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Facy ML, Hebart ML, Oakey H, McEwin RA, Pitchford WS. Genetic parameters for yearling male reproduction traits in tropical composite cattle population. J Anim Sci 2024; 102:skae069. [PMID: 38477357 PMCID: PMC10998458 DOI: 10.1093/jas/skae069] [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: 07/18/2023] [Accepted: 03/12/2024] [Indexed: 03/14/2024] Open
Abstract
Fertility is economically important but is hard to quantify and measure in breeding programs which has led extensive breeding programs to ignore fertility in their selection criteria. While female fertility traits have been extensively researched, male fertility traits have been largely ignored. It is estimated that 20% to 40% of bulls have sub-fertility, reducing the number of calves born and profits, highlighting the importance of investigating bull fertility. The most practical measure of male fertility is a bull breeding soundness evaluation (BBSE) which assesses structure as well as semen quality and quantity. Generally, traits recorded in a BBSE are neither genetically evaluated nor used for selection in breeding programs. All traits recorded during a BBSE were analyzed through a series of univariate and bivariate linear mixed models using a genomic relationship matrix to estimate genetic parameters. All genotype and phenotype data were obtained from a tropical composite commercial cattle population and imputed to 27,638 single-nucleotide polymorphisms (SNPs) with a total of 2,613 genotyped animals with BBSE records ranging from 616 to 826 animals depending on the trait. The heritabilities of the 27 traits recorded during a BBSE ranged from 0.02 to 0.49. Seven of the male fertility traits were recommended to be included in a breeding program based on their heritability and their phenotypic and genetic correlations. These traits are scrotal circumference, percent normal sperm, proximal droplets, distal midpiece reflex, knobbed acrosomes, vacuoles/teratoids, and sheath score. Using these seven traits in a breeding program would result in higher calving rates, increasing production and profitability.
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Affiliation(s)
- Madeliene L Facy
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Michelle L Hebart
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5006, Australia
| | - Rudi A McEwin
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Wayne S Pitchford
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
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Oakey H, Giles LC, Thomson RL, Lê Cao KA, Ashwood P, Brown JD, Knight EJ, Barry SC, Craig ME, Colman PG, Davis EA, Hamilton-Williams EE, Harrison LC, Haynes A, Kim KW, Mallitt KA, McGorm K, Morahan G, Rawlinson WD, Sinnott RO, Soldatos G, Wentworth JM, Couper JJ, Penno MAS. Protocol for a nested case-control study design for omics investigations in the Environmental Determinants of Islet Autoimmunity cohort. Ann Med 2023; 55:2198255. [PMID: 37043275 PMCID: PMC10101668 DOI: 10.1080/07853890.2023.2198255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Background: The Environmental Determinants of Islet Autoimmunity (ENDIA) pregnancy-birth cohort investigates the developmental origins of type 1 diabetes (T1D), with recruitment between 2013 and 2019. ENDIA is the first study in the world with comprehensive data and biospecimen collection during pregnancy, at birth and through childhood from at-risk children who have a first-degree relative with T1D. Environmental exposures are thought to drive the progression to clinical T1D, with pancreatic islet autoimmunity (IA) developing in genetically susceptible individuals. The exposures and key molecular mechanisms driving this progression are unknown. Persistent IA is the primary outcome of ENDIA; defined as a positive antibody for at least one of IAA, GAD, ZnT8 or IA2 on two consecutive occasions and signifies high risk of clinical T1D.Method: A nested case-control (NCC) study design with 54 cases and 161 matched controls aims to investigate associations between persistent IA and longitudinal omics exposures in ENDIA. The NCC study will analyse samples obtained from ENDIA children who have either developed persistent IA or progressed to clinical T1D (cases) and matched control children at risk of developing persistent IA. Control children were matched on sex and age, with all four autoantibodies absent within a defined window of the case's onset date. Cases seroconverted at a median of 1.37 years (IQR 0.95, 2.56). Longitudinal omics data generated from approximately 16,000 samples of different biospecimen types, will enable evaluation of changes from pregnancy through childhood.Conclusions: This paper describes the ENDIA NCC study, omics platform design considerations and planned univariate and multivariate analyses for its longitudinal data. Methodologies for multivariate omics analysis with longitudinal data are discovery-focused and data driven. There is currently no single multivariate method tailored specifically for the longitudinal omics data that the ENDIA NCC study will generate and therefore omics analysis results will require either cross validation or independent validation.KEY MESSAGESThe ENDIA nested case-control study will utilize longitudinal omics data on approximately 16,000 samples from 190 unique children at risk of type 1 diabetes (T1D), including 54 who have developed islet autoimmunity (IA), followed during pregnancy, at birth and during early childhood, enabling the developmental origins of T1D to be explored.
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Affiliation(s)
- Helena Oakey
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Lynne C Giles
- School of Public Health, The University of Adelaide, Adelaide, South Australia, Australia
| | - Rebecca L Thomson
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Pat Ashwood
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - James D Brown
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Emma J Knight
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Simon C Barry
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth A Davis
- Telethon Kids Institute Centre for Child Health Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Emma E Hamilton-Williams
- Faculty of Medicine, Frazer Institute, The University of Queensland Translational Research Institute, Brisbane, Queensland, Australia
| | - Leonard C Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Aveni Haynes
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Ki Wook Kim
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Kylie-Ann Mallitt
- Faculty of Medicine and Health, Sydney School of Public Health, The University of Sydney, Sydney, New South Wales, Australia
- School of Clinical Medicine - Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Kelly McGorm
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information Services, University of Melbourne, Melbourne, Victoria, Australia
| | - Georgia Soldatos
- Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, Victoria, Australia
| | - John M Wentworth
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Jennifer J Couper
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Endocrinology and Diabetes Centre, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Megan A S Penno
- Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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Harrison LC, Bandala‐Sanchez E, Oakey H, Colman PG, Watson K, Kim KW, Wu R, Hamilton‐Williams EE, Stone NL, Haynes A, Thomson RL, Vuillermin PJ, Soldatos G, Rawlinson WD, McGorm KJ, Morahan G, Barry SC, Sinnott RO, Wentworth JM, Couper JJ, Penno MAS. A surge in serum mucosal cytokines associated with seroconversion in children at risk for type 1 diabetes. J Diabetes Investig 2023; 14:1092-1100. [PMID: 37312283 PMCID: PMC10445231 DOI: 10.1111/jdi.14031] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 06/15/2023] Open
Abstract
AIMS/INTRODUCTION Autoantibodies to pancreatic islet antigens identify young children at high risk of type 1 diabetes. On a background of genetic susceptibility, islet autoimmunity is thought to be driven by environmental factors, of which enteric viruses are prime candidates. We sought evidence for enteric pathology in children genetically at-risk for type 1 diabetes followed from birth who had developed islet autoantibodies ("seroconverted"), by measuring mucosa-associated cytokines in their sera. MATERIALS AND METHODS Sera were collected 3 monthly from birth from children with a first-degree type 1 diabetes relative, in the Environmental Determinants of Islet Autoimmunity (ENDIA) study. Children who seroconverted were matched for sex, age, and sample availability with seronegative children. Luminex xMap technology was used to measure serum cytokines. RESULTS Of eight children who seroconverted, for whom serum samples were available at least 6 months before and after seroconversion, the serum concentrations of mucosa-associated cytokines IL-21, IL-22, IL-25, and IL-10, the Th17-related cytokines IL-17F and IL-23, as well as IL-33, IFN-γ, and IL-4, peaked from a low baseline in seven around the time of seroconversion and in one preceding seroconversion. These changes were not detected in eight sex- and age-matched seronegative controls, or in a separate cohort of 11 unmatched seronegative children. CONCLUSIONS In a cohort of children at risk for type 1 diabetes followed from birth, a transient, systemic increase in mucosa-associated cytokines around the time of seroconversion lends support to the view that mucosal infection, e.g., by an enteric virus, may drive the development of islet autoimmunity.
