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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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Tan J, Walford SA, Dennis ES, Llewellyn DJ. Erratum To: Trichomes at the Base of the Petal are Regulated by the Same Transcription Factors as Cotton Seed Fibers. Plant Cell Physiol 2022; 63:441. [PMID: 35077537 DOI: 10.1093/pcp/pcab138] [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] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Jiafu Tan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- University of Technology Sydney, Ultimo, NSW 2007, Australia
| | | | - Elizabeth S Dennis
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- University of Technology Sydney, Ultimo, NSW 2007, Australia
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3
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Liu S, Koebernick JC, Walford SA, Constable GA, Stiller WN, Llewellyn DJ. Correction to: Improved lint yield under field conditions in cotton over-expressing transcription factors regulating fibre initiation. Transgenic Res 2020; 29:551. [PMID: 33052558 DOI: 10.1007/s11248-020-00216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Due to an unfortunate misunderstanding, an extra middle initial erroneously appeared in the original publication and the full name of the first author should read Shi Ming Liu.
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Affiliation(s)
- Shiming Liu
- CSIRO Agriculture and Food, Narrabri, NSW, 2390, Australia.
| | - Jenny C Koebernick
- Auburn University, 202 Funchess Hall, 350 S. College St, Auburn, Al, 36849, USA
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4
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Shen E, Chen T, Zhu X, Fan L, Sun J, Llewellyn DJ, Wilson I, Zhu QH. Expansion of MIR482/2118 by a class-II transposable element in cotton. Plant J 2020; 103:2084-2099. [PMID: 32578284 DOI: 10.1111/tpj.14885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class-II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The 'GosTE' involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.
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Affiliation(s)
- Enhui Shen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xintian Zhu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Danny J Llewellyn
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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5
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Tan J, Walford SA, Dennis ES, Llewellyn DJ. Trichomes at the Base of the Petal Are Regulated by the Same Transcription Factors as Cotton Seed Fibers. Plant Cell Physiol 2020; 61:1590-1599. [PMID: 32579215 DOI: 10.1093/pcp/pcaa082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Many polypetalous plants have a constriction at the base of the petal that leaves a small gap that can provide entry into the young flower bud before the reproductive organs are fully developed. In cotton (Gossypium hirsutum L.), this gap is occluded by tufts of short unicellular trichomes superficially resembling the fibers found on cotton seeds. We are just beginning to understand the developmental regulation of the seed fibers and have previously characterized several MIXTA-like MYB transcription factors (TFs) that are critical for correct seed fiber development but know little about the molecular regulation of other types of cotton trichomes. Here, using RNAi or dominant suppression transgenic cotton lines and natural fiber mutants, we investigated the development and regulation of the petal base trichomes. Petal base trichomes and seed trichomes were also examined across several different species within and outside of the Malvoideae. We found that the petal base trichomes are regulated by the same MYB TFs as cotton seed fibers and, since they are more widely distributed across different taxa than the seed fibers, could have preceded them in the evolution of these important textile fibers produced by some cotton species.
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Affiliation(s)
- Jiafu Tan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- University of Technology Sydney, Ultimo, NSW 2007, Australia
| | | | - Elizabeth S Dennis
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- University of Technology Sydney, Ultimo, NSW 2007, Australia
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Sanchez X, Torregrossa M, Woodman T, Jones G, Llewellyn DJ. Identification of Parameters That Predict Sport Climbing Performance. Front Psychol 2019; 10:1294. [PMID: 31214092 PMCID: PMC6554989 DOI: 10.3389/fpsyg.2019.01294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 05/16/2019] [Indexed: 12/03/2022] Open
Abstract
In recent years, extreme sport-related pursuits including climbing have emerged not only as recreational activities but as competitive sports. Today, sport climbing is a rapidly developing, competitive sport included in the 2020 Olympic Games official program. Given recent developments, the understanding of which factors may influence actual climbing performance becomes critical. The present study aimed at identifying key performance parameters as perceived by experts in predicting actual lead sport climbing performance. Ten male (Mage = 28, SD = 6.6 years) expert climbers (7a+ to 8b on-sight French Rating Scale of Difficulty), who were also registered as climbing coaches, participated in semi-structured interviews. Participants’ responses were subjected to inductive-deductive content analysis. Several performance parameters were identified: passing cruxes, strength and conditioning aspects, interaction with the environment, possessing a good climbing movement repertoire, risk management, route management, mental balance, peer communication, and route preview. Route previewing emerged as critical when it comes to preparing and planning ascents, both cognitively and physically. That is, when optimizing decision making in relation to progressing on the route (ascent strategy forecasting) and when enhancing strategic management in relation to the effort exerted on the route (ascent effort forecasting). Participants described how such planning for the ascent allows them to: select an accurate and comprehensive movement repertoire relative to the specific demands of the route and reject ineffective movements; optimize effective movements; and link different movements upward. As the sport of climbing continues to develop, our findings provide a basis for further research that shall examine further how, each of these performance parameters identified, can most effectively be enhanced and optimized to influence performance positively. In addition, the present study provides a comprehensive view of parameters to consider when planning, designing and delivering holistic and coherent training programs aimed at enhancing climbing performance.
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Affiliation(s)
- Xavier Sanchez
- Department of Health and Sport, Halmstad University, Halmstad, Sweden
| | - M Torregrossa
- Department of Psychology, Autonomous University of Barcelona, Barcelona, Spain
| | - T Woodman
- School of Sport, Health and Exercise Sciences, Bangor University, Bangor, United Kingdom
| | - G Jones
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, United Kingdom
| | - D J Llewellyn
- Medial School, University of Exeter, Exeter, United Kingdom
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7
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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8
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Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q, Llewellyn DJ, Zhang X. GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring. Plant Biotechnol J 2016; 14:951-63. [PMID: 26269378 DOI: 10.1111/pbi.12450] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 05/18/2023]
Abstract
Cotton provides us the most important natural fibre. High fibre quality is the major goal of cotton breeding, and introducing genes conferring longer, finer and stronger fibre from Gossypium barbadense to Gossypium hirsutum is an important breeding strategy. We previously analysed the G. barbadense fibre development mechanism by gene expression profiling and found two homoeologous fibre-specific α-expansins from G. barbadense, GbEXPA2 and GbEXPATR. GbEXPA2 (from the DT genome) is a classical α-expansin, while its homoeolog, GbEXPATR (AT genome), encodes a truncated protein lacking the normal C-terminal polysaccharide-binding domain of other α-expansins and is specifically expressed in G. barbadense. Silencing EXPA in G. hirsutum induced shorter fibres with thicker cell walls. GbEXPA2 overexpression in G. hirsutum had no effect on mature fibre length, but produced fibres with a slightly thicker wall and increased crystalline cellulose content. Interestingly, GbEXPATR overexpression resulted in longer, finer and stronger fibres coupled with significantly thinner cell walls. The longer and thinner fibre was associated with lower expression of a number of secondary wall-associated genes, especially chitinase-like genes, and walls with lower cellulose levels but higher noncellulosic polysaccharides which advocated that a delay in the transition to secondary wall synthesis might be responsible for better fibre. In conclusion, we propose that α-expansins play a critical role in fibre development by loosening the cell wall; furthermore, a truncated form, GbEXPATR, has a more dramatic effect through reorganizing secondary wall synthesis and metabolism and should be a candidate gene for developing G. hirsutum cultivars with superior fibre quality.
