought to identify the responsible predisposition germline variant in an extended high-risk CRC pedigree that exhibited evidence of linkage to the 18q12.2 region (TLOD = +2.81). METHODS DNA from two distantly related carriers of the hypothesized predisposition haplotype on 18q12.2 was sequenced to identify candidate variants. The candidate rare variants shared by the related sequenced subjects were screened in 3,094 CRC cases and 5x population-matched controls from UKBiobank to test for association. Further segregation of the variant was tested via Taqman assay in other sampled individuals in the pedigree. RESULTS Analysis of whole genome sequence data for the two related hypothesized predisposition haplotype carriers, restricted to the shared haplotype boundaries, identified multiple (n = 6) rare candidate non-coding variants that were tested for association with CRC risk in UKBiobank. A rare intronic variant ofCELF4 gene, rs568643870, was significantly associated with CRC (p = 0.004, OR = 5.0), and segregated with CRC in other members of the linked pedigree. CONCLUSION Evidence of segregation in a high-risk pedigree, case-control association in an external dataset, and identification of additional CRC-affected carriers in the linked pedigree support a role for a rareCELF4 intronic variant in CRC risk.
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Affiliation(s)
- Craig C Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - Jeff Stevens
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - Rolando Hernandez
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
| | - Julio C Facelli
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; Center for Clinical and Translational Science, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
| | - Lisa A Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT 84148, USA; Huntsman Cancer Institute, Salt Lake City, UT 84112, USA.
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23
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Zeb M, Tackaberry LE, Massicotte HB, Egger KN, Reimer K, Lu G, Heiss C, Azadi P, Lee CH. Structural elucidation and immuno-stimulatory activity of a novel polysaccharide containing glucuronic acid from the fungus Echinodontium tinctorium. Carbohydr Polym 2021; 258:117700. [PMID: 33593571 DOI: 10.1016/j.carbpol.2021.117700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/17/2022]
Abstract
An immuno-stimulatory polysaccharide (EtISPFa) was purified from water extract of the fungus Echinodontium tinctorium. EtISPFa has an estimated weight average molecular weight (Mw) of 1354 kDa and is composed of glucose (66.2 %), glucuronic acid (10.1 %), mannose (6.7 %), galactose (6.4 %), xylose (5.6 %), rhamnose (3.1 %), fucose (1.8 %), and arabinose (0.2 %). It has multiple glycosidic linkages, with 3-Glcp (19.8 %), 4-GlcpA (10.8 %), 6-Glcp (10.7 %), and 3,6-Glcp (8.7 %) being the most prominent. NMR analysis showed that EtISPFa has a backbone containing mostly of 3-substituted β-glucopyranose with 4-substituted glucopyranosyluronic acid. Short side chains consisting of an average of two β-glycopyranose residues, connected through 1→6 linkages, are attached to the 6-position of about every 4th or 5th backbone glucose residue. EtISPFa is a novel glucuronic acid-containing β-glucan capable of significantly inducing the production of cytokines IL-17, IL-16, MIP-2, G-CSF,GM-CSF, LIF, MIP-1α, MIP-1β, and RANTES in vitro. EtISPFa should be further explored for its immuno-stimulatory activity in vivo.
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Affiliation(s)
- Mehreen Zeb
- Chemistry and Biochemistry Program, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9, Canada.
| | - Linda E Tackaberry
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9, Canada.
| | - Hugues B Massicotte
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9, Canada.
| | - Keith N Egger
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9, Canada.
| | - Kerry Reimer
- Chemistry and Biochemistry Program, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9, Canada.
| | - Grace Lu
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia, 30602, USA.
| | - Christian Heiss
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia, 30602, USA.
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia, 30602, USA.
| | - Chow H Lee
- Chemistry and Biochemistry Program, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9, Canada.
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24
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Collin R, Dugas V, Pelletier AN, Chabot-Roy G, Lesage S. Evidence of genetic epistasis in autoimmune diabetes susceptibility revealed by mouse congenic sublines. Immunogenetics 2021; 73:307-319. [PMID: 33755757 DOI: 10.1007/s00251-021-01214-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
Susceptibility to autoimmune diabetes is a complex genetic trait. Linkage analyses exploiting the NOD mouse, which spontaneously develops autoimmune diabetes, have proved to be a useful tool for the characterization of some of these traits. In a linkage analysis using 3A9 TCR transgenic mice on both B10.BR and NOD.H2k backgrounds, we previously determined that both the Idd2 and Idd13 loci were linked to the proportion of immunoregulatory CD4-CD8- double negative (DN) T cells. In addition to Idd2 and Idd13, five other loci showed weak linkage to the proportion of DN T cells. Of interest, in an interim analysis, a locus on chromosome 12 is linked to DN T cell proportion in both the spleen and the lymph nodes. To determine the impact of this locus on DN T cells, we generated two congenic sublines, which we named Chr12P and Chr12D for proximal and distal, respectively. While 3A9 TCR:insHEL NOD.H2k-Chr12D mice were protected from diabetes, 3A9 TCR:insHEL NOD.H2k-Chr12P showed an increase in diabetes incidence. Yet, the proportion of DN T cells was similar to the parental 3A9 TCR NOD.H2k strain for both of these congenic sublines. A genome-wide two dimensional LOD score analysis reveals genetic epistasis between chromosome 12 and the Idd13 locus. Altogether, this study identified further complex genetic interactions in defining the proportion of DN T cells, along with evidence of genetic epistasis within a locus on chromosome 12 influencing autoimmune susceptibility.
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Affiliation(s)
- Roxanne Collin
- Cellular Immunogenetics laboratory, Division of Immunology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, H1T 2M4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, Quebec, H3C 3J7, Canada
- CellCarta, 201 President Kennedy Avenue, Suite 3900, Montreal, Quebec, H2X 3Y7, Canada
| | - Véronique Dugas
- Cellular Immunogenetics laboratory, Division of Immunology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, H1T 2M4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, Quebec, H3C 3J7, Canada
| | | | - Geneviève Chabot-Roy
- Cellular Immunogenetics laboratory, Division of Immunology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, H1T 2M4, Canada
| | - Sylvie Lesage
- Cellular Immunogenetics laboratory, Division of Immunology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, H1T 2M4, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, Quebec, H3C 3J7, Canada.