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Affiliation(s)
- Leonard C Harrison
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Esther Bandala‐Sanchez
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Helena Oakey
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Peter G Colman
- Department of Diabetes and EndocrinologyRoyal Melbourne HospitalMelbourneVictoriaAustralia
| | - Kelly Watson
- Department of Diabetes and EndocrinologyRoyal Melbourne HospitalMelbourneVictoriaAustralia
| | - Ki Wook Kim
- Virology Research Laboratory, Serology and Virology DivisionNSW Health, Prince of Wales HospitalSydneyNew South WalesAustralia
- Schools of Biomedical Sciences and Biotechnology and Biomolecular Sciences, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Roy Wu
- Virology Research Laboratory, Serology and Virology DivisionNSW Health, Prince of Wales HospitalSydneyNew South WalesAustralia
- Schools of Biomedical Sciences and Biotechnology and Biomolecular Sciences, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | | | - Natalie L Stone
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Aveni Haynes
- Telethon Kids Institute for Child Health Research, Centre for Child Health Researchthe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Rebecca L Thomson
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Peter J Vuillermin
- Faculty of School of MedicineDeakin UniversityGeelongVictoriaAustralia
- Child Health Research UnitBarwon HealthGeelongVictoriaAustralia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
- Diabetes and Vascular Medicine UnitMonash HealthMelbourneVictoriaAustralia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology DivisionNSW Health, Prince of Wales HospitalSydneyNew South WalesAustralia
- Schools of Biomedical Sciences and Biotechnology and Biomolecular Sciences, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Kelly J McGorm
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical ResearchThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Simon C Barry
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information ServicesUniversity of MelbourneMelbourneVictoriaAustralia
| | - John M Wentworth
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
- Department of Diabetes and EndocrinologyRoyal Melbourne HospitalMelbourneVictoriaAustralia
| | - Jennifer J Couper
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Megan AS Penno
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
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McGorm KJ, Brown JD, Roberts AG, Greenbank S, Brasacchio D, Sawyer ACP, Oakey H, Colman PG, Craig ME, Davis EA, Soldatos G, Thomson RL, Wentworth JM, Couper JJ, Penno MAS. Experiences of Caregivers and At-Risk Children Enrolled in a Prospective Pregnancy-Birth Cohort Study into the Causes of Type 1 Diabetes: The ENDIA Study. Children 2023; 10:children10040637. [PMID: 37189886 DOI: 10.3390/children10040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
Background: We sought research experiences of caregivers and their children were enrolled in the Environmental Determinants of Islet Autoimmunity (ENDIA) study. Methods: ENDIA is a pregnancy–birth cohort investigating early-life causes of type 1 diabetes (T1D). Surveys were sent to 1090 families between June 2021 and March 2022 with a median participation of >5 years. Caregivers completed a 12-item survey. Children ≥ 3 years completed a four-item survey. Results: The surveys were completed by 550/1090 families (50.5%) and 324/847 children (38.3%). The research experience was rated as either “excellent” or “good” by 95% of caregivers, and 81% of children were either “ok”, “happy” or “very happy”. The caregivers were motivated by contributing to research and monitoring their children for T1D. Relationships with the research staff influenced the experience. The children most liked virtual reality headsets, toys, and “helping”. Blood tests were least liked by the children and were the foremost reason that 23.4% of the caregivers considered withdrawing. The children valued gifts more than their caregivers. Only 5.9% of responses indicated dissatisfaction with some aspects of the protocol. The self-collection of samples in regional areas, or during the COVID-19 pandemic restrictions, were accepted. Conclusions: This evaluation identified modifiable protocol elements and was conducted to further improve satisfaction. What was important to the children was distinct from their caregivers.
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Shafiei R, Hooper M, McClellan C, Oakey H, Stephens J, Lapierre C, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. Downregulation of barley ferulate 5-hydroxylase dramatically alters straw lignin structure without impact on mechanical properties. Front Plant Sci 2023; 13:1125003. [PMID: 36726680 PMCID: PMC9886061 DOI: 10.3389/fpls.2022.1125003] [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: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Barley is a major cereal crop for temperate climates, and a diploid genetic model for polyploid wheat. Cereal straw biomass is an attractive source of feedstock for green technologies but lignin, a key determinant of feedstock recalcitrance, complicates bio-conversion processes. However, manipulating lignin content to improve the conversion process could negatively affect agronomic traits. An alternative approach is to manipulate lignin composition which influences the physical and chemical properties of straw. This study validates the function of a barley ferulate 5-hydroxylase gene and demonstrates that its downregulation using the RNA-interference approach substantially impacts lignin composition. We identified five barley genes having putative ferulate 5-hydroxylase activity. Downregulation of HvF5H1 substantially reduced the lignin syringyl/guaiacyl (S/G) ratio in straw while the lignin content, straw mechanical properties, plant growth habit, and grain characteristics all remained unaffected. Metabolic profiling revealed significant changes in the abundance of 173 features in the HvF5H1-RNAi lines. The drastic changes in the lignin polymer of transgenic lines highlight the plasticity of barley lignification processes and the associated potential for manipulating and improving lignocellulosic biomass as a feedstock for green technologies. On the other hand, our results highlight some differences between the lignin biosynthetic pathway in barley, a temperate climate grass, and the warm climate grass, rice, and underscore potential diversity in the lignin biosynthetic pathways in grasses.
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Affiliation(s)
- Reza Shafiei
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Matthew Hooper
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Christopher McClellan
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
- Faculty of Sciences, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Jennifer Stephens
- Cell And Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | | | - Yukiko Tsuji
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
- Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium
| | - John Ralph
- Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
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Facy ML, Hebart ML, Oakey H, McEwin RA, Pitchford WS. Genetic relationships among yearling fertility, body composition and weight traits in tropically adapted composite cattle. Anim Prod Sci 2023. [DOI: 10.1071/an22453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Wentworth JM, Oakey H, Craig ME, Couper JJ, Cameron FJ, Davis EA, Lafferty AR, Harris M, Wheeler BJ, Jefferies C, Colman PG, Harrison LC. Decreased occurrence of ketoacidosis and preservation of beta cell function in relatives screened and monitored for type 1 diabetes in Australia and New Zealand. Pediatr Diabetes 2022; 23:1594-1601. [PMID: 36175392 PMCID: PMC9772160 DOI: 10.1111/pedi.13422] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 09/24/2022] [Indexed: 12/29/2022] Open
Abstract
AIMS Islet autoantibody screening of infants and young children in the Northern Hemisphere, together with semi-annual metabolic monitoring, is associated with a lower risk of ketoacidosis (DKA) and improved glucose control after diagnosis of clinical (stage 3) type 1 diabetes (T1D). We aimed to determine if similar benefits applied to older Australians and New Zealanders monitored less rigorously. METHODS DKA occurrence and metabolic control were compared between T1D relatives screened and monitored for T1D and unscreened individuals diagnosed in the general population, ascertained from the Australasian Diabetes Data Network. RESULTS Between 2005 and 2019, 17,105 relatives (mean (SD) age 15.7 (10.8) years; 52% female) were screened for autoantibodies against insulin, glutamic acid decarboxylase, and insulinoma-associated protein 2. Of these, 652 screened positive to a single and 306 to multiple autoantibody specificities, of whom 201 and 215, respectively, underwent metabolic monitoring. Of 178 relatives diagnosed with stage 3 T1D, 9 (5%) had DKA, 7 of whom had not undertaken metabolic monitoring. The frequency of DKA in the general population was 31%. After correction for age, sex and T1D family history, the frequency of DKA in screened relatives was >80% lower than in the general population. HbA1c and insulin requirements following diagnosis were also lower in screened relatives, consistent with greater beta cell reserve. CONCLUSIONS T1D autoantibody screening and metabolic monitoring of older children and young adults in Australia and New Zealand, by enabling pre-clinical diagnosis when beta cell reserve is greater, confers protection from DKA. These clinical benefits support ongoing efforts to increase screening activity in the region and should facilitate the application of emerging immunotherapies.