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Affiliation(s)
- Yang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Filomena A Pettolino
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Shengmei Ji
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Juan Hao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fenglin Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiafu Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Danny J Llewellyn
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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9
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Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann RSN, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia SLR, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp RGJ, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen AJM, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH. GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Mol Psychiatry 2016; 21:189-197. [PMID: 25869804 PMCID: PMC4722802 DOI: 10.1038/mp.2015.37] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [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: 12/18/2013] [Revised: 01/21/2015] [Accepted: 02/11/2015] [Indexed: 01/20/2023]
Abstract
To identify common variants contributing to normal variation in two specific domains of cognitive functioning, we conducted a genome-wide association study (GWAS) of executive functioning and information processing speed in non-demented older adults from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) consortium. Neuropsychological testing was available for 5429-32,070 subjects of European ancestry aged 45 years or older, free of dementia and clinical stroke at the time of cognitive testing from 20 cohorts in the discovery phase. We analyzed performance on the Trail Making Test parts A and B, the Letter Digit Substitution Test (LDST), the Digit Symbol Substitution Task (DSST), semantic and phonemic fluency tests, and the Stroop Color and Word Test. Replication was sought in 1311-21860 subjects from 20 independent cohorts. A significant association was observed in the discovery cohorts for the single-nucleotide polymorphism (SNP) rs17518584 (discovery P-value=3.12 × 10(-8)) and in the joint discovery and replication meta-analysis (P-value=3.28 × 10(-9) after adjustment for age, gender and education) in an intron of the gene cell adhesion molecule 2 (CADM2) for performance on the LDST/DSST. Rs17518584 is located about 170 kb upstream of the transcription start site of the major transcript for the CADM2 gene, but is within an intron of a variant transcript that includes an alternative first exon. The variant is associated with expression of CADM2 in the cingulate cortex (P-value=4 × 10(-4)). The protein encoded by CADM2 is involved in glutamate signaling (P-value=7.22 × 10(-15)), gamma-aminobutyric acid (GABA) transport (P-value=1.36 × 10(-11)) and neuron cell-cell adhesion (P-value=1.48 × 10(-13)). Our findings suggest that genetic variation in the CADM2 gene is associated with individual differences in information processing speed.
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Affiliation(s)
- CA Ibrahim-Verbaas
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands,Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - J Bressler
- Human Genetics Center, School of Public Health, University of
Texas Health Science Center at Houston, Houston, TX, USA,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - S Debette
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,Institut National de la Santé et de la Recherche
Médicale (INSERM), U897, Epidemiology and Biostatistics, University of Bordeaux,
Bordeaux, France,Department of Neurology, Bordeaux University Hospital, Bordeaux,
France,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - M Schuur
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands,Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - AV Smith
- Icelandic Heart Association, Kopavogur, Iceland,Faculty of Medicine, University of Iceland, Reykjavik,
Iceland,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - JC Bis
- Cardiovascular Health Research Unit, Department of Medicine,
University of Washington, Seattle, WA, USA,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - S Trompet
- Department of Cardiology, Leiden University Medical Center,
Leiden, The Netherlands,Department of Gerontology and Geriatrics, Leiden University
Medical Center, Leiden, The Netherlands
| | - JA Smith
- Department of Epidemiology, University of Michigan, Ann Arbor,
MI, USA
| | - C Wolf
- RG Statistical Genetics, Max Planck Institute of Psychiatry,
Munich, Germany
| | - LB Chibnik
- Program in Translational Neuropsychiatric Genomics, Department
of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Y Liu
- Department of Epidemiology, Wake Forest School of Medicine,
Winston-Salem, NC, USA
| | - V Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular
Medicine, University of Edinburgh, Edinburgh, UK
| | - M Kirin
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - K Petrovic
- Department of Neurology, Medical University and General
Hospital of Graz, Graz, Austria
| | - O Polasek
- Department of Public Health, University of Split, Split,
Croatia
| | - L Zgaga
- Department of Public Health and Primary Care, Trinity College
Dublin, Dublin, Ireland
| | - C Fawns-Ritchie
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK
| | - P Hoffmann
- Institute of Neuroscience and Medicine (INM -1), Research
Center Juelich, Juelich, Germany,Division of Medical Genetics, Department of Biomedicine,
University of Basel, Basel, Switzerland,Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - J Karjalainen
- Department of Genetics, University Medical Centre Groningen,
University of Groningen, Groningen, The Netherlands
| | - J Lahti
- Institute of Behavioural Sciences, University of Helsinki,
Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland
| | - DJ Llewellyn
- Institute of Biomedical and Clinical Sciences, University of
Exeter Medical School, Exeter, UK
| | - CO Schmidt
- Institute for Community Medicine, University Medicine
Greifswald, Greifswald, Germany
| | - KA Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia
| | - V Chouraki
- Inserm, U1167, Institut Pasteur de Lille, Université
Lille-Nord de France, Lille, France
| | - Q Sun
- Channing Division of Network Medicine, Department of Medicine,
Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - SM Resnick
- Laboratory of Behavioral Neuroscience, National Institute on
Aging, NIH, Baltimore, MD, USA
| | - LM Rose
- Division of Preventive Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - C Oldmeadow
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - M Stewart
