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Nissan N, Hooker J, Arezza E, Dick K, Golshani A, Mimee B, Cober E, Green J, Samanfar B. Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode. Front Bioinform 2023; 3:1199675. [PMID: 37409347 PMCID: PMC10319130 DOI: 10.3389/fbinf.2023.1199675] [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: 04/03/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
The soybean cyst nematode (SCN) [Heterodera glycines Ichinohe] is a devastating pathogen of soybean [Glycine max (L.) Merr.] that is rapidly becoming a global economic issue. Two loci conferring SCN resistance have been identified in soybean, Rhg1 and Rhg4; however, they offer declining protection. Therefore, it is imperative that we identify additional mechanisms for SCN resistance. In this paper, we develop a bioinformatics pipeline to identify protein-protein interactions related to SCN resistance by data mining massive-scale datasets. The pipeline combines two leading sequence-based protein-protein interaction predictors, the Protein-protein Interaction Prediction Engine (PIPE), PIPE4, and Scoring PRotein INTeractions (SPRINT) to predict high-confidence interactomes. First, we predicted the top soy interacting protein partners of the Rhg1 and Rhg4 proteins. Both PIPE4 and SPRINT overlap in their predictions with 58 soybean interacting partners, 19 of which had GO terms related to defense. Beginning with the top predicted interactors of Rhg1 and Rhg4, we implement a "guilt by association" in silico proteome-wide approach to identify novel soybean genes that may be involved in SCN resistance. This pipeline identified 1,082 candidate genes whose local interactomes overlap significantly with the Rhg1 and Rhg4 interactomes. Using GO enrichment tools, we highlighted many important genes including five genes with GO terms related to response to the nematode (GO:0009624), namely, Glyma.18G029000, Glyma.11G228300, Glyma.08G120500, Glyma.17G152300, and Glyma.08G265700. This study is the first of its kind to predict interacting partners of known resistance proteins Rhg1 and Rhg4, forming an analysis pipeline that enables researchers to focus their search on high-confidence targets to identify novel SCN resistance genes in soybean.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Julia Hooker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Eric Arezza
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jeansur-Richelieu, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - James Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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Belzile F, Jean M, Torkamaneh D, Tardivel A, Lemay MA, Boudhrioua C, Arsenault-Labrecque G, Dussault-Benoit C, Lebreton A, de Ronne M, Tremblay V, Labbé C, O’Donoughue L, St-Amour VTB, Copley T, Fortier E, Ste-Croix DT, Mimee B, Cober E, Rajcan I, Warkentin T, Gagnon É, Legay S, Auclair J, Bélanger R. The SoyaGen Project: Putting Genomics to Work for Soybean Breeders. Front Plant Sci 2022; 13:887553. [PMID: 35557742 PMCID: PMC9087807 DOI: 10.3389/fpls.2022.887553] [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] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The SoyaGen project was a collaborative endeavor involving Canadian soybean researchers and breeders from academia and the private sector as well as international collaborators. Its aims were to develop genomics-derived solutions to real-world challenges faced by breeders. Based on the needs expressed by the stakeholders, the research efforts were focused on maximizing realized yield through optimization of maturity and improved disease resistance. The main deliverables related to molecular breeding in soybean will be reviewed here. These include: (1) SNP datasets capturing the genetic diversity within cultivated soybean (both within a worldwide collection of > 1,000 soybean accessions and a subset of 102 short-season accessions (MG0 and earlier) directly relevant to this group); (2) SNP markers for selecting favorable alleles at key maturity genes as well as loci associated with increased resistance to key pathogens and pests (Phytophthora sojae, Heterodera glycines, Sclerotinia sclerotiorum); (3) diagnostic tools to facilitate the identification and mapping of specific pathotypes of P. sojae; and (4) a genomic prediction approach to identify the most promising combinations of parents. As a result of this fruitful collaboration, breeders have gained new tools and approaches to implement molecular, genomics-informed breeding strategies. We believe these tools and approaches are broadly applicable to soybean breeding efforts around the world.