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Affiliation(s)
- John M Wentworth
- Department of Population Health and Immunity, Walter and Eliza Hall Institute, Parkville, Australia
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Helena Oakey
- Robinson Research Institute, University of Adelaide, South Australia
| | - Maria E Craig
- School of Women’s and Children’s Health, University of New South Wales, Australia
- Children’s Hospital at Westmead, Westmead, Australia
- Charles Perkins Centre Westmead, University of Sydney, Australia
| | - Jennifer J Couper
- Department of Diabetes and Endocrinology, Women’s and Children’s Hospital, North Adelaide, South Australia
| | | | | | | | - Mark Harris
- Queensland Children’s Hospital, South Brisbane, Australia
| | - Benjamin J Wheeler
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, New Zealand
- Department of Paediatrics, Southern District Health Board, Dunedin, New Zealand
| | - Craig Jefferies
- Starship Children’s Health Liggins institute and Department of Paediatrics, University of Auckland, New Zealand
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Parkville, Australia
| | - Leonard C Harrison
- Department of Population Health and Immunity, Walter and Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
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McGorm KJ, Brown JD, Thomson RL, Oakey H, Moore B, Hendry A, Colman PG, Craig ME, Davis EA, Harris M, Harrison LC, Haynes A, Soldatos G, Vuillermin P, Wentworth JM, Couper JJ, Penno MAS. A Long-Term Evaluation of Facebook for Recruitment and Retention in the ENDIA Type 1 Diabetes Pregnancy-Birth Cohort Study. J Diabetes Sci Technol 2022; 17:696-704. [PMID: 35193430 DOI: 10.1177/19322968221079867] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The Environmental Determinants of Islet Autoimmunity (ENDIA) study is an Australia-wide pregnancy-birth cohort study following children who have a first-degree relative with type 1 diabetes (ACTRN1261300794707). A dedicated ENDIA Facebook page was established in 2013 with the aim of enhancing recruitment and supporting participant retention through dissemination of study information. To measure the impact of Facebook, we evaluated the sources of referral to the study, cohort demographics, and withdrawal rates. We also investigated whether engagement with Facebook content was associated with specific post themes. METHODS Characteristics of Facebook versus conventional recruits were compared using linear, logistic, and multinomial logistic regression models. Logistic regression was used to determine the risk of study withdrawal. Data pertaining to 794 Facebook posts over 7.5 years were included in the analysis. RESULTS Facebook was the third largest source of referral (300/1511; 19.9%). Facebook recruits were more frequently Australian-born (P < .001) enrolling postnatally (P = .01) and withdrew from the study at a significantly lower rate compared with conventional recruits (4.7% vs 12.3%; P < .001) after a median of follow-up of 3.3 years. Facebook content featuring stories and images of participants received the highest engagement even though <20% of the 2337 Facebook followers were enrolled in the study. CONCLUSIONS Facebook was a valuable recruitment tool for ENDIA. Compared with conventional recruits, Facebook recruits were three times less likely to withdraw during long-term follow-up and had different sociodemographic characteristics. Facebook content featuring participants was the most engaging. These findings inform social media strategies for future cohort and type 1 diabetes studies. TRIAL REGISTRATION Australia New Zealand Clinical Trials Registry: ACTRN1261300794707.
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Affiliation(s)
- Kelly J McGorm
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
| | - James D Brown
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
| | - Rebecca L Thomson
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
| | - Belinda Moore
- Department of Diabetes & Endocrinology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Alexandra Hendry
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
| | - Peter G Colman
- Department of Diabetes & Endocrinology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Elizabeth A Davis
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia
| | - Mark Harris
- Queensland Children's Hospital, South Brisbane, QLD, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Aveni Haynes
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia
| | - Georgia Soldatos
- Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, VIC, Australia
| | - Peter Vuillermin
- Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
| | - John M Wentworth
- Department of Diabetes & Endocrinology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Jennifer J Couper
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
- Women's and Children's Hospital, Adelaide, SA, Australia
| | - Megan A S Penno
- Robinson Research Institute, Adelaide Medical School, The University of Adelaide, North Adelaide, SA, Australia
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Hall M, Oakey H, Penno MAS, McGorm K, Anderson AJ, Ashwood P, Colman PG, Craig ME, Davis EA, Harris M, Harrison LC, Haynes A, Morbey C, Sinnott RO, Soldatos G, Vuillermin PJ, Wentworth JM, Thomson RL, Couper JJ. Mental Health During Late Pregnancy and Postpartum in Mothers With and Without Type 1 Diabetes: The ENDIA Study. Diabetes Care 2022; 45:dc212335. [PMID: 35107582 DOI: 10.2337/dc21-2335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/15/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Pregnancy and type 1 diabetes are each associated with increased anxiety and depression, but the combined impact on well-being is unresolved. We compared the mental health of women with and without type 1 diabetes during pregnancy and postpartum and examined the relationship between mental health and glycemic control. RESEARCH DESIGN AND METHODS Participants were women enrolled from 2016 to 2020 in the Environmental Determinants of Islet Autoimmunity (ENDIA) study, a pregnancy to birth prospective cohort following children with a first-degree relative with type 1 diabetes. Edinburgh Postnatal Depression Scale (EPDS) and Perceived Stress Scale (PSS) were completed during the third trimester (T3) (median [interquartile range] 34 [32, 36] weeks) and postpartum (14 [13, 16] weeks) by 737 women (800 pregnancies) with (n = 518) and without (n = 282) type 1 diabetes. RESULTS EPDS and PSS scores did not differ between women with and without type 1 diabetes during T3 and postpartum. EPDS scores were marginally higher in T3: predicted mean (95% CI) 5.7 (5.4, 6.1) than postpartum: 5.3 (5.0, 5.6), independent of type 1 diabetes status (P = 0.01). HbA1c levels in type 1 diabetes were 6.3% [5.8, 6.9%] in T3 and did not correlate with EPDS or PSS scores. Reported use of psychotropic medications was similar in women with (n = 44 of 518 [8%]) and without type 1 diabetes (n = 17 of 282 [6%]), as was their amount of physical activity. CONCLUSIONS Overall, mental health in late pregnancy and postpartum did not differ between women with and without type 1 diabetes, and mental health scores were not correlated with glycemic control.
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Affiliation(s)
- Madeleine Hall
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Diabetes and Endocrinology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Megan A S Penno
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Kelly McGorm
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Amanda J Anderson
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Pat Ashwood
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Elizabeth A Davis
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Queensland, Australia
- Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Aveni Haynes
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Claire Morbey
- Hunter Diabetes Centre, Merewether, New South Wales, Australia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information Services, University of Melbourne, Melbourne, Victoria, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, Victoria, Australia
| | - Peter J Vuillermin
- Faculty of Health, School of Medicine, Deakin University, Geelong, Victoria, Australia
- Child Health Research Unit, Barwon Health, Geelong, Victoria, Australia
| | - John M Wentworth
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Rebecca L Thomson
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer J Couper
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Diabetes and Endocrinology, Women's and Children's Hospital, Adelaide, South Australia, Australia
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Bandala-Sanchez E, Roth-Schulze AJ, Oakey H, Penno MAS, Bediaga NG, Naselli G, Ngui KM, Smith AD, Huang D, Zozaya-Valdes E, Thomson RL, Brown JD, Vuillermin PJ, Barry SC, Craig ME, Rawlinson WD, Davis EA, Harris M, Soldatos G, Colman PG, Wentworth JM, Haynes A, Morahan G, Sinnott RO, Papenfuss AT, Couper JJ, Harrison LC. Women with type 1 diabetes exhibit a progressive increase in gut Saccharomyces cerevisiae in pregnancy associated with evidence of gut inflammation. Diabetes Res Clin Pract 2022; 184:109189. [PMID: 35051423 DOI: 10.1016/j.diabres.2022.109189] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/26/2022]
Abstract
AIMS Studies of the gut microbiome have focused on its bacterial composition. We aimed to characterize the gut fungal microbiome (mycobiome) across pregnancy in women with and without type 1 diabetes. METHODS Faecal samples (n = 162) were collected from 70 pregnant women (45 with and 25 without type 1 diabetes) across all trimesters. Fungi were analysed by internal transcribed spacer 1 amplicon sequencing. Markers of intestinal inflammation (faecal calprotectin) and intestinal epithelial integrity (serum intestinal fatty acid binding protein; I-FABP), and serum antibodies to Saccharomyces cerevisiae (ASCA) were measured. RESULTS Women with type 1 diabetes had decreased fungal alpha diversity by the third trimester, associated with an increased abundance of Saccharomyces cerevisiae that was inversely related to the abundance of the anti-inflammatory butyrate-producing bacterium Faecalibacterium prausnitzii. Women with type 1 diabetes had higher concentrations of calprotectin, I-FABP and ASCA. CONCLUSIONS Women with type 1 diabetes exhibit a shift in the gut mycobiome across pregnancy associated with evidence of gut inflammation and impaired intestinal barrier function. The relevance of these findings to the higher rate of pregnancy complications in type 1 diabetes warrants further study.