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25
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Ergun U, Say B, Ergun SG, Percin FE, Inan L, Kaygisiz S, Asal PG, Yurteri B, Struchalin M, Shtokalo D, Ergun MA. Genome-wide association and whole exome sequencing studies reveal a novel candidate locus for restless legs syndrome. Eur J Med Genet 2021; 64:104186. [PMID: 33662638 DOI: 10.1016/j.ejmg.2021.104186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/05/2021] [Accepted: 02/27/2021] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The restless legs syndrome (RLS) is a common heritable neurologic disorder which is characterized by an irresistible desire to move and unpleasant sensations in the legs. METHODS We aim to identify new variants associated with RLS by performing genome-wide linkage and subsequent association analysis of forty member's family with history of RLS. RESULTS We found evidence of linkage for three loci 7q21.11 (HLOD = 3.02), 7q21.13-7q21.3 (HLOD = 3.02) and 7q22.3 (HLOD = 3.09). Fine-mapping of those regions in association study using exome sequencing identified SEMA3A (p-value = 8.5·10-4), PPP1R9A (p-value = 7.2·10-4), PUS7 (p-value = 8.7·10-4), CDHR3 (p-value = 7.2·10-4), HBP1 (p-value = 1.5·10-4) and COG5 (p-value = 1.5·10-4) genes with p-values below significance threshold. CONCLUSION Linkage analysis with subsequent association study of exome variants identified six new genes associated with RLS mapped on 7q21 and q22.
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Affiliation(s)
- Ufuk Ergun
- Kırıkkale University Faculty of Medicine, Department of Neurology, Kırıkkale, Turkey
| | - Bahar Say
- Kırıkkale University Faculty of Medicine, Department of Neurology, Kırıkkale, Turkey
| | - Sezen Guntekin Ergun
- Hacettepe University Faculty of Medicine, Department of Medical Biology, Anakara, Turkey
| | - Ferda Emriye Percin
- Gazi University Faculty of Medicine, Department of Medical Genetics, Ankara, Turkey
| | - Levent Inan
- Ministry of Health Ankara Research and Training Hospital Neurology and Algology Department, Ankara, Turkey
| | - Sukran Kaygisiz
- Ministry of Health Ordu University Traning and Research Hospital, Ordu, Turkey
| | - Pınar Gelener Asal
- Dr. Suat Gunsel University of Kyrenia Hospital, Kyrenia, Turkish Republic of Northern Cyprus
| | - Buket Yurteri
- Hacettepe University Faculty of Medicine, Department of Pediatric Basic Sciences, Ankara, Turkey
| | | | - Dmitry Shtokalo
- AcademGene Ltd, Russia; A.P.Ershov Institute of Informatics Systems SB RAS, Russia
| | - Mehmet Ali Ergun
- Gazi University Faculty of Medicine, Department of Medical Genetics, Ankara, Turkey.
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26
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Wei Z, Yuan Q, Lin H, Li X, Zhang C, Gao H, Zhang B, He H, Liu T, Jie Z, Gao X, Shi S, Wang B, Gao Z, Kong L, Qian Q, Shang L. Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress. BMC Plant Biol 2021; 21:85. [PMID: 33563229 DOI: 10.1186/s12870-021-02857-2852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/26/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. RESULT Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research. CONCLUSIONS The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.
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Affiliation(s)
- Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tianjiao Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhang Jie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xu Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shandang Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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27
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Wei Z, Yuan Q, Lin H, Li X, Zhang C, Gao H, Zhang B, He H, Liu T, Jie Z, Gao X, Shi S, Wang B, Gao Z, Kong L, Qian Q, Shang L. Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress. BMC Plant Biol 2021; 21:85. [PMID: 33563229 PMCID: PMC7874481 DOI: 10.1186/s12870-021-02857-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. RESULT Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research. CONCLUSIONS The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.
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Affiliation(s)
- Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tianjiao Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhang Jie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xu Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shandang Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Abstract
Multiparental populations are located midway between association mapping that relies on germplasm collections and classic linkage analysis, based upon biparental populations. They provide several key advantages such as the possibility to include a higher number of alleles and increased level of recombination with respect to biparental populations, and more equilibrated allelic frequencies than association mapping panels. Moreover, in these populations new allele's combinations arise from recombination that may reveal transgressive phenotypes and make them a useful pre-breeding material. Here we describe the strategies for working with multiparental populations, focusing on nested association mapping populations (NAM) and multiparent advanced generation intercross populations (MAGIC). We provide details from the selection of founders, population development, and characterization to the statistical methods for genetic mapping and quantitative trait detection.
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Affiliation(s)
- Isidore Diouf
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
| | - Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain.
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Stone DL, Beck DB, Manthiram K, Park YH, Chae JJ, Remmers E, Kastner DL. The systemic autoinflammatory diseases: Coming of age with the human genome. J Allergy Clin Immunol 2020; 146:997-1001. [PMID: 32987090 PMCID: PMC11008603 DOI: 10.1016/j.jaci.2020.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022]
Affiliation(s)
| | - David B Beck
- National Human Genome Research Institute, Bethesda, Md
| | | | | | - Jae Jin Chae
- National Human Genome Research Institute, Bethesda, Md
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Whiting RM, Torabi S, Lukens L, Eskandari M. Genomic regions associated with important seed quality traits in food-grade soybeans. BMC Plant Biol 2020; 20:485. [PMID: 33096978 PMCID: PMC7583236 DOI: 10.1186/s12870-020-02681-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/30/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND The production of soy-based food products requires specific physical and chemical characteristics of the soybean seed. Identification of quantitative trait loci (QTL) associated with value-added traits, such as seed weight, seed protein and sucrose concentration, could accelerate the development of competitive high-protein soybean cultivars for the food-grade market through marker-assisted selection (MAS). The objectives of this study were to identify and validate QTL associated with these value-added traits in two high-protein recombinant inbred line (RIL) populations. RESULTS The RIL populations were derived from the high-protein cultivar 'AC X790P' (49% protein, dry weight basis), and two high-yielding commercial cultivars, 'S18-R6' (41% protein) and 'S23-T5' (42% protein). Fourteen large-effect QTL (R2 > 10%) were identified associated with seed protein concentration. Of these QTL, seven QTL were detected in both populations, and eight of them were co-localized with QTL associated with either seed sucrose concentration or seed weight. None of the protein-related QTL was found to be associated with seed yield in either population. Sixteen candidate genes with putative roles in protein metabolism were identified within seven of these protein-related regions: qPro_Gm02-3, qPro_Gm04-4, qPro_Gm06-1, qPro_Gm06-3, qPro_Gm06-6, qPro_Gm13-4 and qPro-Gm15-3. CONCLUSION The use of RIL populations derived from high-protein parents created an opportunity to identify four novel QTL that may have been masked by large-effect QTL segregating in populations developed from diverse parental cultivars. In total, we have identified nine protein QTL that were detected either in both populations in the current study or reported in other studies. These QTL may be useful in the curated selection of new soybean cultivars for optimized soy-based food products.