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - BH Smith
- Medical Research Institute, University of Dundee, Dundee,
UK
| | - V Gudnason
- Icelandic Heart Association, Kopavogur, Iceland,Faculty of Medicine, University of Iceland, Reykjavik,
Iceland
| | - Q Yang
- The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - SS Mirza
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands
| | - JW Jukema
- Department of Cardiology, Leiden University Medical Center,
Leiden, The Netherlands
| | - PL deJager
- Program in Translational Neuropsychiatric Genomics, Department
of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - TB Harris
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, MD, USA
| | - DC Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh,
UK
| | - N Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands
| | - LH Coker
- Division of Public Health Sciences and Neurology, Wake Forest
School of Medicine, Winston-Salem, NC, USA
| | - O Stegle
- Max Planck Institute for Developmental Biology, Max Planck
Institute for Intelligent Systems, Tübingen, Germany
| | - OL Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh,
PA, USA
| | - R Schmidt
- Department of Neurology, Medical University and General
Hospital of Graz, Graz, Austria
| | - A Teumer
- Interfaculty Institute for Genetics and Functional Genomics,
University Medicine Greifswald, Greifswald, Germany
| | - I Ford
- Robertson Center for biostatistics, University of Glasgow,
Glasgow, UK
| | - N Karbalai
- RG Statistical Genetics, Max Planck Institute of Psychiatry,
Munich, Germany
| | - JT Becker
- Department of Neurology, University of Pittsburgh, Pittsburgh,
PA, USA,Department of Psychiatry, University of Pittsburgh, Pittsburgh,
PA, USA,Department of Psychology, University of Pittsburgh, Pittsburgh,
PA, USA
| | | | - R Au
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA
| | - RSN Fehrmann
- Department of Genetics, University Medical Centre Groningen,
University of Groningen, Groningen, The Netherlands
| | - S Herms
- Division of Medical Genetics, Department of Biomedicine,
University of Basel, Basel, Switzerland,Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - M Nalls
- Laboratory of Neurogenetics, National Institute on Aging,
Bethesda, MD, USA
| | - W Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor,
MI, USA
| | - ST Turner
- Division of Nephrology and Hypertension, Department of Internal
Medicine, Mayo Clinic, Rochester, MN, USA
| | - K Yaffe
- Departments of Psychiatry, Neurology and Epidemiology,
University of California, San Francisco and San Francisco VA Medical Center, San Francisco,
CA, USA
| | - K Lohman
- Department of Epidemiology, Wake Forest School of Medicine,
Winston-Salem, NC, USA
| | - JC van Swieten
- Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - SLR Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor,
MI, USA
| | - DS Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - WM Meeks
- Department of Medicine, Division of Geriatrics, University of
Mississippi Medical Center, Jackson, MS, USA
| | - G Heiss
- Department of Epidemiology, Gillings School of Global Public
Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - EG Holliday
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - PW Schofield
- School of Medicine and Public Health, Faculty of Health,
University of Newcastle, Newcastle, SW, Australia
| | - T Tanaka
- Translational Gerontology Branch, National Institute on Aging,
Baltimore, MD, USA
| | - DJ Stott
- Department of Cardiovascular and Medical Sciences, University
of Glasgow, Glasgow, UK
| | - J Wang
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - P Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - AJ Gow
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh,
UK
| | - A Pattie
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK
| | - JM Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Alzheimer Scotland Research Centre, Edinburgh, UK
| | - LJ Hocking
- Division of Applied Medicine, University of Aberdeen, Aberdeen,
UK
| | - NJ Armstrong
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia,Cancer Research Program, Garvan Institute of Medical Research,
Sydney, NSW, Australia,School of Mathematics & Statistics and Prince of Wales
Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - S McLachlan
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - JM Shulman
- Department of Neurology, Baylor College of Medicine, Houston,
TX, USA,Department of Molecular and Human Genetics, The Jan and Dan
Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - LC Pilling
- Epidemiology and Public Health Group, University of Exeter
Medical School, Exeter, UK
| | | | - RJ Scott
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - NA Kochan
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia,Neuropsychiatric Institute, The Prince of Wales Hospital,
Sydney, NSW, Australia
| | - A Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, UK,Institute for Molecular Medicine Finland (FIMM), University of
Helsinki, Helsinki, Finland,Department of Medical Genetics, University of Helsinki and
University Central Hospital, Helsinki, Finland
| | - Y-C Hsieh
- School of Public Health, Taipei Medical University, Taipei,
Taiwan
| | - JG Eriksson
- Folkhälsan Research Centre, Helsinki, Finland,Department of General Practice and Primary Health Care,
University of Helsinki, Helsinki, Finland,National Institute for Health and Welfare, Helsinki,
Finland,Helsinki University Central Hospital, Unit of General Practice,
Helsinki, Finland,Vasa Central Hospital, Vasa, Finland
| | - A Penman
- Center of Biostatistics and Bioinformatics, University of
Mississippi Medical Center, Jackson, MS, USA
| | - RF Gottesman
- Department of Neurology, Johns Hopkins University School of
Medicine, Baltimore, MD, USA
| | - BA Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands
| | - L Yu
- Rush Alzheimer's Disease Center, Rush University Medical
Center, Chicago, IL, USA
| | - AL DeStefano
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - A Beiser
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - M Garcia
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, MD, USA
| | - JI Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los
Angeles, CA, USA,Institute for Translational Genomics and Population Sciences,
Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA,
USA,Division of Genetic Outcomes, Department of Pediatrics,
Harbor-UCLA Medical Center, Torrance, CA, USA
| | - MM Nöthen
- Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany,German Center for Neurodegenerative Diseases (DZNE), Bonn,
Germany
| | - A Hofman
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands
| | - PE Slagboom
- Department of Molecular Epidemiology, Leiden University Medical