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Affiliation(s)
- Esther Bandala-Sanchez
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Alexandra J Roth-Schulze
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Helena Oakey
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Megan A S Penno
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Naiara G Bediaga
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Gaetano Naselli
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Katrina M Ngui
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Alannah D Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dexing Huang
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Enrique Zozaya-Valdes
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Rebecca L Thomson
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - James D Brown
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Peter J Vuillermin
- Faculty of School of Medicine, Deakin University and Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
| | - Simon C Barry
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, NSW Health Pathology, Sydney, NSW, Australia; School of Medical Sciences, Biotechnology and Biomolecular Sciences, Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Elizabeth A Davis
- Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, WA, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia; Queensland Children's Hospital, South Brisbane, QLD, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne and Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, VIC, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - John M Wentworth
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia; Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Aveni Haynes
- Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, WA, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information Services, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology and School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia; Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Jennifer J Couper
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Women's and Children's Hospital, Adelaide, SA, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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Penno MAS, Anderson AJ, Thomson RL, McGorm K, Barry SC, Colman PG, Craig ME, Davis EA, Harris M, Haynes A, Morahan G, Oakey H, Rawlinson WD, Sinnott RO, Soldatos G, Vuillermin PJ, Wentworth JM, Harrison LC, Couper JJ. Evaluation of protocol amendments to the Environmental Determinants of Islet Autoimmunity (ENDIA) study during the COVID-19 pandemic. Diabet Med 2021; 38:e14638. [PMID: 34236734 PMCID: PMC8420199 DOI: 10.1111/dme.14638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/10/2021] [Accepted: 07/07/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Megan A. S. Penno
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Amanda J. Anderson
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Rebecca L. Thomson
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Kelly McGorm
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Simon C. Barry
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Peter G. Colman
- Department of Diabetes and EndocrinologyRoyal Melbourne HospitalMelbourneVICAustralia
| | - Maria E. Craig
- School of Women's and Children's HealthFaculty of MedicineUniversity of New South WalesSydneyNSWAustralia
- Institute of Endocrinology and DiabetesThe Children's Hospital at WestmeadSydneyNSWAustralia
| | - Elizabeth A. Davis
- Telethon Institute for Child Health ResearchCentre for Child Health ResearchThe University of Western AustraliaPerthWAAustralia
| | - Mark Harris
- The University of Queensland Diamantina InstituteFaculty of MedicineThe University of QueenslandTranslational Research InstituteWoolloongabbaQLDAustralia
- Queensland Children’s HospitalSouth BrisbaneQLDAustralia
| | - Aveni Haynes
- Telethon Institute for Child Health ResearchCentre for Child Health ResearchThe University of Western AustraliaPerthWAAustralia
| | - Grant Morahan
- Centre for Diabetes ResearchHarry Perkins Institute of Medical ResearchThe University of Western AustraliaPerthWAAustralia
| | - Helena Oakey
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - William D. Rawlinson
- Virology Research Laboratory, Serology and Virology DivisionSouth Eastern Area Laboratory Services MicrobiologyPrince of Wales HospitalSydneyNSWAustralia
- School of Medical SciencesFaculty of MedicineUniversity of New South WalesSydneyNSWAustralia
| | - Richard O. Sinnott
- Melbourne eResearch GroupSchool of Computing and Information ServicesUniversity of MelbourneMelbourneVICAustralia
| | - Georgia Soldatos
- Monash Centre for Health Research and ImplementationSchool of Public Health and Preventive MedicineMonash UniversityMelbourneVICAustralia
- Diabetes and Vascular Medicine UnitMonash HealthMelbourneVICAustralia
| | - Peter J. Vuillermin
- Faculty of HealthSchool of MedicineDeakin UniversityGeelongVICAustralia
- Child Health Research UnitBarwon HealthGeelongVICAustralia
| | - John M. Wentworth
- Department of Diabetes and EndocrinologyRoyal Melbourne HospitalMelbourneVICAustralia
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVICAustralia
| | | | - Jennifer J. Couper
- Robinson Research InstituteAdelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
- Department of Diabetes and EndocrinologyWomen’s and Children’s HospitalAdelaideSAAustralia
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12
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Hope CM, Huynh D, Wong YY, Oakey H, Perkins GB, Nguyen T, Binkowski S, Bui M, Choo AYL, Gibson E, Huang D, Kim KW, Ngui K, Rawlinson WD, Sadlon T, Couper JJ, Penno MAS, Barry SC. Optimization of Blood Handling and Peripheral Blood Mononuclear Cell Cryopreservation of Low Cell Number Samples. Int J Mol Sci 2021; 22:ijms22179129. [PMID: 34502038 PMCID: PMC8431655 DOI: 10.3390/ijms22179129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Rural/remote blood collection can cause delays in processing, reducing PBMC number, viability, cell composition and function. To mitigate these impacts, blood was stored at 4 °C prior to processing. Viable cell number, viability, immune phenotype, and Interferon-γ (IFN-γ) release were measured. Furthermore, the lowest protective volume of cryopreservation media and cell concentration was investigated. Methods: Blood from 10 individuals was stored for up to 10 days. Flow cytometry and IFN-γ ELISPOT were used to measure immune phenotype and function on thawed PBMC. Additionally, PBMC were cryopreserved in volumes ranging from 500 µL to 25 µL and concentration from 10 × 106 cells/mL to 1.67 × 106 cells/mL. Results: PBMC viability and viable cell number significantly reduced over time compared with samples processed immediately, except when stored for 24 h at RT. Monocytes and NK cells significantly reduced over time regardless of storage temperature. Samples with >24 h of RT storage had an increased proportion in Low-Density Neutrophils and T cells compared with samples stored at 4 °C. IFN-γ release was reduced after 24 h of storage, however not in samples stored at 4 °C for >24 h. The lowest protective volume identified was 150 µL with the lowest density of 6.67 × 106 cells/mL. Conclusion: A sample delay of 24 h at RT does not impact the viability and total viable cell numbers. When long-term delays exist (>4 d) total viable cell number and cell viability losses are reduced in samples stored at 4 °C. Immune phenotype and function are slightly altered after 24 h of storage, further impacts of storage are reduced in samples stored at 4 °C.
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Affiliation(s)
- Christopher M. Hope
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
- Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
| | - Dao Huynh
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Ying Ying Wong
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Griffith Boord Perkins
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Trung Nguyen
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Sabrina Binkowski
- Children’s Diabetes Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (S.B.); (A.Y.L.C.)
| | - Minh Bui
- Child Health Research Unit, Barwon Health, Geelong, VIC 3220, Australia;
| | - Ace Y. L. Choo
- Children’s Diabetes Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (S.B.); (A.Y.L.C.)
| | - Emily Gibson
- School of Women’s and Children’s Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia; (E.G.); (K.W.K.); (W.D.R.)
| | - Dexing Huang
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; (D.H.); (K.N.)
| | - Ki Wook Kim
- School of Women’s and Children’s Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia; (E.G.); (K.W.K.); (W.D.R.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Katrina Ngui
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; (D.H.); (K.N.)
| | - William D. Rawlinson
- School of Women’s and Children’s Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia; (E.G.); (K.W.K.); (W.D.R.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Timothy Sadlon
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Jennifer J. Couper
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
- Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
| | - Megan A. S. Penno
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Simon C. Barry
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
- Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
- Correspondence:
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13
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Stanschewski CS, Rey E, Fiene G, Craine EB, Wellman G, Melino VJ, S. R. Patiranage D, Johansen K, Schmöckel SM, Bertero D, Oakey H, Colque-Little C, Afzal I, Raubach S, Miller N, Streich J, Amby DB, Emrani N, Warmington M, Mousa MAA, Wu D, Jacobson D, Andreasen C, Jung C, Murphy K, Bazile D, Tester M. Quinoa Phenotyping Methodologies: An International Consensus. Plants (Basel) 2021; 10:1759. [PMID: 34579292 PMCID: PMC8472428 DOI: 10.3390/plants10091759] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.
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Affiliation(s)
- Clara S. Stanschewski
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Elodie Rey
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Gabriele Fiene
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Evan B. Craine
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (E.B.C.); (K.M.)
| | - Gordon Wellman
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Vanessa J. Melino
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Dilan S. R. Patiranage
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; (N.E.); (C.J.)
| | - Kasper Johansen
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Sandra M. Schmöckel
- Department Physiology of Yield Stability, Institute of Crop Science, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Daniel Bertero
- Department of Plant Production, School of Agriculture, University of Buenos Aires, Buenos Aires C1417DSE, Argentina;
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Carla Colque-Little
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark; (C.C.-L.); (D.B.A.); (C.A.)
| | - Irfan Afzal
- Department of Agronomy, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee AB15 8QH, UK;
| | - Nathan Miller
- Department of Botany, University of Wisconsin, 430 Lincoln Dr, Madison, WI 53706, USA;
| | - Jared Streich
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (J.S.); (D.J.)
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark; (C.C.-L.); (D.B.A.); (C.A.)
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; (N.E.); (C.J.)
| | - Mark Warmington
- Department of Primary Industries and Regional Development, Agriculture and Food, Kununurra, WA 6743, Australia;
| | - Magdi A. A. Mousa
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Vegetables, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - David Wu
- Shanxi Jiaqi Agri-Tech Co., Ltd., Taiyuan 030006, China;
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (J.S.); (D.J.)
| | - Christian Andreasen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark; (C.C.-L.); (D.B.A.); (C.A.)
