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Wilson IW, Moncuquet P, Yuan Y, Soliveres M, Li Z, Stiller W, Zhu QH. Genetic Mapping and Characterization of Verticillium Wilt Resistance in a Recombinant Inbred Population of Upland Cotton. Int J Mol Sci 2024; 25:2439. [PMID: 38397116 PMCID: PMC10889826 DOI: 10.3390/ijms25042439] [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: 01/30/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Verticillium wilt (VW) is an important and widespread disease of cotton and once established is long-lived and difficult to manage. In Australia, the non-defoliating pathotype of Verticillium dahliae is the most common, and extremely virulent. Breeding cotton varieties with increased VW resistance is the most economical and effective method of controlling this disease and is greatly aided by understanding the genetics of resistance. This study aimed to investigate VW resistance in 240 F7 recombinant inbred lines (RIL) derived from a cross between MCU-5, which has good resistance, and Siokra 1-4, which is susceptible. Using a controlled environment bioassay, we found that resistance based on plant survival or shoot biomass was complex but with major contributions from chromosomes D03 and D09, with genomic prediction analysis estimating a prediction accuracy of 0.73 based on survival scores compared to 0.36 for shoot biomass. Transcriptome analysis of MCU-5 and Siokra 1-4 roots uninfected or infected with V. dahliae revealed that the two cultivars displayed very different root transcriptomes and responded differently to V. dahliae infection. Ninety-nine differentially expressed genes were located in the two mapped resistance regions and so are potential candidates for further identifying the genes responsible for VW resistance.
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Affiliation(s)
- Iain W. Wilson
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | | | - Yuman Yuan
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | - Melanie Soliveres
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | - Zitong Li
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
| | - Warwick Stiller
- CSIRO Agriculture and Food, Locked Bag 59, Narrabri, NSW 2390, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia
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Conaty WC, Broughton KJ, Egan LM, Li X, Li Z, Liu S, Llewellyn DJ, MacMillan CP, Moncuquet P, Rolland V, Ross B, Sargent D, Zhu QH, Pettolino FA, Stiller WN. Cotton Breeding in Australia: Meeting the Challenges of the 21st Century. Front Plant Sci 2022; 13:904131. [PMID: 35646011 PMCID: PMC9136452 DOI: 10.3389/fpls.2022.904131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program is the sole breeding effort for cotton in Australia, developing high performing cultivars for the local industry which is worth∼AU$3 billion per annum. The program is supported by Cotton Breeding Australia, a Joint Venture between CSIRO and the program's commercial partner, Cotton Seed Distributors Ltd. (CSD). While the Australian industry is the focus, CSIRO cultivars have global impact in North America, South America, and Europe. The program is unique compared with many other public and commercial breeding programs because it focuses on diverse and integrated research with commercial outcomes. It represents the full research pipeline, supporting extensive long-term fundamental molecular research; native and genetically modified (GM) trait development; germplasm enhancement focused on yield and fiber quality improvements; integration of third-party GM traits; all culminating in the release of new commercial cultivars. This review presents evidence of past breeding successes and outlines current breeding efforts, in the areas of yield and fiber quality improvement, as well as the development of germplasm that is resistant to pests, diseases and abiotic stressors. The success of the program is based on the development of superior germplasm largely through field phenotyping, together with strong commercial partnerships with CSD and Bayer CropScience. These relationships assist in having a shared focus and ensuring commercial impact is maintained, while also providing access to markets, traits, and technology. The historical successes, current foci and future requirements of the CSIRO cotton breeding program have been used to develop a framework designed to augment our breeding system for the future. This will focus on utilizing emerging technologies from the genome to phenome, as well as a panomics approach with data management and integration to develop, test and incorporate new technologies into a breeding program. In addition to streamlining the breeding pipeline for increased genetic gain, this technology will increase the speed of trait and marker identification for use in genome editing, genomic selection and molecular assisted breeding, ultimately producing novel germplasm that will meet the coming challenges of the 21st Century.