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Affiliation(s)
- François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Martine Jean
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Aurélie Tardivel
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Marc-André Lemay
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Chiheb Boudhrioua
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | | | | | - Amandine Lebreton
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Vanessa Tremblay
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Caroline Labbé
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Louise O’Donoughue
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Vincent-Thomas Boucher St-Amour
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Tanya Copley
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Eric Fortier
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Tom Warkentin
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Éric Gagnon
- Semences Prograin Inc., Saint-Césaire, QC, Canada
- Sevita Genetics, Inkerman, ON, Canada
| | | | | | - Richard Bélanger
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
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3
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Torkamaneh D, Laroche J, Valliyodan B, O'Donoughue L, Cober E, Rajcan I, Vilela Abdelnoor R, Sreedasyam A, Schmutz J, Nguyen HT, Belzile F. Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics. Plant Biotechnol J 2021; 19:324-334. [PMID: 32794321 DOI: 10.1101/534578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/02/2019] [Revised: 07/24/2020] [Accepted: 08/07/2020] [Indexed: 05/27/2023]
Abstract
Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
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Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Louise O'Donoughue
- CÉROM, Centre de recherche Sur Les Grains Inc., Saint-Mathieu de Beloeil, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Ricardo Vilela Abdelnoor
- Brazilian Corporation of Agricultural Research (Embrapa Soja), Warta County, PR, Brazil
- Londrina State University (UEL), Londrina, PR, Brazil
| | | | - Jeremy Schmutz
- Institute for Biotechnology, HudsonAlpha, Huntsville, AL, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
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4
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Torkamaneh D, Laroche J, Valliyodan B, O’Donoughue L, Cober E, Rajcan I, Vilela Abdelnoor R, Sreedasyam A, Schmutz J, Nguyen HT, Belzile F. Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics. Plant Biotechnol J 2021; 19:324-334. [PMID: 32794321 PMCID: PMC7868971 DOI: 10.1111/pbi.13466] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/02/2019] [Revised: 07/24/2020] [Accepted: 08/07/2020] [Indexed: 05/10/2023]
Abstract
Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
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Affiliation(s)
- Davoud Torkamaneh
- Département de PhytologieUniversité LavalQuébec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
- Department of Plant AgricultureUniversity of GuelphGuelphONCanada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Louise O’Donoughue
- CÉROMCentre de recherche Sur Les Grains Inc.Saint‐Mathieu de BeloeilQCCanada
| | - Elroy Cober
- Agriculture and Agri‐Food CanadaOttawaONCanada
| | - Istvan Rajcan
- Department of Plant AgricultureUniversity of GuelphGuelphONCanada
| | - Ricardo Vilela Abdelnoor
- Brazilian Corporation of Agricultural Research (Embrapa Soja)Warta CountyPRBrazil
- Londrina State University (UEL)LondrinaPRBrazil
| | | | - Jeremy Schmutz
- Institute for BiotechnologyHudsonAlphaHuntsvilleALUSA
- Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - François Belzile
- Département de PhytologieUniversité LavalQuébec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébec CityQCCanada
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5