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; (N.E.); (C.J.)
| | - Kevin Murphy
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (E.B.C.); (K.M.)
| | - Didier Bazile
- CIRAD, UMR SENS, 34398 Montpellier, France;
- SENS, CIRAD, IRD, University Paul Valery Montpellier 3, 34090 Montpellier, France
| | - Mark Tester
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
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14
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Roth-Schulze AJ, Penno MAS, Ngui KM, Oakey H, Bandala-Sanchez E, Smith AD, Allnutt TR, Thomson RL, Vuillermin PJ, Craig ME, Rawlinson WD, Davis EA, Harris M, Soldatos G, Colman PG, Wentworth JM, Haynes A, Barry SC, Sinnott RO, Morahan G, Bediaga NG, Smyth GK, Papenfuss AT, Couper JJ, Harrison LC. Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome. Microbiome 2021; 9:167. [PMID: 34362459 PMCID: PMC8349100 DOI: 10.1186/s40168-021-01104-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D. RESULTS Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage. CONCLUSIONS Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means. Video abstract.
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Affiliation(s)
- Alexandra J Roth-Schulze
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Megan A S Penno
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Katrina M Ngui
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Helena Oakey
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Esther Bandala-Sanchez
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Alannah D Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Theo R Allnutt
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Rebecca L Thomson
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Peter J Vuillermin
- Faculty of School of Medicine, Deakin University and Child Health Research Unit, Barwon Health, Geelong, VIC, 3220, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Elizabeth A Davis
- Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, WA, 6009, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
- Queensland Children's Hospital, South Brisbane, QLD, 4101, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne and Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, VIC, 3168, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - John M Wentworth
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, 3050, Australia
| | - Aveni Haynes
- Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, WA, 6009, Australia
| | - Simon C Barry
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information Services, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Naiara G Bediaga
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gordon K Smyth
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology and School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology and School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jennifer J Couper
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
- Women's and Children's Hospital, Adelaide, SA, 5006, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
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15
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Awlia M, Alshareef N, Saber N, Korte A, Oakey H, Panzarová K, Trtílek M, Negrão S, Tester M, Julkowska MM. Genetic mapping of the early responses to salt stress in Arabidopsis thaliana. Plant J 2021; 107:544-563. [PMID: 33964046 DOI: 10.1111/tpj.15310] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single set-up is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from 1 h to 7 days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (Fv' /Fm' ) greatly affected growth maintenance in the early phase of salt stress, whereas the maximum quantum yield (QYmax ) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QYmax and Fv' /Fm' were selected for validation using T-DNA insertion lines. We characterized an unknown protein kinase found in the QYmax locus that reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the candidate genes identified will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses and identifying associations across different traits and time points, which are likely to constitute the genetic components of salinity tolerance.
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Affiliation(s)
- Mariam Awlia
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Nouf Alshareef
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Noha Saber
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Helena Oakey
- Faculty of Sciences, School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | | | - Martin Trtílek
- Photon Systems Instruments (PSI), Drásov, Czech Republic
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Magdalena M Julkowska
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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16
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McEwin RA, Hebart ML, Oakey H, Pitchford WS. Within-breed selection is sufficient to improve terminal crossbred beef marbling: a review of reciprocal recurrent genomic selection. Anim Prod Sci 2021. [DOI: 10.1071/an21085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Reciprocal recurrent selection is the selection of purebreds for crossbred performance and takes advantage of additive and non-additive variance by using pedigreed progeny performance records. Developed in maize, the adoption of this approach in livestock breeding has been limited to the pork and poultry industries; genomic selection may facilitate its extension into the beef industry by replacing pedigree. The literature regarding the relative importance of additive versus non-additive variance and reciprocal recurrent genomic selection models was reviewed. The potential for using reciprocal recurrent genomic selection in a terminal Wagyu × Angus cross scenario was examined. Non-additive variance is more important for fitness traits and accounts for a small proportion of variance related to production traits such as marbling. In general, reciprocal recurrent selection was not significantly better at improving performance of crossbreds than was traditional selection within parental breeds using only additive variance in the studies examined. Simulation studies showed benefits of including dominance or breed-specific allele effects in prediction models but advantages were small as more realistic simulations were examined. On the basis of the evidence, it is likely that in a terminal two-way cross-beef scenario utilising Wagyu sires and Angus dams, where selection emphasis is on marbling, selection of purebreds on the basis of additive variance will allow substantial progress to be realised.
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17
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Facy ML, Hebart ML, Oakey H, McEwin RA, Popplewell GI, Pitchford WS. Evaluation of dominance in tropically adapted composite beef cattle. Anim Prod Sci 2021. [DOI: 10.1071/an21094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Significant opportunities have been identified in the northern Australian beef industry that can improve efficiency and profitability by using composite or crossbred cattle and genomic selection. The improved performance of composite cattle is partly due to heterosis. One of the major genetic bases of heterosis is dominance. Traditionally, dominance is ignored in genetic evaluation but could improve the accuracy of breeding values and help maintain genetic diversity.
Aims
The aim of this study is to describe the impact of including a dominance relationship matrix with different parameterisation methods and including heterozygosity fraction on estimated breeding values for 400-day weight in a composite population.
Methods
Genotype and phenotype data were obtained from 2364 tropical composite animals and were imputed to 27 648 single nucleotide polymorphisms. Genetic parameters and breeding values were estimated for 400-day weight from a linear mixed model using a genomic relationship matrix, heterozygosity fraction and three different parameterisation methods for the dominance relationship matrix, including genotypic, classical and the natural and orthogonal interaction approach. Genetic parameters and breeding values where compared over the three different parameterisation methods.
Key results
The heritability for all models when heterozygosity was not fitted ranged from 0.25 to 0.35, with the genotypic dominance model having the lowest additive heritability. Including heterozygosity fraction in the model as a fixed covariate resulted in substantial (39–49%) reductions in dominance variance across all models but a minimal change in the additive variance and, therefore, heritability (0.29–0.35).
Conclusions and Implications
In a composite population, including heterozygosity fraction in the model was important due to directional dominance. When heterozygosity fraction was not included, the genetic variance was incorrectly partitioned, and the dominance estimates were biased. Including the dominance relationship matrix improved the accuracy of breeding values. Parameterisation methods for forming the dominance relationship matrix are largely a matter of what estimates are required from the models and convenience. The additive values were largely independent of dominance parameterisation when heterozygosity was in the model.
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Abstract
Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.
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Affiliation(s)
- Nadia Al-Tamimi
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Oakey
- School of Agriculture Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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19
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Nguyen DT, Gomez LD, Harper A, Halpin C, Waugh R, Simister R, Whitehead C, Oakey H, Nguyen HT, Nguyen TV, Duong TX, McQueen-Mason SJ. Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw. Biotechnol Biofuels 2020; 13:165. [PMID: 33062051 PMCID: PMC7545568 DOI: 10.1186/s13068-020-01807-8] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. RESULTS We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. CONCLUSIONS Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.
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Affiliation(s)
- Duong T. Nguyen
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
- School of Agriculture and Environment, University of Western Australia (UWA), Crawley, WA Australia
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Andrea Harper
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
| | - Robbie Waugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
- Cell, and Molecular Genetics, The James Hutton Institute (JHI), Invergowrie Dundee, UK
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Adelaide, SA Australia
| | - Rachael Simister
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Caragh Whitehead
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Adelaide, SA Australia
| | - Huong T. Nguyen
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
| | - Tuat V. Nguyen
- Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Tu X. Duong
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
| | - Simon J. McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
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20
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Penno MAS, Oakey H, Augustine P, Taranto M, Barry SC, Colman PG, Craig ME, Davis EA, Giles LC, Harris M, Haynes A, McGorm K, Morahan G, Morbey C, Rawlinson WD, Sinnott RO, Soldatos G, Thomson RL, Vuillermin PJ, Wentworth JM, Harrison LC, Couper JJ. Changes in pancreatic exocrine function in young at-risk children followed to islet autoimmunity and type 1 diabetes in the ENDIA study. Pediatr Diabetes 2020; 21:945-949. [PMID: 32430977 DOI: 10.1111/pedi.13056] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/20/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDS We aimed to monitor pancreatic exocrine function longitudinally in relation to the development of islet autoimmunity (IA) and type 1 diabetes (T1D) in at-risk children with a first-degree relative with T1D, who were followed prospectively in the Environmental Determinants of Islet Autoimmunity (ENDIA) study. METHODS Fecal elastase-1 (FE-1) concentration was measured longitudinally in 85 ENDIA children from median age 1.0 (IQR 0.7,1.3) year. Twenty-eight of 85 children (progressors) developed persistent islet autoantibodies at median age of 1.5 (IQR 1.1,2.5) years, of whom 11 went on to develop clinical diabetes. The other 57 islet autoantibody-negative children (non-progressors) followed similarly were age and gender-matched with the progressors. An adjusted linear mixed model compared FE-1 concentrations in progressors and non-progressors. RESULTS Baseline FE-1 did not differ between progressors and non-progressors, or by HLA DR type or proband status. FE-1 decreased over time in progressors in comparison to non-progressors (Wald statistic 5.46, P = .02); in some progressors the fall in FE-1 preceded the onset of IA. CONCLUSIONS Pancreatic exocrine function decreases in the majority of young at-risk children who progress to IA and T1D.