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Affiliation(s)
| | | | - Lucy M. Egan
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
| | - Xiaoqing Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Zitong Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Shiming Liu
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
| | | | | | | | | | - Brett Ross
- Cotton Seed Distributors Ltd., Wee Waa, NSW, Australia
| | - Demi Sargent
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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Zhu QH, Stiller W, Moncuquet P, Gordon S, Yuan Y, Barnes S, Wilson I. Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant. G3 (Bethesda) 2021; 11:1-14. [PMID: 33704434 PMCID: PMC8022719 DOI: 10.1093/g3journal/jkaa042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022]
Abstract
Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0-6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.
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Affiliation(s)
- Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | | | - Philippe Moncuquet
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - Stuart Gordon
- CSIRO Agriculture and Food, Waurn Ponds, VIC 3216, Australia
| | - Yuman Yuan
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - Scott Barnes
- CSIRO Manufacturing, Waurn Ponds, VIC 3216, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
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Wilson IW, Moncuquet P, Ellis M, White RG, Zhu QH, Stiller W, Llewellyn D. Characterization and Genetic Mapping of Black Root Rot Resistance in Gossypium arboreum L. Int J Mol Sci 2021; 22:ijms22052642. [PMID: 33807984 PMCID: PMC7961528 DOI: 10.3390/ijms22052642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
Black root rot (BRR) is an economically important disease of cotton and other crops, especially in cooler regions with short growing seasons. Symptoms include black discoloration of the roots, reduced number of lateral roots and stunted or slow plant growth. The cultivated tetraploid Gossypium species are susceptible to BRR. Resistance to BRR was identified in G. arboreum accession BM13H and is associated with reduced and restricted hyphal growth and less sporulation. Transcriptome analysis indicates that BM13H responds to infection at early time points 2- and 3-days post-inoculation, but by day 5, few differentially expressed genes are observed between infected and uninfected roots. Inheritance of BM13H resistance to BRR was evaluated in an F6 recombinant inbred population and shows a single semi-dominant locus conferring resistance that was fine mapped to a region on chromosome 1, containing ten genes including five putative resistance-like genes.
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Affiliation(s)
- Iain W. Wilson
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
- Correspondence:
| | - Philippe Moncuquet
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
| | - Marc Ellis
- 133 Route de Beauregard, 74540 Gruffy, France;
| | - Rosemary G. White
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
| | - Warwick Stiller
- CSIRO Agriculture and Food, Locked Bag 59, Narrabri, NSW 2390, Australia;
| | - Danny Llewellyn
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
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Chal J, Al Tanoury Z, Oginuma M, Moncuquet P, Gobert B, Miyanari A, Tassy O, Guevara G, Hubaud A, Bera A, Sumara O, Garnier JM, Kennedy L, Knockaert M, Gayraud-Morel B, Tajbakhsh S, Pourquié O. Recapitulating early development of mouse musculoskeletal precursors of the paraxial mesoderm in vitro. Development 2018; 145:145/6/dev157339. [DOI: 10.1242/dev.157339] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 02/06/2018] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Body skeletal muscles derive from the paraxial mesoderm, which forms in the posterior region of the embryo. Using microarrays, we characterize novel mouse presomitic mesoderm (PSM) markers and show that, unlike the abrupt transcriptome reorganization of the PSM, neural tube differentiation is accompanied by progressive transcriptome changes. The early paraxial mesoderm differentiation stages can be efficiently recapitulated in vitro using mouse and human pluripotent stem cells. While Wnt activation alone can induce posterior PSM markers, acquisition of a committed PSM fate and efficient differentiation into anterior PSM Pax3+ identity further requires BMP inhibition to prevent progenitors from drifting to a lateral plate mesoderm fate. When transplanted into injured adult muscle, these precursors generated large numbers of immature muscle fibers. Furthermore, exposing these mouse PSM-like cells to a brief FGF inhibition step followed by culture in horse serum-containing medium allows efficient recapitulation of the myogenic program to generate myotubes and associated Pax7+ cells. This protocol results in improved in vitro differentiation and maturation of mouse muscle fibers over serum-free protocols and enables the study of myogenic cell fusion and satellite cell differentiation.