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Affiliation(s)
- Rachel M Whiting
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
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Hayat A, Hussain S, Bilal M, Kausar M, Almuzzaini B, Abbas S, Tanveer A, Khan A, Siddiqi S, Foo JN, Ahmad F, Khan F, Khan B, Anees M, Mäkitie O, Alfadhel M, Ahmad W, Umair M. Biallelic variants in four genes underlying recessive osteogenesis imperfecta. Eur J Med Genet 2020; 63:103954. [PMID: 32413570 DOI: 10.1016/j.ejmg.2020.103954] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/08/2020] [Accepted: 05/09/2020] [Indexed: 12/12/2022]
Abstract
Osteogenesis imperfecta (OI) is an inherited heterogeneous rare skeletal disorder characterized by increased bone fragility and low bone mass. The disorder mostly segregates in an autosomal dominant manner. However, several rare autosomal recessive and X-linked forms, caused by mutations in 18 different genes, have also been described in the literature. Here, we present five consanguineous families segregating OI in an autosomal recessive pattern. Affected individuals in the five families presented severe forms of skeletal deformities. It included frequent bone fractures with abnormal healing, short stature, facial dysmorphism, osteopenia, joint laxity, and severe scoliosis. In order to search for the causative variants, DNA of at least one affected individual in three families (A-C) were subjected to whole exome sequencing (WES). In two other families (D-E), linkage analysis using highly polymorphic microsatellite markers was followed by Sanger sequencing. Sequence analysis revealed two novels and three previously reported disease-causing variants. The two novel homozygous variants including [c.824G > A; p.(Cys275Tyr)] in the SP7 gene and [c.397C > T, p.(Gln133*)] in the SERPINF1 gene were identified in families A and B, respectively. The three previously reported homozygous variants including [c.497G > A; p.(Arg166His)] in the SPARC gene, (c.359-3C > G; intron 2) and [c.677C > T; p.(Ser226Leu)] in the WNT1 gene were identified in family C, D, and E. In conclusion, our findings provided additional evidence of involvement of homozygous sequence variants in the SP7, SERPINF1, SPARC and WNT1 genes causing severe OI. It also highlights the importance of extensive genetic investigations to search for the culprit gene in each case of skeletal deformity.
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Affiliation(s)
- Amir Hayat
- Department Biochemistry, Faculty of Life and Chemical Sciences, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Shabir Hussain
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Mehran Kausar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Rehman College of Allied Health Sciences, RMI, Phase-5, Hayatabad, Peshawar, Pakistan
| | - Bader Almuzzaini
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, P.O. Box 3660, Riyadh, 11481, Saudi Arabia
| | - Safdar Abbas
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Adeena Tanveer
- National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amjad Khan
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085, Strasbourg, France; Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg, France
| | - Saima Siddiqi
- Institute of Biomedical & Genetic Engineering (IB&GE), Mauve area, G-9, Islamabad, Pakistan
| | - Jia Nee Foo
- Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Farooq Ahmad
- Department of Chemistry, Women University Swabi, Swabi, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Feroz Khan
- Department of Zoology and Biology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Bushra Khan
- Department Biochemistry, Faculty of Life and Chemical Sciences, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Mariam Anees
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, P.O. Box 3660, Riyadh, 11481, Saudi Arabia
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, P.O. Box 3660, Riyadh, 11481, Saudi Arabia.
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Thambugala D, Menzies JG, Knox RE, Campbell HL, McCartney CA. Genetic analysis of loose smut (Ustilago tritici) resistance in Sonop spring wheat. BMC Plant Biol 2020; 20:314. [PMID: 32620083 PMCID: PMC7333308 DOI: 10.1186/s12870-020-02525-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/25/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND The genetics of resistance to loose smut of wheat (Triticum aestivum L.) caused by the fungus Ustilago tritici (Pers.) Rostr. is not well understood. This study examines loose smut resistance in Sonop (TD-14), a South African spring wheat variety. A doubled haploid (DH) population of 163 lines derived from the cross Diamont/TD-14 was studied. The parents and progenies were inoculated with U. tritici races T2, T9, and T39 individually in growth facilities at Morden and Swift Current, Canada. Loose smut incidence (LSI) and partial loose smut resistance (PLSR) were assessed. RESULTS A whole genome linkage map was developed consisting of 11,519 SNP loci found on 31 linkage groups spanning 2845 cM. A new major resistance gene Ut11 was located to the distal end of chromosome arm 7BS. Ut11 conferred resistance to U. tritici race T2, but not races T9 and T39. Quantitative trait locus (QTL) mapping identified four QTL controlling LSI in the Diamont/TD-14 DH population on chromosomes 3B, 4B, 5B, and 7B (at Ut11) with TD-14 contributing the resistance alleles at three of these loci. The major QTL QUt.mrc-5B was effective against all three races and explained up to 81% of the phenotypic variation. The only QTL identified for PLSR coincided with the LSI QTL QUt.mrc-5B indicating that this locus affected both loose smut incidence and partial smutting of spikes. CONCLUSIONS A race-specific resistance gene Ut11 and a broadly effective resistance QTL QUt.mrc-5B were the main loci controlling loose smut resistance in the differential line TD-14 (cultivar Sonop). This study provides insight into the genetics of loose smut resistance in spring wheat Sonop and the single nucleotide polymorphism (SNP) markers linked to the resistance gene Ut11 and QTL QUt.mrc-5B will be useful for selecting loose smut resistance in breeding programs.
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Affiliation(s)
- Dinushika Thambugala
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB Canada
| | - Jim G. Menzies
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB Canada
| | - Ron E. Knox
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK Canada
| | - Heather L. Campbell
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK Canada
| | - Curt A. McCartney
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB Canada
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Zhao ZQ, Sheng XG, Yu HF, Wang JS, Shen YS, Gu HH. Identification of QTLs associated with curd architecture in cauliflower. BMC Plant Biol 2020; 20:177. [PMID: 32321422 PMCID: PMC7178959 DOI: 10.1186/s12870-020-02377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Curd architecture is one of the most important characters determining the curd morphology of cauliflower. However, the genetic mechanism dissection of this complex trait at molecular level is lacking. Genes/QTLs responsible for the morphological differences between present-day loose-curd and compact-curd cauliflower haven't been well revealed. RESULTS Herein, by using a common compact-curd parent and two loose-curd parents, we developed two double haploid (DH) populations including 122 and 79 lines, respectively. For each population, we decomposed the curd architecture concept into four parameters (basal diameter, stalk length, stalk angle and curd solidity), and collected corresponding phenotypic data for each parameter across two environments. The Kosambi function and composite interval mapping algorithm were conducted to construct the linkage map and analyze the QTLs associated with curd architecture parameters. A total of 20 QTLs were detected with the minimum likelihood of odd (LOD) values ranging from 2.61 to 8.38 and the percentage of the phenotypic variance explained by each QTL (PVE) varying between 7.69 and 25.10%. Of these, two QTLs controlling stalk length (qSL.C6-1, qSL.C6-2) and two QTLs controlling curd solidity (qCS.C6-1 and qCS.C6-2) were steadily expressed in both environments. Further, qSL.C6-1, qSL.C6-2, qCS.C6-1 and qCS.C6-4 fell into the same chromosomal region of the reference genome, indicating that these loci are involved in pleiotropic effects or are tightly linked. CONCLUSION The current study identified a series of QTLs associated with curd architecture parameters, which might contribute essentially to the formation of present-day loose-curd cauliflower that is widely cultivated in China. These results may pave the way for intensive deciphering the molecular mechanisms of curd development and for marker-assisted selection of curd morphology in cauliflower breeding.