Center, Leiden, The Netherlands
| | - RGJ Westendorp
- Leiden Academy of Vitality and Ageing, Leiden, The
Netherlands
| | - BM Buckley
- Department of Pharmacology and Therapeutics, University College
Cork, Cork, Ireland
| | - PA Wolf
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA
| | - AG Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands,Department of Internal Medicine, Erasmus University Medical
Center, Rotterdam, The Netherlands
| | - BM Psaty
- Cardiovascular Health Research Unit, Department of Medicine,
University of Washington, Seattle, WA, USA,Department of Epidemiology, University of Washington, Seattle,
WA, USA,Department of Health Services, University of Washington,
Seattle, WA, USA,Group Health Research Institute, Group Health, Seattle, WA,
USA
| | - HJ Grabe
- Department of Psychiatry and Psychotherapy, University Medicine
Greifswald, HELIOS-Hospital Stralsund, Stralsund, Germany
| | - S Bandinelli
- Geriatric Unit, Azienda Sanitaria Firenze (ASF), Florence,
Italy
| | - DI Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - F Grodstein
- Channing Division of Network Medicine, Department of Medicine,
Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - K Räikkönen
- Institute of Behavioural Sciences, University of Helsinki,
Helsinki, Finland
| | - J-C Lambert
- Inserm, U1167, Institut Pasteur de Lille, Université
Lille-Nord de France, Lille, France
| | - DJ Porteous
- Centre for Genomic and Experimental Medicine, Institute of
Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - JF Price
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - PS Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW
Medicine, University of New South Wales, Sydney, Australia,Neuropsychiatric Institute, The Prince of Wales Hospital,
Sydney, NSW, Australia
| | - L Ferrucci
- Translational Gerontology Branch, National Institute on Aging,
Baltimore, MD, USA
| | - JR Attia
- Hunter Medical Research Institute and Faculty of Health,
University of Newcastle, Newcastle, NSW, Australia
| | - I Rudan
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - C Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular
Medicine, University of Edinburgh, Edinburgh, UK
| | - AF Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular
Medicine, University of Edinburgh, Edinburgh, UK
| | - JF Wilson
- Centre for Population Health Sciences, University of Edinburgh,
Edinburgh, UK
| | - S Cichon
- Division of Medical Genetics, Department of Biomedicine,
University of Basel, Basel, Switzerland,Department of Genomics, Life and Brain Research Center,
Institute of Human Genetics, University of Bonn, Bonn, Germany,Institute of Neuroscience and Medicine (INM-1), Research Center
Juelich, Juelich, Germany
| | - L Franke
- Department of Genetics, University Medical Centre Groningen,
University of Groningen, Groningen, The Netherlands
| | - H Schmidt
- Department of Neurology, Medical University and General
Hospital of Graz, Graz, Austria
| | - J Ding
- Department of Internal Medicine, Wake Forest University School
of Medicine, Winston-Salem, NC, USA
| | - AJM de Craen
- Department of Gerontology and Geriatrics, Leiden University
Medical Center, Leiden, The Netherlands
| | - M Fornage
- Institute for Molecular Medicine and Human Genetics Center,
University of Texas Health Science Center at Houston, Houston, TX, USA
| | - DA Bennett
- Rush Alzheimer's Disease Center, Rush University Medical
Center, Chicago, IL, USA
| | - IJ Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, The
University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh,
UK
| | - MA Ikram
- Department of Neurology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands,Department of Radiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - LJ Launer
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, MD, USA
| | - AL Fitzpatrick
- Department of Epidemiology, University of Washington, Seattle,
WA, USA
| | - S Seshadri
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA,The National Heart Lung and Blood Institute's Framingham Heart
Study, Framingham, MA, USA
| | - CM van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus
University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The
Netherlands
| | - TH Mosley
- Department of Medicine and Neurology, University of Mississippi
Medical Center, Jackson, MS, USA
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10
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Liu S, Lacape JM, Constable GA, Llewellyn DJ. Inheritance and QTL Mapping of Leaf Nutrient Concentration in a Cotton Inter-Specific Derived RIL Population. PLoS One 2015; 10:e0128100. [PMID: 26020945 PMCID: PMC4447399 DOI: 10.1371/journal.pone.0128100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/23/2015] [Indexed: 11/19/2022] Open
Abstract
Developing and deploying cotton cultivars with high nutrient uptake, use efficiency and tolerance to nutrient related soil stresses is desirable to assist sustainable soil management. Genetic variation, heritability, selection response and quantitative trait loci (QTLs) were investigated for five macronutrients (P, K, Ca, Mg, S) and five micronutrients (Fe, Mn, B, Zn, and Cu) in a recombinant inbred line (RIL) population from an inter-specific cross between Gossypium hirsutum cv. Guazuncho 2, and G. barbadense accession VH8-4602. Na and K/Na ratio were also studied as the imbalance between Na and other nutrients is detrimental to cotton growth and development. The concentrations of nutrients were measured for different plant parts of the two parents and for leaf samples of the whole population collected at early to peak flowering in field experiments over two years in a sodic Vertosol soil. Parental contrast was large for most nutrient concentrations in leaves when compared with other plant parts. Segregation for leaf nutrient concentration was observed within the population with transgression for P, K, K/Na ratio and all micronutrients. Genotypic difference was the major factor behind within-population variation for most nutrients, while narrow sense heritability was moderate (0.27 for Mn and Cu, and 0.43 for B). At least one significant QTL was identified for each nutrient except K and more than half of those QTLs were clustered on chromosomes 14, 18 and 22. Selection response was predicted to be low for P and all micronutrients except B, high for K, Na and B, and very high for K/Na ratio. Correlations were more common between macronutrients, Na and K/Na ratio where the nature and strength of the relations varied (r=-0.69 to 0.76). We conclude that there is sufficient genetic diversity between these two tetraploid cotton species that could be exploited to improve cotton nutrient status by introgressing species-unique favourable alleles.