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Affiliation(s)
- Jérome Chal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Ziad Al Tanoury
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Masayuki Oginuma
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Philippe Moncuquet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Bénédicte Gobert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Anagenesis Biotechnologies, Parc d'innovation, Illkirch Graffenstaden 67400, France
| | - Ayako Miyanari
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Olivier Tassy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Getzabel Guevara
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Alexis Hubaud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Agata Bera
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Olga Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Leif Kennedy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Marie Knockaert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Barbara Gayraud-Morel
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Shahragim Tajbakhsh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
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Oginuma M, Moncuquet P, Xiong F, Karoly E, Chal J, Guevorkian K, Pourquié O. A Gradient of Glycolytic Activity Coordinates FGF and Wnt Signaling during Elongation of the Body Axis in Amniote Embryos. Dev Cell 2017; 40:342-353.e10. [PMID: 28245921 DOI: 10.1016/j.devcel.2017.02.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/23/2016] [Accepted: 01/31/2017] [Indexed: 12/17/2022]
Abstract
Mammalian embryos transiently exhibit aerobic glycolysis (Warburg effect), a metabolic adaptation also observed in cancer cells. The role of this particular type of metabolism during vertebrate organogenesis is currently unknown. Here, we provide evidence for spatiotemporal regulation of glycolysis in the posterior region of mouse and chicken embryos. We show that a posterior glycolytic gradient is established in response to graded transcription of glycolytic enzymes downstream of fibroblast growth factor (FGF) signaling. We demonstrate that glycolysis controls posterior elongation of the embryonic axis by regulating cell motility in the presomitic mesoderm and by controlling specification of the paraxial mesoderm fate in the tail bud. Our results suggest that glycolysis in the tail bud coordinates Wnt and FGF signaling to promote elongation of the embryonic axis.
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Affiliation(s)
- Masayuki Oginuma
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch 67400, France; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Philippe Moncuquet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch 67400, France
| | - Fengzhu Xiong
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Edward Karoly
- Metabolon, 617 Davis Drive, Suite 400, Morrisville, NC 27560, USA
| | - Jérome Chal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch 67400, France; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Karine Guevorkian
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch 67400, France; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch 67400, France; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA.
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7
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Hook SE, Kroon FJ, Metcalfe S, Greenfield PA, Moncuquet P, McGrath A, Smith R, Warne MSJ, Turner RD, McKeown A, Westcott DA. Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses. Environ Toxicol Chem 2017; 36:103-112. [PMID: 27219023 DOI: 10.1002/etc.3505] [Citation(s) in RCA: 5] [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: 08/11/2015] [Revised: 11/23/2015] [Accepted: 05/22/2016] [Indexed: 06/05/2023]
Abstract
Most catchments discharging into the Great Barrier Reef lagoon have elevated loads of suspended sediment, nutrients, and pesticides, including photosystem II inhibiting herbicides, associated with upstream agricultural land use. To investigate potential impacts of declining water quality on fish physiology, RNA sequencing (RNASeq) was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from 2 of these tropical river catchments in Queensland, Australia. The Daintree and Tully Rivers differ in upstream land uses, as well as sediment, nutrient, and pesticide loads, with the area of agricultural land use and contaminant loads lower in the Daintree. In fish collected from the Tully River, transcripts involved in fatty acid metabolism, amino acid metabolism, and citrate cycling were also more abundant, suggesting elevated circulating cortisol concentrations, whereas transcripts involved in immune responses were less abundant. Fish from the Tully also had an increased abundance of transcripts associated with xenobiotic metabolism. Previous laboratory-based studies observed similar patterns in fish and amphibians exposed to the agricultural herbicide atrazine. If these transcriptomic patterns are manifested at the whole organism level, the differences in water quality between the 2 rivers may alter fish growth and fitness. Environ Toxicol Chem 2017;36:103-112. © 2016 SETAC.