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Affiliation(s)
- Zhen-Qing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Xiao-Guang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Hui-Fang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Jian-Sheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Yu-Sen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Hong-Hui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
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Lahaye M, Falourd X, Laillet B, Le Gall S. Cellulose, pectin and water in cell walls determine apple flesh viscoelastic mechanical properties. Carbohydr Polym 2019; 232:115768. [PMID: 31952582 DOI: 10.1016/j.carbpol.2019.115768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
Abstract
The viscoelastic mechanical properties are important quality traits for fleshy fruit uses. The contribution of cell wall polysaccharides chemistry and organization on their variability was studied in six varieties of apple. Correlation between damping and storage modulus of plasmolyzed tissue distinguished better apple varieties on their viscoelasticity than fresh samples. Galactose, arabinose and uronic acids correlated positively with the storage modulus of fresh apple samples (E'f). These corresponded to 4-linked galactan but no specific arabinose linkage. Galacturonic acid branched on O-3 and terminal rhamnose correlated negatively with E'f. These correlations formed two groups of fruit except for branched methyl-esterified galacturonic. Solid-state 13C NMR spectroscopy analyses showed that E'f correlated negatively with cellulose C4 T1ρH relaxation and positively with pectin methyl esters THH proton diffusion. The results point to the key roles of pectin structure and hydration and cellulose microfibrils distribution on apple mechanical properties.
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Kuipers AL, Wojczynski MK, Barinas-Mitchell E, Minster RL, Wang L, Feitosa MF, Kulminski A, Thyagarajan B, Lee JH, Province MA, Newman AB, Zmuda JM. Genome-wide linkage analysis of carotid artery traits in exceptionally long-lived families. Atherosclerosis 2019; 291:19-26. [PMID: 31634740 DOI: 10.1016/j.atherosclerosis.2019.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/03/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Atherosclerosis develops with age and is partially controlled by genetics. Research to date has identified common variants with small effects on atherosclerosis related traits. We aimed to use family-based genome-wide linkage analysis to identify chromosomal regions potentially harboring rare variants with larger effects for atherosclerosis related traits. METHODS Participants included 2205 individuals from the Long Life Family Study (LLFS), which recruited families with exceptional longevity from Boston, New York, Pittsburgh, and Denmark. Participants underwent B-mode ultrasonography of the carotid arteries to measure intima-media thickness (IMT), inter-adventitial diameter (IAD), and plaque presence and severity. We conducted residual heritability and genome-wide linkage analyses adjusted for age, age2, sex, and field center using pedigree-based maximum-likelihood methods in SOLAR. RESULTS All carotid traits were significantly heritable with a range of 0.68 for IAD to 0.38 for IMT. We identified three chromosomal regions with linkage to IAD (3q13; max LOD 5.3), plaque severity (17q22-q23, max LOD 3.2), and plaque presence (17q24, max LOD 3.1). No common allelic variants within these linkage peaks were associated with the carotid artery traits. CONCLUSIONS We identified three chromosomal regions with evidence of linkage to carotid artery diameter and atherosclerotic plaque in exceptionally long-lived families. Since common allelic variants within our linkage peaks did not account for our findings, future follow-up resequencing of these regions in LLFS families should help advance our understanding of atherosclerosis, CVD, and healthy vascular aging.
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Affiliation(s)
- Allison L Kuipers
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Mary K Wojczynski
- Department of Genetics, Washington University in St Louis, St. Louis, MO, USA
| | | | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lihua Wang
- Department of Genetics, Washington University in St Louis, St. Louis, MO, USA
| | - Mary F Feitosa
- Department of Genetics, Washington University in St Louis, St. Louis, MO, USA
| | | | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Joseph H Lee
- Sergievsky Center, Taub Institute, Departments of Epidemiology and Neurology, Columbia University, New York, NY, USA
| | - Michael A Province
- Department of Genetics, Washington University in St Louis, St. Louis, MO, USA
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph M Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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Ulloa M, De Santiago LM, Hulse-Kemp AM, Stelly DM, Burke JJ. Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection. Mol Genet Genomics 2020; 295:155-76. [PMID: 31620883 DOI: 10.1007/s00438-019-01611-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/22/2019] [Indexed: 01/09/2023]
Abstract
To provision the world sustainably, modern society must increase overall crop production, while conserving and preserving natural resources. Producing more with diminishing water resources is an especially daunting endeavor. Toward the goal of genetically improving drought resilience of cultivated Upland cotton (Gossypium hirsutum L.), this study addresses the genetics of differential yield components referred to as productivity and fiber quality traits under regular-water versus low-water (LW) field conditions. We used ten traits to assess water stress deficit, which included six productivity and four fiber quality traits on two recombinant inbred line (RIL) populations from reciprocally crossed cultivars, Phytogen 72 and Stoneville 474. To facilitate genetic inferences, we genotyped RILs with the CottonSNP63K array, assembled high-density linkage maps of over 7000 SNPs and then analyzed quantitative trait variations. Analysis of variance revealed significant differences for all traits (p < 0.05) in these RIL populations. Although the LW irrigation regime significantly reduced all traits, except lint percent, the RILs exhibited a broad phenotypic spectrum of heritable differences across the water regimes. Transgressive segregation occurred among the RILs, suggesting the possibility of genetic gain through phenotypic selection for drought resilience and perhaps through marker-based selection. Analyses revealed more than 150 quantitative trait loci (QTLs) associated with productivity and fiber quality traits (p < 0.005) on different genomic regions of the cotton genome. The multiple-QTL models analysis with LOD > 3.0 detected 21 QTLs associated with productivity and 22 QTLs associated with fiber quality. For fiber traits, strong clustering and QTL associations occurred in c08 and its homolog c24 as well as c10, c14, and c21. Using contemporary genome sequence assemblies and bioinformatically related information, the identification of genomic regions associated with responses to plant stress/drought elevates the possibility of using marker-assisted and omics-based selection to enhance breeding for drought resilient cultivars and identifying candidate genes and networks. RILs with different responses to drought indicated that it is possible to maintain high fiber quality under LW conditions or reduce the of LW impact on quality. The heritable variation among elite bi-parental RILs for productivity and quality under field drought conditions, and their association of QTLs, and thus specific genomic regions, indicate opportunities for breeding-based gains in water resource conservation, i.e., enhancing cotton's agricultural sustainability.