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Affiliation(s)
- Shiming Liu
- CSIRO Agriculture Flagship, Narrabri, NSW 2390, Australia
- * E-mail:
| | | | | | - Danny J. Llewellyn
- CSIRO Agriculture Flagship, P.O. Box 1600, Canberra, ACT 2601, Australia
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11
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Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda) 2015; 5:1187-209. [PMID: 25908569 PMCID: PMC4478548 DOI: 10.1534/g3.115.018416] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [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] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/11/2015] [Indexed: 11/18/2022]
Abstract
High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - Jana Lemm
- TraitGenetics GmbH, 06466 Gatersleben, Germany
| | | | - Hamid Ashrafi
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Ramesh Buyyarapu
- Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268
| | - David D Fang
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - James Frelichowski
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Lori L Hinze
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Penny K Riggs
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Jodi A Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776
| | - Joshua A Udall
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Shirley S Wang
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Qian-Hao Zhu
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Sumit K Bag
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Robert L Byers
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | | | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - David B Harker
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Md S Islam
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762
| | - Don C Jones
- Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513
| | | | - Danny J Llewellyn
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Richard G Percy
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Alan E Pepper
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Krishan Mohan Rai
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Samir V Sawant
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Sunil Kumar Singh
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Andrew Spriggs
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Jen M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Fei Wang
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Scott M Yourstone
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Xiuting Zheng
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | | | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Iain W Wilson
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - David M Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
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12
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Annweiler C, Dursun E, Féron F, Gezen-Ak D, Kalueff AV, Littlejohns T, Llewellyn DJ, Millet P, Scott T, Tucker KL, Yilmazer S, Beauchet O. 'Vitamin D and cognition in older adults': updated international recommendations. J Intern Med 2015; 277:45-57. [PMID: 24995480 DOI: 10.1111/joim.12279] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Hypovitaminosis D, a condition that is highly prevalent in older adults aged 65 years and above, is associated with brain changes and dementia. Given the rapidly accumulating and complex contribution of the literature in the field of vitamin D and cognition, clear guidance is needed for researchers and clinicians. METHODS International experts met at an invitational summit on 'Vitamin D and Cognition in Older Adults'. Based on previous reports and expert opinion, the task force focused on key questions relating to the role of vitamin D in Alzheimer's disease and related disorders. Each question was discussed and voted using a Delphi-like approach. RESULTS The experts reached an agreement that hypovitaminosis D increases the risk of cognitive decline and dementia in older adults and may alter the clinical presentation as a consequence of related comorbidities; however, at present, vitamin D level should not be used as a diagnostic or prognostic biomarker of Alzheimer's disease due to lack of specificity and insufficient evidence. This population should be screened for hypovitaminosis D because of its high prevalence and should receive supplementation, if necessary; but this advice was not specific to cognition. During the debate, the possibility of 'critical periods' during which vitamin D may have its greatest impact on the brain was addressed; whether hypovitaminosis D influences cognition actively through deleterious effects and/or passively by loss of neuroprotection was also considered. CONCLUSIONS The international task force agreed on five overarching principles related to vitamin D and cognition in older adults. Several areas of uncertainty remain, and it will be necessary to revise the proposed recommendations as new findings become available.
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Affiliation(s)
- C Annweiler
- Department of Neuroscience, Division of Geriatric Medicine and Memory Clinic, UPRES EA 4638, UNAM, Angers University Hospital, Angers, France; Department of Medical Biophysics, Robarts Research Institute, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, ON, Canada
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Le TN, Schumann U, Smith NA, Tiwari S, Au PCK, Zhu QH, Taylor JM, Kazan K, Llewellyn DJ, Zhang R, Dennis ES, Wang MB. DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol 2014; 15:458. [PMID: 25228471 PMCID: PMC4189188 DOI: 10.1186/s13059-014-0458-3] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 09/01/2014] [Indexed: 11/12/2022] Open
Abstract
Background DNA demethylases regulate DNA methylation levels in eukaryotes. Arabidopsis encodes four DNA demethylases, DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), DEMETER-LIKE 2 (DML2), and DML3. While DME is involved in maternal specific gene expression during seed development, the biological function of the remaining DNA demethylases remains unclear. Results We show that ROS1, DML2, and DML3 play a role in fungal disease resistance in Arabidopsis. A triple DNA demethylase mutant, rdd (ros1 dml2 dml3), shows increased susceptibility to the fungal pathogen Fusarium oxysporum. We identify 348 genes differentially expressed in rdd relative to wild type, and a significant proportion of these genes are downregulated in rdd and have functions in stress response, suggesting that DNA demethylases maintain or positively regulate the expression of stress response genes required for F. oxysporum resistance. The rdd-downregulated stress response genes are enriched for short transposable element sequences in their promoters. Many of these transposable elements and their surrounding sequences show localized DNA methylation changes in rdd, and a general reduction in CHH methylation, suggesting that RNA-directed DNA methylation (RdDM), responsible for CHH methylation, may participate in DNA demethylase-mediated regulation of stress response genes. Many of the rdd-downregulated stress response genes are downregulated in the RdDM mutants nrpd1 and nrpe1, and the RdDM mutants nrpe1 and ago4 show enhanced susceptibility to F. oxysporum infection. Conclusions Our results suggest that a primary function of DNA demethylases in plants is to regulate the expression of stress response genes by targeting promoter transposable element sequences. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0458-3) contains supplementary material, which is available to authorized users.
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Littlejohns TJ, Kos K, Henley WE, Cherubini A, Ferrucci L, Lang IA, Langa KM, Melzer D, Llewellyn DJ. OP01 Serum leptin and risk of cognitive decline in elderly Italians: a prospective cohort study. Br J Soc Med 2014. [DOI: 10.1136/jech-2014-204726.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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15
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Bedon F, Ziolkowski L, Walford SA, Dennis ES, Llewellyn DJ. Members of the MYBMIXTA-like transcription factors may orchestrate the initiation of fiber development in cotton seeds. Front Plant Sci 2014; 5:179. [PMID: 24860577 PMCID: PMC4028877 DOI: 10.3389/fpls.2014.00179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/14/2014] [Indexed: 05/24/2023]
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Osabe K, Clement JD, Bedon F, Pettolino FA, Ziolkowski L, Llewellyn DJ, Finnegan EJ, Wilson IW. Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues. PLoS One 2014; 9:e86049. [PMID: 24465864 PMCID: PMC3896429 DOI: 10.1371/journal.pone.0086049] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 12/05/2013] [Indexed: 12/19/2022] Open
Abstract
In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.
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Liu Q, Talbot M, Llewellyn DJ. Pectin methylesterase and pectin remodelling differ in the fibre walls of two gossypium species with very different fibre properties. PLoS One 2013; 8:e65131. [PMID: 23755181 PMCID: PMC3673955 DOI: 10.1371/journal.pone.0065131] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/22/2013] [Indexed: 01/30/2023] Open
Abstract
Pectin, a major component of the primary cell walls of dicot plants, is synthesized in Golgi, secreted into the wall as methylesters and subsequently de-esterified by pectin methylesterase (PME). Pectin remodelling by PMEs is known to be important in regulating cell expansion in plants, but has been poorly studied in cotton. In this study, genome-wide analysis showed that PMEs are a large multi-gene family (81 genes) in diploid cotton (Gossypium raimondii), an expansion over the 66 in Arabidopsis and suggests the evolution of new functions in cotton. Relatively few PME genes are expressed highly in fibres based on EST abundance and the five most abundant in fibres were cloned and sequenced from two cotton species. Their significant sequence differences and their stage-specific expression in fibres within a species suggest sub-specialisation during fibre development. We determined the transcript abundance of the five fibre PMEs, total PME enzyme activity, pectin content and extent of de-methylesterification of the pectin in fibre walls of the two cotton species over the first 25-30 days of fibre growth. There was a higher transcript abundance of fibre-PMEs and a higher total PME enzyme activity in G. barbadense (Gb) than in G. hirsutum (Gh) fibres, particularly during late fibre elongation. Total pectin was high, but de-esterified pectin was low during fibre elongation (5-12 dpa) in both Gh and Gb. De-esterified pectin levels rose thereafter when total PME activity increased and this occurred earlier in Gb fibres resulting in a lower degree of esterification in Gb fibres between 17 and 22 dpa. Gb fibres are finer and longer than those of Gh, so differences in pectin remodelling during the transition to wall thickening may be an important factor in influencing final fibre diameter and length, two key quality attributes of cotton fibres.