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Affiliation(s)
- Sharon E Hook
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Kirrawee, New South Wales, Australia
| | - Frederieke J Kroon
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Suzanne Metcalfe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, Queensland, Australia
| | - Paul A Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, New South Wales, Australia
| | - Philippe Moncuquet
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Australian Capital Territory, Australia
| | - Annette McGrath
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Australian Capital Territory, Australia
| | - Rachael Smith
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Michael St J Warne
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Ryan D Turner
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Adam McKeown
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Smithfield, Queensland, Australia
| | - David A Westcott
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Atherton, Queensland, Australia
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8
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Chal J, Oginuma M, Al Tanoury Z, Gobert B, Sumara O, Hick A, Bousson F, Zidouni Y, Mursch C, Moncuquet P, Tassy O, Vincent S, Miyanari A, Bera A, Garnier JM, Guevara G, Hestin M, Kennedy L, Hayashi S, Drayton B, Cherrier T, Gayraud-Morel B, Gussoni E, Relaix F, Tajbakhsh S, Pourquié O. Differentiation of pluripotent stem cells to muscle fiber to model Duchenne muscular dystrophy. Nat Biotechnol 2015; 33:962-9. [PMID: 26237517 DOI: 10.1038/nbt.3297] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/23/2015] [Indexed: 12/22/2022]
Abstract
During embryonic development, skeletal muscles arise from somites, which derive from the presomitic mesoderm (PSM). Using PSM development as a guide, we establish conditions for the differentiation of monolayer cultures of mouse embryonic stem (ES) cells into PSM-like cells without the introduction of transgenes or cell sorting. We show that primary and secondary skeletal myogenesis can be recapitulated in vitro from the PSM-like cells, providing an efficient, serum-free protocol for the generation of striated, contractile fibers from mouse and human pluripotent cells. The mouse ES cells also differentiate into Pax7(+) cells with satellite cell characteristics, including the ability to form dystrophin(+) fibers when grafted into muscles of dystrophin-deficient mdx mice, a model of Duchenne muscular dystrophy (DMD). Fibers derived from ES cells of mdx mice exhibit an abnormal branched phenotype resembling that described in vivo, thus providing an attractive model to study the origin of the pathological defects associated with DMD.
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Affiliation(s)
- Jérome Chal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - Masayuki Oginuma
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Ziad Al Tanoury
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Bénédicte Gobert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Olga Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Aurore Hick
- Anagenesis Biotechnologies, Parc d'innovation, Illkirch Graffenstaden, France
| | - Fanny Bousson
- Anagenesis Biotechnologies, Parc d'innovation, Illkirch Graffenstaden, France
| | - Yasmine Zidouni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Caroline Mursch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Philippe Moncuquet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Olivier Tassy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Stéphane Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Ayako Miyanari
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Agata Bera
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Getzabel Guevara
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - Marie Hestin
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - Leif Kennedy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | - Shinichiro Hayashi
- UPMC Paris 06, UMRS 787, INSERM, Avenir team, Pitié-Salpêtrière, Paris, France.,Institut de Myologie, Paris, France
| | - Bernadette Drayton
- UPMC Paris 06, UMRS 787, INSERM, Avenir team, Pitié-Salpêtrière, Paris, France.,Institut de Myologie, Paris, France
| | - Thomas Cherrier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France
| | | | - Emanuela Gussoni
- Division of Genetics and Genomics Boston Children's Hospital, Boston, Massachusetts, USA
| | - Frédéric Relaix
- UPMC Paris 06, UMRS 787, INSERM, Avenir team, Pitié-Salpêtrière, Paris, France.,Institut de Myologie, Paris, France
| | | | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden, France.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Kansas City, Missouri, USA
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9
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Cesari S, Bernoux M, Moncuquet P, Kroj T, Dodds PN. A novel conserved mechanism for plant NLR protein pairs: the "integrated decoy" hypothesis. Front Plant Sci 2014; 5:606. [PMID: 25506347 DOI: 10.3389/fpls.2014.00606/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/17/2014] [Indexed: 05/26/2023]
Abstract
Plant immunity is often triggered by the specific recognition of pathogen effectors by intracellular nucleotide-binding, leucine-rich repeat receptors (NLR). Plant NLRs contain an N-terminal signaling domain that is mostly represented by either a Toll-interleukin1 receptor (TIR) domain or a coiled coil (CC) domain. In many cases, single NLR proteins are sufficient for both effector recognition and signaling activation. However, many paired NLRs have now been identified where both proteins are required to confer resistance to pathogens. Recent detailed studies on the Arabidopsis thaliana TIR-NLR pair RRS1 and RPS4 and on the rice CC-NLR pair RGA4 and RGA5 have revealed for the first time how such protein pairs function together. In both cases, the paired partners interact physically to form a hetero-complex receptor in which each partner plays distinct roles in effector recognition or signaling activation, highlighting a conserved mode of action of NLR pairs across both monocotyledonous and dicotyledonous plants. We also describe an "integrated decoy" model for the function of these receptor complexes. In this model, a plant protein targeted by an effector has been duplicated and fused to one member of the NLR pair, where it acts as a bait to trigger defense signaling by the second NLR upon effector binding. This mechanism may be common to many other plant NLR pairs.