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Peddareddygari LR, Kramer PD, Hanna PA, Levenstien MA, Grewal RP. Genetic Analysis of a Large Family with Migraine, Vertigo, and Motion Sickness. Can J Neurol Sci 2019; 46:512-7. [PMID: 31258098 DOI: 10.1017/cjn.2019.64] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Migraine is a common disorder most typically presenting as headache and often associated with vertigo and motion sickness. It is a genetically complex condition with multiple genes ultimately contributing to the predisposition and development of this episodic neurological disorder. We identified a large American family of 29 individuals of which 17 members suffered from at least one of these disorders, migraine, vertigo, or motion sickness. Many of these individuals suffered from several simultaneously. We hypothesized that vertigo and motion sickness may involve genes that are independent to those directly contributing to migraine susceptibility. METHODS Genome-wide linkage analysis performed using 400 microsatellite repeat markers spaced at 10 cM throughout the genome. The members of this family were phenotyped for each condition, migraine, vertigo, and motion sickness and analyzed separately. Statistical analysis was performed using two-point and multipoint linkage analysis employing a number of models including autosomal recessive or dominant patterns of inheritance with high and low genetic penetrance. RESULTS We identified a novel locus for migraine, 9q13-q22 (maximum two-point logarithm of odds [LOD] score-2.51). In addition, there are suggestive LOD scores that localize to different chromosomes for each phenotype; vertigo (chromosome 18, LOD score of 1.82) and motion sickness (chromosome 4, LOD score of 2.09). CONCLUSIONS Our analysis supports our hypothesis that the migraine-associated vertigo and motion sickness may involve distinct susceptibility genes.
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Huang C, Yan J, Zhan L, Zhao M, Zhou J, Gao H, Xie W, Li Y, Chai W. Linkage and sequence analysis of neutral oligosaccharides by negative-ion MALDI tandem mass spectrometry with laser-induced dissociation. Anal Chim Acta 2019; 1071:25-35. [PMID: 31128752 DOI: 10.1016/j.aca.2019.04.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 11/25/2022]
Abstract
Mass spectrometry (MS) has become the primary method for high-sensitivity structural determination of oligosaccharides. Fragmentation in the negative-ion MS can provide a wealth of structural information and these can be used for sequence determination. However, although negative-ion MS of neutral oligosaccharide using the deprotonated molecule [M-H]- as the precursor has been very successful for electrospray ionization (ESI), it has only limited success for matrix-assisted laser desorption/ionization (MALDI). In the present study, the features of negative-ion MALDI primary spectra were investigated in detail and the product-ion spectra using [M-H]- and [M+Cl]- as the precursors were carefully compared. The formation of [M-H]- was the main difficulty for MALDI while [M+Cl]- was proved to be useful as alternative precursor anion for MALDI-MS/MS to produce similar fragmentation for sequencing of neutral oligosaccharides. N-(1-naphthyl)ethylenediamine dihydrochloride was then used as both the matrix and the Cl- dopant to evaluate the extent of structural information that can be obtained by negative-ion fragmentation from [M+Cl]- using laser-induced dissociation (LID)-MS/MS for linkage assignment of gluco-oligosaccharides and for typing of blood-group ABO(H) and Lewis antigens on either type 1 or type 2 backbone-chains.
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Affiliation(s)
- Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; GuangDong Bio-healtech Advanced, Foshan, 528315, China
| | - Jingyu Yan
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry, Dalian, 116023, China
| | - Lingpeng Zhan
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Min Zhao
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Jinyu Zhou
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Huanyu Gao
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Wenchun Xie
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; GuangDong Bio-healtech Advanced, Foshan, 528315, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Wengang Chai
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
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Lan T, Yang B, Zhang X, Wang T, Lu Q. Statistical Methods and Software for Substance Use and Dependence Genetic Research. Curr Genomics 2019; 20:172-183. [PMID: 31929725 PMCID: PMC6935956 DOI: 10.2174/1389202920666190617094930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Substantial substance use disorders and related health conditions emerged dur-ing the mid-20th century and continue to represent a remarkable 21st century global burden of disease. This burden is largely driven by the substance-dependence process, which is a complex process and is influenced by both genetic and environmental factors. During the past few decades, a great deal of pro-gress has been made in identifying genetic variants associated with Substance Use and Dependence (SUD) through linkage, candidate gene association, genome-wide association and sequencing studies. METHODS Various statistical methods and software have been employed in different types of SUD ge-netic studies, facilitating the identification of new SUD-related variants. CONCLUSION In this article, we review statistical methods and software that are currently available for SUD genetic studies, and discuss their strengths and limitations.
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Affiliation(s)
| | | | | | - Tong Wang
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
| | - Qing Lu
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
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Pham LV, Jensen SB, Fahnøe U, Pedersen MS, Tang Q, Ghanem L, Ramirez S, Humes D, Serre SBN, Schønning K, Bukh J, Gottwein JM. HCV genotype 1-6 NS3 residue 80 substitutions impact protease inhibitor activity and promote viral escape. J Hepatol 2019; 70:388-397. [PMID: 30395912 DOI: 10.1016/j.jhep.2018.10.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 09/13/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Protease inhibitors (PIs) are of central importance in the treatment of patients with chronic hepatitis C virus (HCV) infection. HCV NS3 protease (NS3P) position 80 displays polymorphisms associated with resistance to the PI simeprevir for HCV genotype 1a. We investigated the effects of position-80-substitutions on fitness and PI-resistance for HCV genotypes 1-6, and analyzed evolutionary mechanisms underlying viral escape mediated by pre-existing Q80K. METHODS The fitness of infectious NS3P recombinants of HCV genotypes 1-6, with engineered position-80-substitutions, was studied by comparison of viral spread kinetics in Huh-7.5 cells in culture. Median effective concentration (EC50) and fold resistance for PIs simeprevir, asunaprevir, paritaprevir, grazoprevir, glecaprevir and voxilaprevir were determined in short-term treatment assays. Viral escape was studied by long-term treatment of genotype 1a recombinants with simeprevir, grazoprevir, glecaprevir and voxilaprevir and of genotype 3a recombinants with glecaprevir and voxilaprevir, next generation sequencing, NS3P substitution linkage and haplotype analysis. RESULTS Among tested PIs, only glecaprevir and voxilaprevir showed pan-genotypic activity against the original genotype 1-6 culture viruses. Variants with position-80-substitutions were all viable, but fitness depended on the specific substitution and the HCV isolate. Q80K conferred resistance to simeprevir across genotypes but had only minor effects on the activity of the remaining PIs. For genotype 1a, pre-existing Q80K mediated accelerated escape from simeprevir, grazoprevir and to a lesser extent glecaprevir, but not voxilaprevir. For genotype 3a, Q80K mediated accelerated escape from glecaprevir and voxilaprevir. Escape was mediated by rapid and genotype-, PI- and PI-concentration-dependent co-selection of clinically relevant resistance associated substitutions. CONCLUSIONS Position-80-substitutions had relatively low fitness cost and the potential to promote HCV escape from clinically relevant PIs in vitro, despite having a minor impact on results in classical short-term resistance assays. LAY SUMMARY Among all clinically relevant hepatitis C virus protease inhibitors, voxilaprevir and glecaprevir showed the highest and most uniform activity against cell culture infectious hepatitis C virus with genotype 1-6 proteases. Naturally occurring amino acid changes at protease position 80 had low fitness cost and influenced sensitivity to simeprevir, but not to other protease inhibitors in short-term treatment assays. Nevertheless, the pre-existing change Q80K had the potential to promote viral escape from protease inhibitors during long-term treatment by rapid co-selection of additional resistance changes, detected by next generation sequencing.