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Miranda C, Scaboo A, Cober E, Denwar N, Bilyeu K. The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments. BMC Plant Biol 2020; 20:65. [PMID: 32033536 PMCID: PMC7006184 DOI: 10.1186/s12870-020-2276-y] [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] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Soybean is native to the temperate zones of East Asia. Poor yields of soybean in West African countries may be partially attributed to inadequate adaptation of soybean to tropical environments. Adaptation will require knowledge of the effects of allelic combinations of major maturity genes (E1, E2, and E3) and stem architecture. The long juvenile trait (J) influences soybean flowering time in short, ~ 12 h days, which characterize tropical latitudes. Soybean plant architecture includes determinate or indeterminate stem phenotypes controlled by the Dt1 gene. Understanding the influence of these genetic components on plant development and adaptation is key to optimize phenology and improve soybean yield potential in tropical environments. RESULTS Soybean lines from five recombinant inbred populations were developed that varied in their combinations of targeted genes. The soybean lines were field tested in multiple environments and characterized for days to flowering (DTF), days to maturity (DTM), and plant height in locations throughout northern Ghana, and allelic combinations were determined for each line for associating genotype with phenotype. The results revealed significant differences based on genotype for DTF and DTM and allowed the comparison of different variant alleles of those genes. The mutant alleles of J and E1 had significant impact on DTF and DTM, and alleles of those genes interacted with each other for DTF but not DTM. The Dt1 gene significantly influenced plant height but not DTF or DTM. CONCLUSIONS This research identified major and minor effect alleles of soybean genes that can be combined to control DTF, DTM, and plant height in short day tropical environments in Ghana. These phenotypes contribute to adaptation to a low latitude environment that can be optimized in a soybean breeding program with targeted selection of desired allele combinations. The knowledge of the genetic control of these traits will enhance molecular breeding to produce optimally adapted soybean varieties targeted to tropical environments.
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Affiliation(s)
- Carrie Miranda
- USDA/ARS Plant Genetics Research Unit, 110 Waters Hall, University of Missouri, Columbia, MO 65211 USA
| | - Andrew Scaboo
- Division of Plant Sciences, 110 Waters Hall, University of Missouri, Columbia, MO 65211 USA
| | - Elroy Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6 Canada
| | - Nicholas Denwar
- CSIR-Savanna Agricultural Research Institute, P. O. Box 52, Tamale, Ghana
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, 110 Waters Hall, University of Missouri, Columbia, MO 65211 USA
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6
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Kato S, Sayama T, Taguchi-Shiobara F, Kikuchi A, Ishimoto M, Cober E. Effect of change from a determinate to a semi-determinate growth habit on the yield and lodging resistance of soybeans in the northeast region of Japan. Breed Sci 2019; 69:151-159. [PMID: 31086493 PMCID: PMC6507727 DOI: 10.1270/jsbbs.18112] [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] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/23/2018] [Indexed: 05/20/2023]
Abstract
Although an indeterminate growth habit is attractive to develop high-yield soybean varieties with higher number of pods (Glycine max (L). Merr.), lodging in indeterminate varieties remains a problem in Japan. As the semi-determinate varieties have shorter main stem length than the indeterminate varieties, this trait can be useful to improve varieties with high yield and low lodging risk. We introduced the genes Dt1 and Dt2, which regulate stem growth habit, into three determinate varieties by backcrossing and evaluated the resulting effects on yield and lodging tendency under four different growing environments. The yield and lodging degree of the semi-determinate and indeterminate lines were higher and more severe than those of the determinate lines. Despite the lower overall lodging score, the semi-determinate lines had marginally lower overall yield than that of the indeterminate lines. However, the effect of introduction of semi-determinate traits on yield and lodging degree was different in the three backgrounds, with the yield of semi-determinate lines being the highest and the difference in lodging degree between the semi-determinate and determinate lines being under 1.0 in one background. Therefore, semi-determinate growth habit has potential to develop high yielding varieties with low lodging risk.