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Affiliation(s)
- Qinxiang Liu
- Plant Industry, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Mark Talbot
- Plant Industry, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Danny J. Llewellyn
- Plant Industry, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
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Brouwer-Brolsma EM, Bischoff-Ferrari HA, Bouillon R, Feskens EJM, Gallagher CJ, Hypponen E, Llewellyn DJ, Stoecklin E, Dierkes J, Kies AK, Kok FJ, Lamberg-Allardt C, Moser U, Pilz S, Saris WH, van Schoor NM, Weber P, Witkamp R, Zittermann A, de Groot LCPGM. Vitamin D: do we get enough? A discussion between vitamin D experts in order to make a step towards the harmonisation of dietary reference intakes for vitamin D across Europe. Osteoporos Int 2013; 24:1567-77. [PMID: 23229471 DOI: 10.1007/s00198-012-2231-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/22/2012] [Indexed: 02/06/2023]
Abstract
UNLABELLED On September 29, 2011, acknowledged experts in the field of vitamin D, mainly European, were brought together in order to discuss the recent scientific advances in relation to vitamin D: the current requirements and associations with various health outcomes. In this article, the discussions resulting from the meeting are summarized. INTRODUCTION Several groups at risk for developing vitamin D insufficiency have been identified. Accordingly, reviews indicate that a significant percentage of the population worldwide have serum 25-hydroxyvitamin D levels below 50 nmol/l. In addition to the role of vitamin D in bone health, recent studies suggest that it may play a pivotal role in other systems, e.g., the cardiovascular system, pancreas, muscle, immune system and brain. Most evidence, however, is obtained from observational studies and yet inconclusive. METHODS To exchange and broaden knowledge on the requirements for vitamin D and its effect on various health outcomes, a workshop entitled "Vitamin D Expert Meeting: Do we get enough?", was organized. RESULTS Despite low vitamin D levels worldwide, consensus on the definition of deficiency is not yet reached. In order to define cut-off points for vitamin D whilst taking into account extraskeletal health effects, randomized controlled trials in these fields are warranted. The experts do emphasize that there is evidence to suggest an important role for vitamin D in the maintenance of optimal bone health at all ages and that vitamin D supplementation, in most studies co-administered with calcium, reduces fracture risk in the senior population. CONCLUSION To reach a serum 25-hydroxyvitamin D level of 50 nmol/l older adults aged ≥65 years are therefore recommended to meet a mean daily vitamin D intake of 20 μg (800 IU), which is best achieved with a supplement.
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Affiliation(s)
- E M Brouwer-Brolsma
- Division of Human Nutrition, Wageningen University and Research Centre, P.O. Box 8129, 6700, EV, Wageningen, The Netherlands.
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19
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Lang IA, Goodwin V, Hubbard R, Llewellyn DJ. OP87 Healthy Behaviours in Middle Age and Long-Term Consequences for Mortality, Physical and Cognitive Function, and Mental Health. Br J Soc Med 2012. [DOI: 10.1136/jech-2012-201753.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Abstract
Gossypium hirsutum L. (cotton) fibres are specialized trichomes a few centimetres in length that grow from the seed coat. Few genes directly involved in the differentiation of these epidermal cells have been identified. These include GhMYB25-like and GhMYB25, two related MYB transcription factors that regulate fibre cell initiation and expansion. We have also identified a putative homeodomain leucine zipper (HD-ZIP) transcription factor, GhHD-1, expressed in trichomes and early fibres that might play a role in cotton fibre initiation. Here, we characterize GhHD-1 homoeologues from tetraploid G. hirsutum and show, using reporter constructs and quantitative real-time PCR (qRT-PCR), that they are expressed predominantly in epidermal tissues during early fibre development, and in other tissues bearing epidermal trichomes. Silencing of GhHD-1 reduced trichome formation and delayed the timing of fibre initiation. Constitutive overexpression of GhHD-1 increased the number of fibres initiating on the seed, but did not affect leaf trichomes. Expression of GhHD-1 in cotton silenced for different fibre MYBs suggest that in ovules it acts downstream of GhMYB25-like, but is unaffected in GhMYB25- or GhMYB109-silenced plants. Microarray analysis of silencing and overexpression lines of GhHD-1 indicated that it potentially regulates the levels of ethylene and reactive oxidation species (ROS) through a WRKY transcription factor and calcium-signalling pathway genes to activate downstream genes necessary for cell expansion and elongation.
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21
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Pilling LC, Harries LW, Powell J, Llewellyn DJ, Ferrucci L, Melzer D. Genomics and successful aging: grounds for renewed optimism? J Gerontol A Biol Sci Med Sci 2012; 67:511-9. [PMID: 22454374 DOI: 10.1093/gerona/gls091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Successful aging depends in part on delaying age-related disease onsets until later in life. Conditions including coronary artery disease, Alzheimer's disease, prostate cancer, and type 2 diabetes are moderately heritable. Genome-wide association studies have identified many risk associated single-nucleotide polymorphisms for these conditions, but much heritability remains unaccounted for. Nevertheless, a great deal is being learned. METHODS Here, we review age-related disease associated single-nucleotide polymorphisms and identify key underlying pathways including lipid handling, specific immune processes, early tissue development, and cell cycle control. RESULTS Most age-related disease associated single-nucleotide polymorphisms do not affect coding regions of genes or protein makeup but instead influence regulation of gene expression. Recent evidence indicates that evolution of gene regulatory sites is fundamental to interspecies differences. Animal models relevant to human aging may therefore need to focus more on gene regulation rather than testing major disruptions to fundamental pathway genes. Recent larger scale human studies of in vivo genome-wide expression (notably from the InCHIANTI aging study) have identified changes in splicing, the "fine tuning" of protein sequences, as a potentially important factor in decline of cellular function with age. Studies of expression with muscle strength and cognition have shown striking concordance with certain mice models of muscle repair and beta-amyloid phagocytosis respectively. CONCLUSIONS The emerging clearer picture of the genetic architecture of age-related diseases in humans is providing new insights into the underlying pathophysiological pathways involved. Translation of genomics into new approaches to prevention, tests and treatments to extend successful aging is therefore likely in the coming decades.