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Affiliation(s)
- Long V Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Sanne Brun Jensen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Martin Schou Pedersen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Qi Tang
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lubna Ghanem
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Daryl Humes
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Stéphanie B N Serre
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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Lim SJ, Wan Aida WM, Schiehser S, Rosenau T, Böhmdorfer S. Structural elucidation of fucoidan from Cladosiphon okamuranus (Okinawa mozuku). Food Chem 2019; 272:222-226. [PMID: 30309536 DOI: 10.1016/j.foodchem.2018.08.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/26/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
Abstract
Fucoidan is a sulphated polysaccharide, made up mainly of l-fucose, which is found in brown seaweeds. Its chemical structure is diverse and depends on maturity, species and geographical location. The objective of this study was to elucidate the chemical structure of fucoidan from Cladosiphon okamuranus harvested in Japan. The fucoidan was subject to purification prior to monosaccharide profiling, sulphate content determination, and linkage analysis. Our results showed that Japanese Cladosiphon okamuranus fucoidan contained 70.13 ± 0.22 wt% fucose and 15.16 ± 1.17 wt% sulphate. Other minor monosaccharides found were d-xylose, d-galactose, d-mannose, d-glucose, d-arabinose, d-rhamnose and d-glucuronic acid. Linkage analysis revealed that fucopyranoside units along the backbone are linked, through α-1,3-glycosidic bonds, with fucose branching at C-2, and one sulphate group at C-4 per every three fucose units, i.e. the structure of fucoidan from Japanese Cladosiphon okamuranus is [→3)-α-fuc(1→]0.52[→3)-α-fuc-4-OSO3-(1→]0.33[→2)-α-fuc]0.14.
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Affiliation(s)
- Seng Joe Lim
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Wan Mustapha Wan Aida
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Sonja Schiehser
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Division of Chemistry of Renewable Resources, Muthgasse 18, A-1190 Vienna, Austria.
| | - Thomas Rosenau
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Division of Chemistry of Renewable Resources, Muthgasse 18, A-1190 Vienna, Austria.
| | - Stefan Böhmdorfer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Division of Chemistry of Renewable Resources, Muthgasse 18, A-1190 Vienna, Austria.
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Abstract
Quantitative cosegregation analysis can help evaluate the pathogenicity of genetic variants. However, genetics professionals without statistical training often use simple methods, reporting only qualitative findings. We evaluate the potential utility of quantitative cosegregation in the clinical setting by comparing three methods. One thousand pedigrees each were simulated for benign and pathogenic variants in BRCA1 and MLH1 using United States historical demographic data to produce pedigrees similar to those seen in the clinic. These pedigrees were analyzed using two robust methods, full likelihood Bayes factors (FLB) and cosegregation likelihood ratios (CSLR), and a simpler method, counting meioses. Both FLB and CSLR outperform counting meioses when dealing with pathogenic variants, though counting meioses is not far behind. For benign variants, FLB and CSLR greatly outperform as counting meioses is unable to generate evidence for benign variants. Comparing FLB and CSLR, we find that the two methods perform similarly, indicating that quantitative results from either of these methods could be combined in multifactorial calculations. Combining quantitative information will be important as isolated use of cosegregation in single families will yield classification for less than 1% of variants. To encourage wider use of robust cosegregation analysis, we present a website ( http://www.analyze.myvariant.org ) which implements the CSLR, FLB, and Counting Meioses methods for ATM, BRCA1, BRCA2, CHEK2, MEN1, MLH1, MSH2, MSH6, and PMS2. We also present an R package, CoSeg, which performs the CSLR analysis on any gene with user supplied parameters. Future variant classification guidelines should allow nuanced inclusion of cosegregation evidence against pathogenicity.
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Affiliation(s)
- John Michael O Rañola
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA.
| | - Quanhui Liu
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98105, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA
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Apolis L, Olivas J, Srinivasan P, Kushwaha AK, Desai SA. Multiple genetic loci define Ca ++ utilization by bloodstream malaria parasites. BMC Genomics 2019; 20:47. [PMID: 30651090 PMCID: PMC6335690 DOI: 10.1186/s12864-018-5418-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/27/2018] [Indexed: 11/30/2022] Open
Abstract
Background Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilization by genetically distinct lines of P. falciparum. These differences, if identified, may provide insights into molecular mechanisms. Results Dose response studies with the Ca++ chelator EGTA (ethylene glycol-bis(β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid) revealed stable differences in Ca++ requirement for six geographically divergent parasite lines used in previous genetic crosses, with the largest difference seen between the parents of the HB3 x Dd2 cross. Genetic mapping of Ca++ requirement yielded complex inheritance in 34 progeny clones with a single significant locus on chromosome 7 and possible contributions from other loci. Although encoded by a gene in the significant locus and a proposed Ca++ target, PfCRT (P. falciparum chloroquine resistance transporter), the primary determinant of clinical resistance to the antimalarial drug chloroquine, does not appear to contribute to this quantitative trait. Stage-specific application of extracellular EGTA also excluded determinants associated with merozoite egress and erythrocyte reinvasion. Conclusions We have identified differences in Ca++ utilization amongst P. falciparum lines. These differences are under genetic regulation, segregating as a complex trait in genetic cross progeny. Ca++ uptake and utilization throughout the bloodstream asexual cycle of malaria parasites represents an unexplored target for therapeutic intervention.
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Affiliation(s)
- Liana Apolis
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.,Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Joanna Olivas
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Prakash Srinivasan
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.,Department Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Baltimore, MD, USA
| | - Ambuj K Kushwaha
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Sanjay A Desai
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
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Angelini C, Lispi L, Salvoro C, Mostacciuolo ML, Vazza G. Clinical and genetic characterization of an Italian family with slow-channel syndrome. Neurol Sci 2018; 40:503-507. [PMID: 30542963 DOI: 10.1007/s10072-018-3645-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The slow-channel congenital myasthenic syndrome (SCCMS) is a postsynaptic form of congenital myasthenic syndromes (CMSs), a clinically heterogeneous group of disorders caused by genetic defects leading to an abnormal signal transmission at the endplate. METHODS We report clinical and molecular data of a multigenerational family in which the presentation of a progressive proximal-distal weakness with ocular involvement led to a number of different clinical diagnoses. RESULTS A comprehensive genetic study which included whole-genome linkage analysis and whole-exome sequencing identified a heterozygous missense substitution (c.721C>T, p.L241F) in the ε subunit of the acetylcholine receptor (CHRNE) that was consistent with clinical weakness in all patients. DISCUSSION SCCMS is characterized by a broad and heterogeneous clinical phenotype in which disease onset, symptoms, severity, and progression can be highly variable even between family members. The identification of a CHRNE mutation allowed to make the definitive diagnosis of CMS in this family and contributed to define the clinical spectrum of this disease.