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Affiliation(s)
- Megan A S Penno
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Priya Augustine
- Department of Diabetes and Endocrinology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Mario Taranto
- PathWest Laboratories, Fiona Stanley Hospital Network, Murdoch, Western Australia, Australia
| | - Simon C Barry
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Elizabeth A Davis
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Lynne C Giles
- Robinson Research Institute, School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.,Endocrinology Department, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Aveni Haynes
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Kelly McGorm
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Claire Morbey
- Hunter Diabetes Centre, Newcastle, New South Wales, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, Prince of Wales Hospital, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information Services, University of Melbourne, Melbourne, Victoria, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, Victoria, Australia
| | - Rebecca L Thomson
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Peter J Vuillermin
- Faculty of Health, School of Medicine, Deakin University, Geelong, Victoria, Australia.,Child Health Research Unit, Barwon Health, Geelong, Victoria, Australia
| | - John M Wentworth
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Leonard C Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Jennifer J Couper
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.,Department of Diabetes and Endocrinology, Women's and Children's Hospital, Adelaide, South Australia, Australia
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21
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Barakate A, Keir E, Oakey H, Halpin C. Stimulation of homologous recombination in plants expressing heterologous recombinases. BMC Plant Biol 2020; 20:336. [PMID: 32677892 PMCID: PMC7364528 DOI: 10.1186/s12870-020-02545-7] [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: 11/18/2019] [Accepted: 07/08/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Current excitement about the opportunities for gene editing in plants have been prompted by advances in CRISPR/Cas and TALEN technologies. CRISPR/Cas is widely used to knock-out or modify genes by inducing targeted double-strand breaks (DSBs) which are repaired predominantly by error-prone non-homologous end-joining or microhomology-mediated end joining resulting in mutations that may alter or abolish gene function. Although such mutations are random, they occur at sufficient frequency to allow useful mutations to be routinely identified by screening. By contrast, gene knock-ins to replace entire genes with alternative alleles or copies with specific characterised modifications, is not yet routinely possible. Gene replacement (or gene targeting) by homology directed repair occurs at extremely low frequency in higher plants making screening for useful events unfeasible. Homology directed repair might be increased by inhibiting non-homologous end-joining and/or stimulating homologous recombination (HR). Here we pave the way to increasing gene replacement efficiency by evaluating the effect of expression of multiple heterologous recombinases on intrachromosomal homologous recombination (ICR) in Nicotiana tabacum plants. RESULTS We expressed several bacterial and human recombinases in different combinations in a tobacco transgenic line containing a highly sensitive β-glucuronidase (GUS)-based ICR substrate. Coordinated simultaneous expression of multiple recombinases was achieved using the viral 2A translational recoding system. We found that most recombinases increased ICR dramatically in pollen, where HR will be facilitated by the programmed DSBs that occur during meiosis. DMC1 expression produced the greatest stimulation of ICR in primary transformants, with one plant showing a 1000-fold increase in ICR frequency. Evaluation of ICR in homozygous T2 plant lines revealed increases in ICR of between 2-fold and 380-fold depending on recombinase(s) expressed. By comparison, ICR was only moderately increased in vegetative tissues and constitutive expression of heterologous recombinases also reduced plant fertility. CONCLUSION Expression of heterologous recombinases can greatly increase the frequency of HR in plant reproductive tissues. Combining such recombinase expression with the use of CRISPR/Cas9 to induce DSBs could be a route to radically improving gene replacement efficiency in plants.
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Affiliation(s)
- Abdellah Barakate
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the JHI, Invergowrie, Dundee, DD2 5DA, Scotland
- Current address: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Ewan Keir
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the JHI, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the JHI, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the JHI, Invergowrie, Dundee, DD2 5DA, Scotland.
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Houston K, Qiu J, Wege S, Hrmova M, Oakey H, Qu Y, Smith P, Situmorang A, Macaulay M, Flis P, Bayer M, Roy S, Halpin C, Russell J, Schreiber M, Byrt C, Gilliham M, Salt DE, Waugh R. Barley sodium content is regulated by natural variants of the Na + transporter HvHKT1;5. Commun Biol 2020; 3:258. [PMID: 32444849 PMCID: PMC7244711 DOI: 10.1038/s42003-020-0990-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 01/15/2020] [Accepted: 04/28/2020] [Indexed: 12/04/2022] Open
Abstract
During plant growth, sodium (Na+) in the soil is transported via the xylem from the root to the shoot. While excess Na+ is toxic to most plants, non-toxic concentrations have been shown to improve crop yields under certain conditions, such as when soil K+ is low. We quantified grain Na+ across a barley genome-wide association study panel grown under non-saline conditions and identified variants of a Class 1 HIGH-AFFINITY-POTASSIUM-TRANSPORTER (HvHKT1;5)-encoding gene responsible for Na+ content variation under these conditions. A leucine to proline substitution at position 189 (L189P) in HvHKT1;5 disturbs its characteristic plasma membrane localisation and disrupts Na+ transport. Under low and moderate soil Na+, genotypes containing HvHKT1:5P189 accumulate high concentrations of Na+ but exhibit no evidence of toxicity. As the frequency of HvHKT1:5P189 increases significantly in cultivated European germplasm, we cautiously speculate that this non-functional variant may enhance yield potential in non-saline environments, possibly by offsetting limitations of low available K+.
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Affiliation(s)
- Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Jiaen Qiu
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Stefanie Wege
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Life Science, Huaiyin Normal University, 223300, Huaian, China
| | - Helena Oakey
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Yue Qu
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Pauline Smith
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Micha Bayer
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Stuart Roy
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot Dry Climate, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Caitlin Byrt
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- Research School of Biology, 46 Sullivans Creek Road, The Australian National University, Canberra, ACT, 2601, Australia
| | - Matt Gilliham
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road Invergowrie, Dundee, DD2 5DA, Scotland, UK.
- School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK.
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23
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Ward B, Brien C, Oakey H, Pearson A, Negrão S, Schilling RK, Taylor J, Jarvis D, Timmins A, Roy SJ, Tester M, Berger B, van den Hengel A. High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare). Plant J 2019; 98:555-570. [PMID: 30604470 PMCID: PMC6850118 DOI: 10.1111/tpj.14225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 08/25/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 05/11/2023]
Abstract
To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study.
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Affiliation(s)
- Ben Ward
- Australian Center for Visual TechnologiesUniversity of AdelaideAdelaideSA5005Australia
| | - Chris Brien
- Australian Plant Phenomics FacilityThe Plant AcceleratorSchool of Agriculture Food & WineUniversity of AdelaideUrrbraeSA5064Australia
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Phenomics and Bioinformatics Research CentreSchool of Information Technology and Mathematical SciencesUniversity of South AustraliaAdelaide5001Australia
| | - Helena Oakey
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
| | - Allison Pearson
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- ARC Centre of Excellence in Plant Energy BiologyThe University of AdelaidePMB 1, Glen OsmondAdelaideSouth Australia5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Rhiannon K. Schilling
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Julian Taylor
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
| | - David Jarvis
- Division of Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Andy Timmins
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Stuart J. Roy
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
- Australian Centre for Plant Functional GenomicsPMB 1, Glen OsmondAdelaideSouth Australia5064Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Bettina Berger
- Australian Plant Phenomics FacilityThe Plant AcceleratorSchool of Agriculture Food & WineUniversity of AdelaideUrrbraeSA5064Australia
- School of Agriculture Food & Wine and Waite Research InstituteUniversity of AdelaideUrrbraeSA5064Australia
| | - Anton van den Hengel
- Australian Center for Visual TechnologiesUniversity of AdelaideAdelaideSA5005Australia
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24
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Daly P, McClellan C, Maluk M, Oakey H, Lapierre C, Waugh R, Stephens J, Marshall D, Barakate A, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. Plant Biotechnol J 2019; 17:594-607. [PMID: 30133138 PMCID: PMC6381794 DOI: 10.1111/pbi.13001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 11/02/2017] [Accepted: 08/18/2018] [Indexed: 05/12/2023]
Abstract
Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by ~50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by ~50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.