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Affiliation(s)
- Shin Kato
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO),
297 Uenodai, Kariwano, Daisen, Akita 019-2112,
Japan
- Corresponding author (e-mail: )
| | - Takashi Sayama
- Western Region Agricultural Research Center, NARO,
1-3-1 Senyuu, Zentsuji, Kagawa 765-8508,
Japan
| | | | - Akio Kikuchi
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO),
297 Uenodai, Kariwano, Daisen, Akita 019-2112,
Japan
| | - Masao Ishimoto
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Elroy Cober
- Ottawa Research Development Centre, Agriculture and Agri-Food Canada,
960 Carling Ave., Ottawa, Ontario K1A0C6,
Canada
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Nambiar P, Cober E, Johnson L, Brizendine KD. Fatal Fusarium infection manifesting as osteomyelitis following previous treatment with amphotericin B in a multi-visceral transplant: Case report and review of Fusarium infections in solid organ transplantation. Transpl Infect Dis 2018; 20:e12872. [PMID: 29512240 DOI: 10.1111/tid.12872] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/06/2017] [Accepted: 01/01/2018] [Indexed: 12/16/2022]
Abstract
Invasive fusariosis in solid organ transplant is uncommon and usually presents as localized infection with favorable outcomes compared to hematologic malignancies or bone marrow transplants. We report the first case of Fusarium osteomyelitis in a patient following multi-visceral transplant and review Fusarium in organ transplant recipients and Fusarium bone and joint infections. Our case underscores the importance of early recognition and multidisciplinary approach to treatment and highlights potential failure to eradicate with amphotericin B monotherapy.
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Affiliation(s)
- P Nambiar
- Department of Medicine, Section of Infectious Disease, Louisiana State University Health System, Shreveport, LA, USA
| | - E Cober
- Department of Infectious Disease, Cleveland Clinic, Cleveland, OH, USA
| | - L Johnson
- Department of Infectious Disease, Cleveland Clinic, Cleveland, OH, USA
| | - K D Brizendine
- Department of Infectious Disease, Cleveland Clinic, Cleveland, OH, USA.,Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
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8
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Torkamaneh D, Laroche J, Tardivel A, O'Donoughue L, Cober E, Rajcan I, Belzile F. Comprehensive description of genomewide nucleotide and structural variation in short-season soya bean. Plant Biotechnol J 2018; 16:749-759. [PMID: 28869792 PMCID: PMC5814582 DOI: 10.1111/pbi.12825] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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: 05/19/2017] [Revised: 07/21/2017] [Accepted: 08/14/2017] [Indexed: 05/22/2023]
Abstract
Next-generation sequencing (NGS) and bioinformatics tools have greatly facilitated the characterization of nucleotide variation; nonetheless, an exhaustive description of both SNP haplotype diversity and of structural variation remains elusive in most species. In this study, we sequenced a representative set of 102 short-season soya beans and achieved an extensive coverage of both nucleotide diversity and structural variation (SV). We called close to 5M sequence variants (SNPs, MNPs and indels) and noticed that the number of unique haplotypes had plateaued within this set of germplasm (1.7M tag SNPs). This data set proved highly accurate (98.6%) based on a comparison of called genotypes at loci shared with a SNP array. We used this catalogue of SNPs as a reference panel to impute missing genotypes at untyped loci in data sets derived from lower density genotyping tools (150 K GBS-derived SNPs/530 samples). After imputation, 96.4% of the missing genotypes imputed in this fashion proved to be accurate. Using a combination of three bioinformatics pipelines, we uncovered ~92 K SVs (deletions, insertions, inversions, duplications, CNVs and translocations) and estimated that over 90% of these were accurate. Finally, we noticed that the duplication of certain genomic regions explained much of the residual heterozygosity at SNP loci in otherwise highly inbred soya bean accessions. This is the first time that a comprehensive description of both SNP haplotype diversity and SV has been achieved within a regionally relevant subset of a major crop.