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Affiliation(s)
- Corrado Angelini
- Fondazione Hospital S.Camillo Institute for Research and Health Care, Venice, Italy.
| | - Ludovico Lispi
- Neurology and Neurophysiopathology Unit, ASO San Camillo-Forlanini Hospital of Rome, Rome, Italy
| | | | | | - Giovanni Vazza
- Department of Biology, University of Padova, Padova, Italy
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Yao X, Wu K, Yao Y, Bai Y, Ye J, Chi D. Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color ( Psc) in hulless barley. Hereditas 2018; 155:37. [PMID: 30473656 PMCID: PMC6240233 DOI: 10.1186/s41065-018-0072-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/18/2018] [Indexed: 01/24/2023] Open
Abstract
Background Colored hulless barley are more suitable in food processing compared to normal (yellow) varieties because it is rich in bioactive compounds and produces higher extraction pearling fractions. Therefore, seed coat color is an important agronomic trait for the breeding and study of hulless barley. Results Genotyping-by-sequencing single-nucleotide polymorphism (GBS-SNP) analysis of a doubled haploid (DH) mapping population (Nierumuzha × Kunlun10) was conducted to map the purple seed coat color genes (Psc). A high-density genetic map of hulless barley was constructed, which contains 3662 efficient SNP markers with 1129 bin markers. Seven linkage groups were resolved, which had a total length of 645.56 cM. Chromosome length ranged from 60.21 cM to 127.21 cM, with average marker density of 0.57 cM. A total of five loci accounting for 3.79% to 23.86% of the observed phenotypic variation for Psc were detected using this high-density map. Five structural candidate genes (F3’M, HID, UF3GT, UFGT and 5MAT) and one regulatory factor (Ant1) related to flavonoid or anthocyanin biosynthesis were identified.. Conclusions Five structural candidate genes and one regulatory factor related to flavonoid or anthocyanin biosynthesis have been identified using a high-density genetic map of hulless barley. This study lays the foundation for map-based cloning of Psc but provides a valuable tool for studying marker-trait associations and its application to marker-assisted breeding of hulless barley. Electronic supplementary material The online version of this article (10.1186/s41065-018-0072-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohua Yao
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Kunlun Wu
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Youhua Yao
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Yixiong Bai
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Jingxiu Ye
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China
| | - Dezhao Chi
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
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Blondell L, Blackburn A, Kos MZ, Blangero J, Göring HHH. Contribution of Inbred Singletons to Variance Component Estimation of Heritability and Linkage. Hum Hered 2018; 83:92-99. [PMID: 30391948 DOI: 10.1159/000492830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES An interesting consequence of consanguinity is that the inbred singleton becomes informative for genetic variance. We determine the contribution of an inbred singleton to variance component analysis of heritability and linkage. METHODS Statistical theory for the power of variance component analysis of quantitative traits is used to determine the expected contribution of an inbred singleton to likelihood-ratio tests of heritability and linkage. RESULTS In variance component models, an inbred singleton contributes relatively little to a test of heritability but can contribute substantively to a test of linkage. For small-to-moderate quantitative trait locus (QTL) effects and a level of inbreeding comparable to matings between first cousins (the preferred form of union in many human populations), an inbred singleton can carry nearly 25% of the information of a non-inbred sib pair. In more highly inbred contexts available with experimental animal populations, nonhuman primate colonies, and some human subpopulations, the contribution of an inbred singleton relative to a sib pair can exceed 50%. CONCLUSIONS Inbred individuals, even in isolation from other members of a sample, can contribute to variance component estimation and tests of heritability and linkage. Under certain conditions, the informativeness of the inbred singleton can approach that of a non-inbred sib pair.
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Affiliation(s)
- Lucy Blondell
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, University of Texas Rio Grande Valley, San Antonio, Texas, USA,
| | - August Blackburn
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, University of Texas Rio Grande Valley, San Antonio, Texas, USA
| | - Mark Z Kos
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, University of Texas Rio Grande Valley, San Antonio, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, University of Texas Rio Grande Valley, San Antonio, Texas, USA
| | - Harald H H Göring
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, University of Texas Rio Grande Valley, San Antonio, Texas, USA
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Chang Y, Hee S, Lee W, Li H, Chang T, Lin M, Hung Y, Lee I, Hung K, Assimes T, Knowles JW, Nong J, Lee P, Chiu Y, Chuang L. Genome-wide scan for circulating vascular adhesion protein-1 levels: MACROD2 as a potential transcriptional regulator of adipogenesis. J Diabetes Investig 2018; 9:1067-1074. [PMID: 29364582 PMCID: PMC6123039 DOI: 10.1111/jdi.12805] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/10/2018] [Accepted: 01/15/2018] [Indexed: 12/28/2022] Open
Abstract
AIMS/INTRODUCTION Vascular adhesion protein-1 (VAP-1) is a membrane-bound amine oxidase highly expressed in mature adipocytes and released into the circulation. VAP-1 has been strongly implicated in several pathological processes, including diabetes, inflammation, hypertension, hepatic steatosis and renal diseases, and is an important disease marker and therapeutic target. Here, we aimed to identify the genetic loci for circulating VAP-1 levels. MATERIALS AND METHODS We carried out a genomic-wide linkage scan for the quantitative trait locus of circulating VAP-1 levels in 1,100 Han Chinese individuals from 398 families in the Stanford Asian Pacific Program for Hypertension and Insulin Resistance study. Regional association fine mapping was carried out using additional single-nucleotide polymorphisms. RESULTS The estimated heritability of circulating VAP-1 levels is high (h2 = 69%). The most significant quantitative trait locus for circulating VAP-1 was located at 38 cM on chromosome 20, with a maximum empirical logarithm of odds score of 4.11 (P = 6.86 × 10-6 ) in females. Regional single-nucleotide polymorphism fine mapping within a 1-unit support region showed the strongest association signals in the MACRO domain containing 2 (MACROD2) gene in females (P = 5.38 × 10-6 ). Knockdown of MACROD2 significantly suppressed VAP-1 expression in human adipocytes, as well as the expression of key adipogenic genes. Furthermore, MACROD2 expression was found to be positively associated with VAP-1 in human visceral adipose tissue. CONCLUSION MACROD2 is a potential genetic determinant of serum VAP-1 levels, probably through transcriptional regulation of adipogenesis.