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Affiliation(s)
- Paul Daly
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Present address:
Fungal PhysiologyWesterdijk Fungal Biodiversity Institute and Fungal Molecular PhysiologyUtrecht UniversityUtrechtThe Netherlands
| | - Christopher McClellan
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Marta Maluk
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Helena Oakey
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Faculty of SciencesSchool of Agriculture, Food and WineUniversity of AdelaideAdelaideAustralia
| | - Catherine Lapierre
- UMR1318 INRA‐AgroParistechIJPBUniversite Paris‐SaclayVersailles CedexFrance
| | - Robbie Waugh
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Cell and Molecular SciencesJames Hutton InstituteDundeeUK
| | | | - David Marshall
- Information and Computational SciencesJames Hutton InstituteDundeeUK
| | - Abdellah Barakate
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Yukiko Tsuji
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Geert Goeminne
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - John Ralph
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Claire Halpin
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
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25
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Abstract
Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers.
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Affiliation(s)
- Helena Oakey
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Brian Cullis
- National Institute for Applied Statistics Research Australia, University of Wollongong, NSW, 2522, Australia
| | - Robin Thompson
- Rothamsted Research, Harpenden, Hertfordshire AL5 3JQ, UK
| | - Jordi Comadran
- Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
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26
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Phillips D, Jenkins G, Macaulay M, Nibau C, Wnetrzak J, Fallding D, Colas I, Oakey H, Waugh R, Ramsay L. The effect of temperature on the male and female recombination landscape of barley. New Phytol 2015; 208:421-9. [PMID: 26255865 DOI: 10.1111/nph.13548] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [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: 03/24/2015] [Accepted: 06/01/2015] [Indexed: 05/02/2023]
Abstract
Barley (Hordeum vulgare) is a crop of global significance. However, a third of the genes of barley are largely inaccessible to conventional breeding programmes as crossovers are localised to the ends of the chromosomes. This work examines whether crossovers can be shifted to more proximal regions simply by elevating growth temperature. We utilised a genome-wide marker set for linkage analysis combined with cytological mapping of crossover events to examine the recombination landscape of plants grown at different temperatures. We found that barley shows heterochiasmy, that is, differences between female and male recombination frequencies. In addition, we found that elevated temperature significantly changes patterns of recombination in male meiosis only, with a repositioning of Class I crossovers determined by cytological mapping of HvMLH3 foci. We show that the length of synaptonemal complexes in male meiocytes increases in response to temperature. The results demonstrate that the distribution of crossover events are malleable and can be shifted to proximal regions by altering the growth temperature. The shift in recombination is the result of altering the distribution of Class I crossovers, but the higher recombination at elevated temperatures is potentially not the result of an increase in Class I events.
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Affiliation(s)
- Dylan Phillips
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth, University, Aberystwyth, SY23 3DA, UK
| | - Glyn Jenkins
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth, University, Aberystwyth, SY23 3DA, UK
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Candida Nibau
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth, University, Aberystwyth, SY23 3DA, UK
| | - Joanna Wnetrzak
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth, University, Aberystwyth, SY23 3DA, UK
| | - Derek Fallding
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth, University, Aberystwyth, SY23 3DA, UK
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Helena Oakey
- Information and Computational Sciences, The James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
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27
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Houston K, Russell J, Schreiber M, Halpin C, Oakey H, Washington JM, Booth A, Shirley N, Burton RA, Fincher GB, Waugh R. A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys. BMC Genomics 2014; 15:907. [PMID: 25326272 PMCID: PMC4213503 DOI: 10.1186/1471-2164-15-907] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/24/2014] [Indexed: 11/10/2022] Open
Abstract
Background (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed above recommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on human health. Results We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes. Conclusions We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containing CslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-907) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland.
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28
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Barakate A, Higgins JD, Vivera S, Stephens J, Perry RM, Ramsay L, Colas I, Oakey H, Waugh R, Franklin FCH, Armstrong SJ, Halpin C. The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley. Plant Cell 2014; 26:729-40. [PMID: 24563202 PMCID: PMC3967036 DOI: 10.1105/tpc.113.121269] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/17/2014] [Accepted: 02/02/2014] [Indexed: 05/18/2023]
Abstract
In many cereal crops, meiotic crossovers predominantly occur toward the ends of chromosomes and 30 to 50% of genes rarely recombine. This limits the exploitation of genetic variation by plant breeding. Previous reports demonstrate that chiasma frequency can be manipulated in plants by depletion of the synaptonemal complex protein ZIPPER1 (ZYP1) but conflict as to the direction of change, with fewer chiasmata reported in Arabidopsis thaliana and more crossovers reported for rice (Oryza sativa). Here, we use RNA interference (RNAi) to reduce the amount of ZYP1 in barley (Hordeum vulgare) to only 2 to 17% of normal zygotene levels. In the ZYP1(RNAi) lines, fewer than half of the chromosome pairs formed bivalents at metaphase and many univalents were observed, leading to chromosome nondisjunction and semisterility. The number of chiasmata per cell was reduced from 14 in control plants to three to four in the ZYP1-depleted lines, although the localization of residual chiasmata was not affected. DNA double-strand break formation appeared normal, but the recombination pathway was defective at later stages. A meiotic time course revealed a 12-h delay in prophase I progression to the first labeled tetrads. Barley ZYP1 appears to function similarly to ZIP1/ZYP1 in yeast and Arabidopsis, with an opposite effect on crossover number to ZEP1 in rice, another member of the Poaceae.
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Affiliation(s)
- Abdellah Barakate
- Division of Plant Sciences, College of Life Sciences,
University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - James D. Higgins
- School of Biosciences, University of Birmingham,
Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Sebastian Vivera
- Division of Plant Sciences, College of Life Sciences,
University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - Jennifer Stephens
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - Ruth M. Perry
- School of Biosciences, University of Birmingham,
Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Luke Ramsay
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - Isabelle Colas
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - Helena Oakey
- Division of Plant Sciences, College of Life Sciences,
University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - Robbie Waugh
- Division of Plant Sciences, College of Life Sciences,
University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
| | - F. Chris H. Franklin
- School of Biosciences, University of Birmingham,
Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Susan J. Armstrong
- School of Biosciences, University of Birmingham,
Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences,
University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA,
United Kingdom
- Address correspondence to
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29
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Oakey H, Shafiei R, Comadran J, Uzrek N, Cullis B, Gomez LD, Whitehead C, McQueen-Mason SJ, Waugh R, Halpin C. Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling. Biotechnol Biofuels 2013; 6:185. [PMID: 24359577 PMCID: PMC3878416 DOI: 10.1186/1754-6834-6-185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/06/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND In this study, a multi-parent population of barley cultivars was grown in the field for two consecutive years and then straw saccharification (sugar release by enzymes) was subsequently analysed in the laboratory to identify the cultivars with the highest consistent sugar yield. This experiment was used to assess the benefit of accounting for both the multi-phase and multi-environment aspects of large-scale phenotyping experiments with field-grown germplasm through sound statistical design and analysis. RESULTS Complementary designs at both the field and laboratory phases of the experiment ensured that non-genetic sources of variation could be separated from the genetic variation of cultivars, which was the main target of the study. The field phase included biological replication and plot randomisation. The laboratory phase employed re-randomisation and technical replication of samples within a batch, with a subset of cultivars chosen as duplicates that were randomly allocated across batches. The resulting data was analysed using a linear mixed model that incorporated field and laboratory variation and a cultivar by trial interaction, and ensured that the cultivar means were more accurately represented than if the non-genetic variation was ignored. The heritability detected was more than doubled in each year of the trial by accounting for the non-genetic variation in the analysis, clearly showing the benefit of this design and approach. CONCLUSIONS The importance of accounting for both field and laboratory variation, as well as the cultivar by trial interaction, by fitting a single statistical model (multi-environment trial, MET, model), was evidenced by the changes in list of the top 40 cultivars showing the highest sugar yields. Failure to account for this interaction resulted in only eight cultivars that were consistently in the top 40 in different years. The correspondence between the rankings of cultivars was much higher at 25 in the MET model. This approach is suited to any multi-phase and multi-environment population-based genetic experiment.