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Affiliation(s)
- Davoud Torkamaneh
- Département de PhytologieUniversité LavalQuebec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuebec CityQCCanada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuebec CityQCCanada
| | - Aurélie Tardivel
- Département de PhytologieUniversité LavalQuebec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuebec CityQCCanada
- CÉROMCentre de Recherche Sur Les Grains Inc.Saint‐Mathieu de BeloeilQCCanada
| | - Louise O'Donoughue
- CÉROMCentre de Recherche Sur Les Grains Inc.Saint‐Mathieu de BeloeilQCCanada
| | - Elroy Cober
- Agriculture and Agri‐Food CanadaOttawaONCanada
| | - Istvan Rajcan
- Department of Plant Agriculture, Crop Science Bldg.University of GuelphGuelphONCanada
| | - François Belzile
- Département de PhytologieUniversité LavalQuebec CityQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuebec CityQCCanada
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9
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Saeed H, Gagnon C, Cober E, Gleddie S. Data on the epitope mapping of soybean A2 and A3 glycinin. Data Brief 2016; 8:123-31. [PMID: 27294180 PMCID: PMC4889876 DOI: 10.1016/j.dib.2016.05.027] [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: 04/11/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 11/28/2022] Open
Abstract
The data information provided in this article relate to our research article “Using patient serum to epitope map soybean glycinins reveals common epitopes shared with many legumes and tree nuts” (Saeed et al., 2016) [1]. Here we provide western blot detection of glycinin subunits by soy-sensitive human sera, ELISA screens with overlapping synthetic peptides (epitope mapping), and various database/server epitope searches.
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Affiliation(s)
- Hanaa Saeed
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Christine Gagnon
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Steve Gleddie
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
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10
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Saeed H, Gagnon C, Cober E, Gleddie S. Using patient serum to epitope map soybean glycinins reveals common epitopes shared with many legumes and tree nuts. Mol Immunol 2016; 70:125-33. [PMID: 26766775 DOI: 10.1016/j.molimm.2015.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 10/08/2015] [Revised: 11/23/2015] [Accepted: 12/13/2015] [Indexed: 11/15/2022]
Abstract
Soybean consumption is increasing in many Western diets; however, recent reviews suggest that the prevalence of soy allergy can be as high as 0.5% for the general population and up to 13% for children. The immunoglobulin-E (IgE) binding of sera from six soy-sensitive adult human subjects to soybean proteins separated by 2D gel electrophoresis was studied. Synthetic peptide sets spanning the mature glycinin subunit A2 and A3 primary sequences were used to map the IgE-binding regions. Putative epitopes identified in this study were also localized on glycinin hexamer models using bioinformatics software. We identified linear IgE-binding epitopes of the major storage protein Gly m 6 by screening individual soy-sensitive patient sera. These epitopes were then further analysed by 3D in silico model localization and compared to other plant storage protein epitopes. Web-based software applications were also used to study the ability to accurately predict epitopes with mixed results. A total of nine putative IgE-binding epitopes were identified in the glycinin A3 (A3.1-A3.3) and A2 (A2.1-A2.6) subunits. Most patients' sera IgE bound to only one or two epitopes, except for one patient's serum which bound to four different A2 epitopes. Two epitopes (A3.2 and A2.4) overlapped with a previously identified epitope hot spot of 11S globulins from other plant species. Most epitopes were predicted to be exposed on the surface of the 3D model of the glycinin hexamer. Amino acid sequence alignments of soybean acidic glycinins and other plant globulins revealed one dominant epitope hot spot among the four reported hot spots. This study may be helpful for future development of soy allergy immunotherapy and diagnosis.
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Affiliation(s)
- Hanaa Saeed
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Christine Gagnon
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada
| | - Steve Gleddie
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario K1A 0C6, Canada.
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Sonah H, O'Donoughue L, Cober E, Rajcan I, Belzile F. Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean. Plant Biotechnol J 2015; 13:211-21. [PMID: 25213593 DOI: 10.1111/pbi.12249] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [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: 02/17/2014] [Revised: 06/24/2014] [Accepted: 07/29/2014] [Indexed: 05/18/2023]
Abstract
Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.