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Affiliation(s)
- L C Pilling
- Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
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22
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Xu SM, Brill E, Llewellyn DJ, Furbank RT, Ruan YL. Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion, reduces seed abortion, and enhances fiber production. Mol Plant 2012; 5:430-41. [PMID: 22115917 DOI: 10.1093/mp/ssr090] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sucrose synthase (Sus) is a key enzyme in the breakdown of sucrose and is considered a biochemical marker for sink strength, especially in crop species, based on mutational and gene suppression studies. It remains elusive, however, whether, or to what extent, increase in Sus activity may enhance sink development. We aimed to address this question by expressing a potato Sus gene in cotton where Sus expression has been previously shown to be critical for normal seed and fiber development. Segregation analyses at T1 generation followed by studies in homozygous progeny lines revealed that increased Sus activity in cotton (1) enhanced leaf expansion with the effect evident from young leaves emerging from shoot apex; (2) improved early seed development, which reduced seed abortion, hence enhanced seed set, and (3) promoted fiber elongation. In young leaves of Sus overexpressing lines, fructose concentrations were significantly increased whereas, in elongating fibers, both fructose and glucose levels were increased. Since hexoses contribute little to osmolality in leaves, in contrast to developing fibers, it is concluded that high Sus activity promotes leaf development independently of osmotic regulation, probably through sugar signaling. The analyses also showed that doubling the Sus activity in 0-d cotton seeds increased their fresh weight by about 30%. However, further increase in Sus activity did not lead to any further increase in seed weight, indicating an upper limit for the Sus overexpression effect. Finally, based on the observed additive effect on fiber yield from increased fiber length and seed number, a new strategy is proposed to increase cotton fiber yield by improving seed development as a whole, rather than solely focusing on manipulating fiber growth.
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Affiliation(s)
- Shou-Min Xu
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
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Abstract
BACKGROUND The prevalence of psychological distress and common mental disorders has been shown to peak in midlife but analyses have ignored the association of poor material circumstances with prevalence. This study aimed to test the hypothesis that the midlife prevalence peak occurs only in lower-income households. METHOD Pooled data were used from the annual Health Survey for England, a nationally representative cross-sectional study, on community-dwelling individuals aged ≥ 16 years from years 1997 to 2006 (n=100 457). 12-item General Health Questionnaire scores, reported mental illness diagnoses and receipt of relevant medication were assessed in relation to household income and age. Analyses were separated by gender and adjusted for age, ethnicity, smoking, social class, education and co-morbidities. RESULTS Prevalence of psychological distress, diagnoses and treatments rose with age until early middle age and declined subsequently. In analyses conducted separately by income categories, this pattern was marked in low-income groups but absent in high-income groups. Income-related inequalities in the prevalence of psychological distress were greatest in midlife; for example, in men aged 45-54 years the odds ratio of receiving psychiatric medication in the lowest income group compared with the highest was 7.50 [95% confidence interval (CI) 4.24-13.27] and in women aged 45-54 years the odds ratio of reporting mental illness was 10.25 (95% CI 6.16-17.05). CONCLUSIONS An increased prevalence of psychological distress, common mental disorder diagnoses and treatment in midlife is not a universal phenomenon but is found only in those in low-income households. This implies the phenomenon is not inevitable but is potentially manageable or preventable.
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Affiliation(s)
- I A Lang
- PenCLAHRC, Peninsula Medical School, University of Exeter, Exeter, UK.
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24
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Ridgway MC, Giulian R, Sprouster DJ, Kluth P, Araujo LL, Llewellyn DJ, Byrne AP, Kremer F, Fichtner PFP, Rizza G, Amekura H, Toulemonde M. Role of thermodynamics in the shape transformation of embedded metal nanoparticles induced by swift heavy-ion irradiation. Phys Rev Lett 2011; 106:095505. [PMID: 21405636 DOI: 10.1103/physrevlett.106.095505] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Indexed: 05/30/2023]
Abstract
Swift heavy-ion irradiation of elemental metal nanoparticles (NPs) embedded in amorphous SiO(2) induces a spherical to rodlike shape transformation with the direction of NP elongation aligned to that of the incident ion. Large, once-spherical NPs become progressively more rodlike while small NPs below a critical diameter do not elongate but dissolve in the matrix. We examine this shape transformation for ten metals under a common irradiation condition to achieve mechanistic insight into the transformation process. Subtle differences are apparent including the saturation of the elongated NP width at a minimum sustainable, metal-specific value. Elongated NPs of lesser width are unstable and subject to vaporization. Furthermore, we demonstrate the elongation process is governed by the formation of a molten ion-track in amorphous SiO(2) such that upon saturation the elongated NP width never exceeds the molten ion-track diameter.
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Affiliation(s)
- M C Ridgway
- Research School of Physics and Engineering, Australian National University, Canberra, Australia
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25
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Abstract
MYB transcription factors have been implicated in regulation of the development of ovule epidermal cells into the elongated seed fibres of cotton. An R2R3 MYB, GhMYB25-like, identified from its reduced expression in a fibreless mutant of cotton (Xu142 fl), is here shown to play a key role in the very early stages of fibre cell differentiation. A GhMYB25-like promoter-GUS construct was expressed predominantly in the epidermal layers of cotton ovules before anthesis (-3days post-anthesis, dpa), increasing in expression in 0-dpa ovules, primarily in those epidermal cells expanding into fibres, and then in elongating fibres at +3dpa, declining thereafter. This was consistent with GhMYB25-like transcript abundance during fibre development. RNA interference suppression of GhMYB25-like resulted in cotton plants with fibreless seeds, but normal trichomes elsewhere, phenocopying the Xu142 fl mutant. Like Xu142 fl these plants had reduced expression of the fibre-expressed MYBs, GhMYB25 and GhMYB109, indicating that GhMYB25-like is upstream from those MYBs. This hierarchy was supported by the absence of any change in transcript level of GhMYB25-like in GhMYB25- and GhMYB109-silenced transgenic lines. Transgenic cotton with an additional copy of the native gene had elevated expression of GhMYB25-like in ovules, but no obvious increase in fibre initials, suggesting that there may be other factors that interact with GhMYB25-like to differentiate epidermal cells into fibre cells.