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Affiliation(s)
- Helena Oakey
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Reza Shafiei
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Nicola Uzrek
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Brian Cullis
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
- Computational Informatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2600, Australia
| | - Leonardo D Gomez
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Caragh Whitehead
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Simon J McQueen-Mason
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Robbie Waugh
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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30
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Abstract
OBJECTIVE To evaluate maternal and neonatal outcomes associated with birth at term by week of gestational age and also by onset of labor. DESIGN Cohort study. SETTING A state-wide perinatal outcome database. POPULATION 28,626 women with spontaneous onset of labor, induction of labor for recognized indications and induction of labor for non-recognized indications. METHODS Cohort study utilizing a validated dataset comparing outcomes with type of onset of labor using a log binomial model. MAIN OUTCOME MEASURES Cesarean section, assisted vaginal birth, important measures of maternal and neonatal morbidity. RESULTS Induction of labor for non-recognized indications was associated with a significantly increased risk of a range of outcomes, including cesarean section (RR 1.67, 95% CI 1.55-1.80). The lowest risk of adverse maternal and infant outcome occurred with birth between 38 and 39 weeks and with the spontaneous onset of labor. CONCLUSIONS Induction of labor for non-recognized indications at term is associated with an increased risk of adverse outcomes. Caution is warranted with a liberal policy of induction of labor at term in an otherwise uncomplicated pregnancy.
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Affiliation(s)
- Rosalie M Grivell
- Discipline of Obstetrics and Gynaecology, University of Adelaide, South Australia, Australia.
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31
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Middleton PF, Crowther CA, Doyle LW, Bubner T, Oakey H, Morris J, Askie L, Davis PG, Flenady V. S44– Rapid development and implementation of guidelines for infant neuroprotection with antenatal magnesium sulfate (MgSO4). Otolaryngol Head Neck Surg 2010. [DOI: 10.1016/j.otohns.2010.04.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | | | - Lex W. Doyle
- University of Melbourne, Parkville, Victoria, Australia
| | - Tanya Bubner
- The University of Adelaide, North Adelaide, South Australia, Australia
| | - Helena Oakey
- The University of Adelaide, North Adelaide, South Australia, Australia
| | - Jonathan Morris
- The University of Sydney, Sydney, New South Wales, Australia
| | - Lisa Askie
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Peter G. Davis
- The University of Melbourne, Parkville, Victoria, Australia
| | - Vicki Flenady
- Mater Hospital, Woolloongabba, Queensland, Australia
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32
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Abstract
OBJECTIVE Gestational diabetes mellitus (GDM) may cause obesity in the offspring. The objective was to assess the effect of treatment for mild GDM on the BMI of 4- to 5-year-old children. RESEARCH DESIGN AND METHODS Participants were 199 mothers who participated in a randomized controlled trial of the treatment of mild GDM during pregnancy and their children. Trained nurses measured the height and weight of the children at preschool visits in a state-wide surveillance program in the state of South Australia. The main outcome measure was age- and sex-specific BMI Z score based on standards of the International Obesity Task Force. RESULTS At birth, prevalence of macrosomia (birth weight >or=4,000 g) was 5.3% among the 94 children whose mothers were in the intervention group, and 21.9% among the 105 children in the routine care control group. At 4- to 5-years-old, mean (SD) BMI Z score was 0.49 (1.20) in intervention children and 0.41 (1.40) among controls. The difference between treatment groups was 0.08 (95% CI -0.29 to 0.44), an estimate minimally changed by adjustment for maternal race, parity, age, and socio-economic index (0.08 [-0.29 to 0.45]). Evaluating BMI >or=85th percentile rather than continuous BMI Z score gave similarly null results. CONCLUSIONS Although treatment of GDM substantially reduced macrosomia at birth, it did not result in a change in BMI at age 4- to 5-years-old.
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Affiliation(s)
- Matthew W Gillman
- Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.
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33
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Oakey H, Verbyla AP, Cullis BR, Wei X, Pitchford WS. Joint modeling of additive and non-additive (genetic line) effects in multi-environment trials. Theor Appl Genet 2007; 114:1319-32. [PMID: 17426958 DOI: 10.1007/s00122-007-0515-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 01/25/2007] [Indexed: 05/14/2023]
Abstract
A statistical approach for the analysis of multi-environment trials (METs) is presented, in which selection of best performing lines, best parents, and best combination of parents can be determined. The genetic effect of a line is partitioned into additive, dominance and residual non-additive effects. The dominance effects are estimated through the incorporation of the dominance relationship matrix, which is presented under varying levels of inbreeding. A computationally efficient way of fitting dominance effects is presented which partitions dominance effects into between family dominance and within family dominance line effects. The overall approach is applicable to inbred lines, hybrid lines and other general population structures where pedigree information is available.
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Affiliation(s)
- Helena Oakey
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
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34
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Oakey H, Verbyla A, Pitchford W, Cullis B, Kuchel H. Joint modeling of additive and non-additive genetic line effects in single field trials. Theor Appl Genet 2006; 113:809-19. [PMID: 16896718 DOI: 10.1007/s00122-006-0333-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 06/03/2006] [Indexed: 05/11/2023]
Abstract
A statistical approach is presented for selection of best performing lines for commercial release and best parents for future breeding programs from standard agronomic trials. The method involves the partitioning of the genetic effect of a line into additive and non-additive effects using pedigree based inter-line relationships, in a similar manner to that used in animal breeding. A difference is the ability to estimate non-additive effects. Line performance can be assessed by an overall genetic line effect with greater accuracy than when ignoring pedigree information and the additive effects are predicted breeding values. A generalized definition of heritability is developed to account for the complex models presented.
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Affiliation(s)
- Helena Oakey
- BiometricsSA, School of Agriculture and Wine, University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia.
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35
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Abstract
This study was conducted to investigate the effects of paternal heat stress on the development in vitro of preimplantation embryos in the mouse. Female C57/CBA mice were superovulated using eCG/hCG and mated either to an untreated (control) male mouse or to one that had been exposed for 24 h to an ambient temperature of 36 +/- 0.1 degrees C and 62 +/- 0.4% relative humidity, between 3 and 42 days previously. Putative zygotes were collected from the oviducts of mated mice, 25-28 h after hCG injection, and cultured in vitro. Embryo development was evaluated at 24-h intervals for up to 120 h. Paternal heat stress significantly reduced the proportion of embryos that developed normally during 24-120 h of in vitro culture, when zygotes were sired by males which had been heat stressed between 7 and 35 days prior to mating. Maximum impairment to development (including nondevelopment, abnormal and dying/dead embryos) occurred in those embryos sired by males at days 14 and 21 after heating. Embryo development returned to control levels by day 42 after heat stress. Furthermore, whilst all stages of embryo development were affected by paternal heat stress, the proportion of embryos at the two-cell stage appeared to be most severely affected. Four-cell to morula stages and the morula to blastocyst stage also demonstrated impairment at days 14, 21, 28 and 35 after heating. These results demonstrate that a single episode of paternal heat stress significantly reduces the development of preimplantation embryos, and this is not recovered until day 42 after heating. The present results also support previous work demonstrating that sperm from the epididymis as well as germ cells in the testis are susceptible to damage by heat stress, with both spermatids and spermatocytes being the most vulnerable.
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Affiliation(s)
- B Zhu
- Faculty of Veterinary Science, University of Sydney, Camden, NSW, Australia.
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36
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Carey AH, Claussen U, Lüdecke HJ, Horsthemke B, Ellis D, Oakey H, Wilson D, Burn J, Williamson R, Scambler PJ. Interstitial deletions in DiGeorge syndrome detected with microclones from 22q11. Mamm Genome 1992; 3:101-5. [PMID: 1617213 DOI: 10.1007/bf00431253] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DiGeorge syndrome in humans is characterized by immunodeficiency, heart defects, mental retardation and facial dysmorphism; cytogenetic analysis has shown that deletions at 22q11 occur in approximately 25% of cases. To generate DNA markers from this region, we have microdissected and microcloned band q11 of human Chromosome (Chr) 22. Nineteen thousand clones were obtained from material dissected from 20 chromosome fragments. Seventeen of 61 clones analyzed (28%) were repetitive, 27 (44%) gave no signal, and 17 (28%) detected single copy sequences of which ten mapped to Chr 22. Two of these were found to be deleted in patients with DiGeorge syndrome and either monosomy for 22q11-pter or visible interstitial deletions of 22q11. These two markers are also hemizygous in patients with no visible chromosomal abnormality, demonstrating that submicroscopic deletions are common in DiGeorge syndrome patients.
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Affiliation(s)
- A H Carey
- Department of Biochemistry and Molecular Genetics, St. Mary's Hospital Medical School, Imperial College London, UK
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