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Affiliation(s)
- Humira Sonah
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
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Kaul DR, Stoelben S, Cober E, Ojo T, Sandusky E, Lischka P, Zimmermann H, Rubsamen-Schaeff H. First report of successful treatment of multidrug-resistant cytomegalovirus disease with the novel anti-CMV compound AIC246. Am J Transplant 2011; 11:1079-84. [PMID: 21521474 DOI: 10.1111/j.1600-6143.2011.03530.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report the first case of cytomegalovirus (CMV) disease treated with AIC246, a novel anti-CMV compound which targets the viral terminase complex and remains active against virus resistant to DNA polymerase inhibitors. A lung transplant recipient developed refractory multidrug-resistant CMV disease involving the lungs, gastrointestinal tract and retina. His disease progressed despite treatment with all DNA polymerase inhibitors; multiple agents reported to have activity against CMV in case series, and reduction in his immunosuppressive medications. AIC246 which is in clinical development was obtained for emergency use, and combined with additional reduction in immunosuppression resulted in rapid clinical, virological and radiological resolution of disease. The patient has remained free of CMV disease or viremia off treatment for greater than 3 months. In summary AIC246, while still in development, may be a promising alternative to current therapies.
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Affiliation(s)
- D R Kaul
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
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Jegadeesan S, Yu K, Poysa V, Gawalko E, Morrison MJ, Shi C, Cober E. Mapping and validation of simple sequence repeat markers linked to a major gene controlling seed cadmium accumulation in soybean [Glycine max (L.) Merr]. Theor Appl Genet 2010; 121:283-94. [PMID: 20224890 DOI: 10.1007/s00122-010-1309-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 02/21/2010] [Indexed: 05/03/2023]
Abstract
Daily consumption of cadmium (Cd) contaminated foods poses a risk to human health. Cultivar selection is an important method to limit Cd uptake and accumulation; however, analyzing grain Cd concentration is costly and time-consuming. Developing markers for low Cd accumulation will facilitate marker assisted selection (MAS). Inheritance studies using a threshold value of 0.2 mg kg(-1) for low and high and an F(2:3) population showed that low Cd accumulation in soybean seed is under the control of a major gene (Cda1, proposed name) with the allele for low accumulation being dominant. A recombinant inbred line (RIL) population (F(6:8)) derived from the cross AC Hime (high Cd accumulation) and Westag-97 (low Cd accumulation) was used to identify the DNA markers linked to Cda gene(s) or quantitative trait loci (QTLs) controlling low Cd accumulation. We screened 171 simple sequence repeat (SSR) primers that showed polymorphism between parents on the 166 RILs. Of these, 40 primers were newly developed from the soybean genomic DNA sequence. Seven SSR markers, SatK138, SatK139, SatK140 (0.5 cM), SatK147, SacK149, SaatK150 and SattK152 (0.3 cM), were linked to Cda1 in soybean seed. All the linked markers were mapped to the same linkage group (LG) K. The closest flanking SSR markers linked to Cda1 were validated using a parallel population (RILs) involving Leo x Westag-97. Linked markers were also validated with diverse soybean genotypes differing in their seed Cd concentration and showed that SSR markers SatK147, SacK149, and SattK152 clearly differentiated the high and low Cd accumulating genotypes tested. To treat Cd uptake as a quantitative trait, QTL analysis using a linkage map constructed with 161 markers identified a major QTL associated with low Cd concentration in the seeds. The QTL was also mapped to the same location as Cda1 on LG-K. This QTL accounted for 57.3% of the phenotypic variation. Potential candidate genes (genes with known or predicted function that could influence the seed Cd concentration) like protein kinase, putative Adagio-like protein, and plasma membrane H(+)-ATPase were found to be located in the locus of interest. Of the four SSR markers located in the region, SattK152 was localized in the plasma membrane H(+)-ATPase gene. SSR markers closely linked to Cda1 in seeds of soybean were identified and have potential to be used for MAS to develop low Cd accumulating cultivars in a breeding program.
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Affiliation(s)
- Souframanien Jegadeesan
- Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, Ontario, Canada
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