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Affiliation(s)
- Yi‐Cheng Chang
- Graduate Institute of Medical Genomics and ProteomicsCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
- Institute of Biomedical ScienceAcademia SinicaTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
| | - Siow‐Wey Hee
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
| | - Wei‐Jei Lee
- Department of SurgeryMin‐Sheng General HospitalTaoyuanTaiwan
| | - Hung‐Yuan Li
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
| | - Tien‐Jyun Chang
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
| | | | - Yi‐Jen Hung
- Division of Endocrinology & MetabolismTri‐Service General HospitalNational Defense Medical CenterTaipeiTaiwan
| | - I‐Te Lee
- Department of Internal MedicineDivision of Endocrinology and MetabolismTaichung Veterans General HospitalTaichungTaiwan
| | - Kuan‐Yi Hung
- Institute of Population Health SciencesNational Health Research InstitutesZhunan, MiaoliTaiwan
| | - Themistocles Assimes
- Division of Cardiovascular Medicine and Cardiovascular InstituteDepartment of MedicineStanford University StanfordStanfordCaliforniaUSA
| | - Joshua W Knowles
- Division of Cardiovascular Medicine and Cardiovascular InstituteDepartment of MedicineStanford University StanfordStanfordCaliforniaUSA
| | - Jiun‐Yi Nong
- Graduate Institute of Molecular MedicineCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Po‐Chu Lee
- Department of General SurgeryNational Taiwan University HospitalTaipeiTaiwan
| | - Yen‐Feng Chiu
- Institute of Population Health SciencesNational Health Research InstitutesZhunan, MiaoliTaiwan
| | - Lee‐Ming Chuang
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
- Graduate Institute of Molecular MedicineCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
- Graduate Institute of Clinical MedicineCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
- Graduate of Epidemiology and Preventive MedicineCollege of Public HealthNational Taiwan UniversityTaipeiTaiwan
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48
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Cheng R, Tang M, Martinez I, Ayodele T, Baez P, Reyes-Dumeyer D, Lantigua R, Medrano M, Jimenez-Velazquez I, Lee JH, Beecham GW, Reitz C. Linkage analysis of multiplex Caribbean Hispanic families loaded for unexplained early-onset cases identifies novel Alzheimer's disease loci. Alzheimers Dement (Amst) 2018; 10:554-562. [PMID: 30406174 PMCID: PMC6215058 DOI: 10.1016/j.dadm.2018.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction Less than 10% of early-onset Alzheimer's disease (EOAD) is explained by known mutations. Methods We conducted genetic linkage analysis of 68 well-phenotyped Caribbean Hispanic families without clear inheritance patterns or mutations in APP, PSEN1, and PSEN2 and with two or more individuals with EOAD. Results We identified 16 (logarithm of odds > 3.6) linked regions, including eight novel loci for EOAD (2p15, 5q14.1, 11p15.1, 13q21.22, 13q33.1, 16p12.1, 20p12.1, and 20q11.21) and eight regions previously associated with late-onset Alzheimer's disease. The strongest signal was observed at 16p12.1 (25 cM, 33 Mb; heterogeneity logarithm of odds = 5.3), ∼3 Mb upstream of the ceroid lipofuscinosis 3 (CLN3) gene associated with juvenile neuronal ceroid lipofuscinosis (JNCL), which functions in retromer trafficking and has been reported to alter intracellular processing of the amyloid precursor protein. Discussion This study supports the notion that the genetic architectures of unexplained EOAD and late-onset AD overlap partially, but not fully.
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Affiliation(s)
- Rong Cheng
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.,The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Min Tang
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.,The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Izri Martinez
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Temitope Ayodele
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Penelope Baez
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Dolly Reyes-Dumeyer
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Rafael Lantigua
- Department of Medicine, Columbia University, New York, NY, USA
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | - Ivonne Jimenez-Velazquez
- Department of Internal Medicine, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Joseph H Lee
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.,The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.,Department of Epidemiology, Columbia University, New York, NY, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.,The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.,Department of Epidemiology, Columbia University, New York, NY, USA.,Department of Neurology, Columbia University, New York, NY, USA
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49
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Huang YL, Jhou BY, Chen SF, Khoo KH. Identifying Specific and Differentially Linked Glycosyl Residues in Mammalian Glycans by Targeted LC-MS Analysis. ANAL SCI 2018; 34:1049-1054. [PMID: 30146545 DOI: 10.2116/analsci.18scp01] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Glycans, which are widespread in nature, consist of a large number of monosaccharides linked via glycosidic bonds. Due to the complex nature of glycan structures on glycoproteins, assessing the configuration and positions of the glycosidic linkages of a glycan is a subject of considerable interest. In this study, a method for accomplishing this using partially O-methylated alditols (PMAs) from glycans combined with LC-MS analysis is reported. N-Glycans were first per-methylated with methyl iodide, and the levels of methylation were further confirmed by MALDI-TOF. PMAs were then produced via complete hydrolysis and reduction. PMAs derived from Fetuin N-glycan and Lewisa antigen carbohydrates were successfully detected by LC-MS analysis. This analysis can be performed without the need for an additional derivatization step for GC analysis, and should be suitable for use in conjunction with a LC-MS-based analysis platform.
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Affiliation(s)
- Yi-Li Huang
- Department of Chemistry, National Taiwan Normal University
| | - Bing-Yi Jhou
- Department of Chemistry, National Taiwan Normal University
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University
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50
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Hackett CA, Milne L, Smith K, Hedley P, Morris J, Simpson CG, Preedy K, Graham J. Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening. BMC Genet 2018; 19:59. [PMID: 30111279 PMCID: PMC6094467 DOI: 10.1186/s12863-018-0666-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. To improve our understanding of the genetic control of raspberry fruit development an enhanced genetic linkage map was developed and used to examine ripening phenotypic data. RESULTS In this study we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Latham reference mapping population using genotyping by sequencing (GbS). Alignment to a newly sequenced draft reference genome of red raspberry, cultivar (cv.) Glen Moy, identified 8019 single nucleotide polymorphisms (SNPs). After stringent filtering to take account of read coverage over all the progeny individuals, association with a single chromosome, heterozygosity and marker regression mapping, 2348 high confidence SNPs were retained and integrated with an existing raspberry genetic map. The linkage map contained many more SNPs segregating in Latham than in Glen Moy. This caused difficulties in quantitative trait loci (QTL) mapping with standard software and a novel analysis based on a hidden Markov model was used to improve the mapping. QTL mapping using the newly generated dense genetic map not only corroborated previously identified genetic locations but also provided additional genetic elements controlling fruit ripening in raspberry. CONCLUSION The high-density GbS map located the QTL peaks more precisely than in earlier studies, aligned the QTLs with Glen Moy genome scaffolds, narrowed the range of potential candidate genes to these regions that can be utilised in other populations or in gene expression studies to confirm their role and increased the repertoire of markers available to understand the genetic control of fruit ripening traits.
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Affiliation(s)
| | - Linda Milne
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Kay Smith
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Pete Hedley
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Jenny Morris
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Craig G. Simpson
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Katharine Preedy
- Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD25DA Scotland
| | - Julie Graham
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
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