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Affiliation(s)
- Stella Cesari
- Institut National de la Recherche Agronomique, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen Interactions Montpellier, France ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen Interactions Montpellier, France ; Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia
| | - Maud Bernoux
- Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia
| | - Philippe Moncuquet
- Commonwealth Scientific and Industrial Research Organisation, Digital Productivity and Service Canberra, ACT, Australia
| | - Thomas Kroj
- Institut National de la Recherche Agronomique, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen Interactions Montpellier, France ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen Interactions Montpellier, France
| | - Peter N Dodds
- Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia
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10
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Hook SE, Johnston EL, Nair S, Roach AC, Moncuquet P, Twine NA, Raftos DA. Next generation sequence analysis of the transcriptome of Sydney rock oysters (Saccostrea glomerata) exposed to a range of environmental stressors. Mar Genomics 2014; 18 Pt B:109-11. [PMID: 25151890 DOI: 10.1016/j.margen.2014.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 11/15/2022]
Abstract
Sydney rock oysters (Saccostrea glomerata) were exposed to environmental stressors at contaminated field sites or in a controlled laboratory setting. RNA seq transcriptome data were generated for the gill and digestive gland using Roche's 454 pyrosequencing technology. 28,685 contigs were de novo assembled which encoded 11,671 different protein products. The data will act as a reference for future studies in ecology, immunology and environmental toxicology.
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Affiliation(s)
- Sharon E Hook
- CSIRO Centre for Environmental Contaminants Research, Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia.
| | - Emma L Johnston
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Sham Nair
- Department of Biological Sciences, Macquarie University, Sydney, 2109 NSW, Australia
| | - Anthony C Roach
- NSW Dept of Environment, Climate Change & Water (DECCW), Australia
| | | | - Natalie A Twine
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - David A Raftos
- Department of Biological Sciences, Macquarie University, Sydney, 2109 NSW, Australia
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11
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Hook SE, Twine NA, Simpson SL, Spadaro DA, Moncuquet P, Wilkins MR. 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes. Aquat Toxicol 2014; 153:73-88. [PMID: 24434169 DOI: 10.1016/j.aquatox.2013.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 05/20/2023]
Abstract
Next generation sequencing using Roche's 454 pyrosequencing platform can be used to generate genomic information for non-model organisms, although there are bioinformatic challenges associated with these studies. These challenges are compounded by a lack of a standardized protocol to either assemble data or to evaluate the quality of a de novo transcriptome. This study presents an assembly of the control and toxicant responsive transcriptome of Melita plumulosa, an Australian amphipod commonly used in ecotoxicological studies. RNA was harvested from control amphipods, juvenile amphipods, and from amphipods exposed to either metal or diesel contaminated sediments. This RNA was used as the basis for a 454 based transcriptome sequencing effort. Sequencing generated 1.3 million reads from control, juvenile, metal-exposed and diesel-exposed amphipods. Different read filtering and assembly protocols were evaluated to generate an assembly that (i) had an optimal number of contigs; (ii) had long contigs; (iii) contained a suitable representation of conserved genes; and (iv) had long ortholog alignment lengths relative to the length of each contig. A final assembly, generated using fixed-length trimming based on the sequence quality scores, followed by assembly using the MIRA algorithm, produced the best results. The 26,625 contigs generated via this approach were annotated using Blast2GO, and the differential expression between treatments and control was determined by mapping with BWA followed by DESeq. Although the mapping generated low coverage, many differentially expressed contigs, including some with known developmental or toxicological function, were identified. This study demonstrated that 454 pyrosequencing is an effective means of generating reference transcriptome information for organisms, such as the amphipod M. plumulosa, that have no genomic information available in databases or in closely related sequenced species. It also demonstrated how optimization of read filtering protocols and assembly approaches changes the utility of results obtained from next generation sequencing studies, and establishes criteria to determine the quality of a de novo assembly in species lacking a reference genome. This new transcriptomic knowledge provides the genomic foundation for the creation of microarray and qPCR assays, serving as a reference transcriptome in future RNAseq studies, and allowing both the biology and ecotoxicology of this organism to be better understood. This approach will allow genomics-based methodology to be applied to a wider range of environmentally relevant species.
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Affiliation(s)
- Sharon E Hook
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia.
| | - Natalie A Twine
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Stuart L Simpson
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia
| | - David A Spadaro
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia
| | - Philippe Moncuquet
- CSIRO Mathematics, Informatics, and Statistics, Acton, ACT, 2601, Australia
| | - Marc R Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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12
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Hook SE, Osborn HL, Gissi F, Moncuquet P, Twine NA, Wilkins MR, Adams MS. RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium. Mar Genomics 2014; 16:45-53. [DOI: 10.1016/j.margen.2013.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/29/2013] [Accepted: 12/18/2013] [Indexed: 01/17/2023]
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13
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Cesari S, Bernoux M, Moncuquet P, Kroj T, Dodds PN. A novel conserved mechanism for plant NLR protein pairs: the "integrated decoy" hypothesis. Front Plant Sci 2014; 5:606. [PMID: 25506347 PMCID: PMC4246468 DOI: 10.3389/fpls.2014.00606] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/17/2014] [Indexed: 05/18/2023]
Abstract
Plant immunity is often triggered by the specific recognition of pathogen effectors by intracellular nucleotide-binding, leucine-rich repeat receptors (NLR). Plant NLRs contain an N-terminal signaling domain that is mostly represented by either a Toll-interleukin1 receptor (TIR) domain or a coiled coil (CC) domain. In many cases, single NLR proteins are sufficient for both effector recognition and signaling activation. However, many paired NLRs have now been identified where both proteins are required to confer resistance to pathogens. Recent detailed studies on the Arabidopsis thaliana TIR-NLR pair RRS1 and RPS4 and on the rice CC-NLR pair RGA4 and RGA5 have revealed for the first time how such protein pairs function together. In both cases, the paired partners interact physically to form a hetero-complex receptor in which each partner plays distinct roles in effector recognition or signaling activation, highlighting a conserved mode of action of NLR pairs across both monocotyledonous and dicotyledonous plants. We also describe an "integrated decoy" model for the function of these receptor complexes. In this model, a plant protein targeted by an effector has been duplicated and fused to one member of the NLR pair, where it acts as a bait to trigger defense signaling by the second NLR upon effector binding. This mechanism may be common to many other plant NLR pairs.
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Affiliation(s)
- Stella Cesari
- Institut National de la Recherche Agronomique, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen InteractionsMontpellier, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen InteractionsMontpellier, France
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Maud Bernoux
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Philippe Moncuquet
- Commonwealth Scientific and Industrial Research Organisation, Digital Productivity and ServiceCanberra, ACT, Australia
| | - Thomas Kroj
- Institut National de la Recherche Agronomique, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen InteractionsMontpellier, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen InteractionsMontpellier, France
- *Correspondence: Thomas Kroj, Institut National de la Recherche Agronomique, Unité Mixtes de Recherche Biology and Genetics of Plant-Pathogen Interactions, TA A-54/K, Campus International de Baillarguet, 34398 Montpellier, France e-mail:
| | - Peter N. Dodds
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
- Peter N. Dodds, CSIRO Agriculture, Clunies Ross Street, GPO Box 1600, Canberra, ACT 2601, Australia e-mail:
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