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MESH Headings
- Amino Acid Sequence
- Cloning, Molecular
- Cotton Fiber
- DNA, Plant/genetics
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Gossypium/genetics
- Gossypium/metabolism
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Ovule/genetics
- Ovule/metabolism
- Ovule/ultrastructure
- Plant Epidermis/genetics
- Plant Epidermis/metabolism
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Promoter Regions, Genetic
- RNA Interference
- Sequence Alignment
- Sequence Analysis, DNA
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species. Plant Signal Behav 2010; 5:1006-9. [PMID: 20724824 PMCID: PMC3115181 DOI: 10.4161/psb.5.8.12231] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [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: 04/30/2010] [Accepted: 04/30/2010] [Indexed: 05/18/2023]
Abstract
Waterlogging is a serious impediment to crop productivity worldwide which acts to reduce oxygen levels in the rhizosphere due to the low diffusion rate of molecular oxygen in water. Plants respond to low oxygen through rapid and specific changes at both the transcriptional and translational levels. Transcriptional changes to low-oxygen (hypoxia) stress have been studied in a number of plant species using whole genome microarrays. Using transcriptome data from root tissue from early time points (4-5 h) from cotton (Gossypium hirsutum), Arabidopsis and gray poplar (Populus x canescens), we have identified a core set of orthologous genes that responded to hypoxia in similar ways between species, and others that showed species specific responses . Responses to hypoxia were most similar between Arabidopsis and cotton, while the waterlogging tolerant poplar species exhibited some significant differences.
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Affiliation(s)
- Jed A Christianson
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, Southern Crop Protection and Food Research Centre, London, Ontario, Canada
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Abstract
Pre-ascent climbing route visual inspection (route preview) has been suggested as a key climbing performance parameter although its role has never been verified experimentally. We examined the efficacy of this perceptual-cognitive skill on indoor sport climbing performance. Twenty-nine male climbers, divided into intermediate, advanced and expert climbing level groups, climbed two indoor sport routes matching their climbing level and, where applicable, routes below their climbing level. At each level, one route was climbed with a preview, where participants benefited from a 3-min pre-ascent climbing route visual inspection. Performance was assessed in terms of output (route completion) and form (number and duration of moves and stops). Route preview did not influence the output performance. Climbers using visual inspection were no more likely to finish the ascent than those without the option of using visual inspection. Conversely, route preview did influence form performance; climbers made fewer, and shorter stops during their ascent following a preview of the route. Form performances differences remained when baseline ability levels were taken into account, although for shorter duration of stops only with expert climbers benefiting most from route preview. The ability to visually inspect a climb before its ascent may represent an essential component of performance optimization.
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Affiliation(s)
- X Sanchez
- Department of Psychology, Faculty of Behavioural and Social Sciences, University of Groningen, Groningen, The Netherlands.
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Llewellyn DJ, Langa KM, Friedland RP, Lang IA. Serum albumin concentration and cognitive impairment. Curr Alzheimer Res 2010; 7:91-6. [PMID: 20205675 DOI: 10.2174/156720510790274392] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 05/05/2009] [Indexed: 11/22/2022]
Abstract
Results from clinical samples suggest low serum albumin may be associated with cognitive impairment, though evidence from population-based studies is inconclusive. Participants were 1,752 adults (699 men and 1,053 women) aged 65 years and over from the Health Survey for England 2000, a nationally representative population-based study. Cognitive impairment was assessed using the Abbreviated Mental Test Score. The cross-sectional relation of serum albumin quartiles to cognitive impairment was modelled using logistic regression. Two hundred and twelve participants were cognitively impaired (68 men and 144 women). Odds ratios (95% confidence intervals) for cognitive impairment in the first (2.2-3.8 g/dl), second (3.9-4.0 g/dl), and third (4.1-4.3 g/dl) quartiles of serum albumin compared with the fourth (4.4-5.3 g/dl) were 2.5 (1.3-5.1), 1.7 (0.9-3.5), and 1.5 (0.7-2.9), after adjustment for age, sex, education and additional risk factors for cognitive impairment (p for linear trend = 0.002). A highly similar pattern of associations was observed for men and women. Our data provide new evidence to suggest that low serum albumin is independently associated with increased odds of cognitive impairment in the elderly population.
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Affiliation(s)
- D J Llewellyn
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 2SR, UK.
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Christianson JA, Dennis ES, Llewellyn DJ, Wilson IW. ATAF NAC transcription factors: regulators of plant stress signaling. Plant Signal Behav 2010; 5:428-32. [PMID: 20118664 PMCID: PMC7080423 DOI: 10.4161/psb.5.4.10847] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
NAC proteins are one of the largest classes of plant-specific transcriptional regulators. Since the first NAC gene NO APICAL MERSITEM (NAM) was identified from petunia in 1996 1, NAC genes have been implicated in important plant developmental processes like boundary cell formation in shoot apical mersitems 1, 2, secondary cell wall formation, 3 and lateral root development. 4 However, recent work indicates that NAC genes are also important regulators in stress responses. Nowhere is this more evident than the ATAF subgroup of NAC domain transcription factors. This mini-review aims at highlighting recent evidence of the importance of the ATAF-like NAC group in a diverse array of stress related signaling processes.
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Affiliation(s)
- Jed A Christianson
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, Southern Crop Protection and Food Research Centre, London, ON, Canada
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Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.). Plant Cell Physiol 2010; 51:21-37. [PMID: 19923201 DOI: 10.1093/pcp/pcp163] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Waterlogging stress causes yield reduction in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging caused significant reductions in stem elongation, shoot mass, root mass and leaf number, and altered the expression of 1,012 genes (4% of genes assayed) in root tissue as early as 4 h after flooding. Many of these genes were associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global gene expression in leaf tissues, significantly changing the expression of 1,305 genes (5% of genes assayed) after 24 h of flooding. Genes affected were associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism The implications of these results for the development of waterlogging-tolerant cotton are discussed.
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Abstract
Little is still known about the developmental control of the long seed coat trichomes of cotton (Gossypium hirsutum L.). In Arabidopsis, leaf trichome initiation is regulated by a group of well-defined transcription factors that includes MYB and homeodomain types. Many MYBs are expressed in fibres, but their roles in fibre development remain unclear. We analysed the function of one MYB transcription factor, GhMYB25, identified from transcriptome comparisons between wild-type and fibreless cotton mutants. A GhMYB25 promoter-GUS construct in transgenic cotton was expressed in the epidermis of ovules, developing fibre initials and fibres, in the trichomes of a number of tissues including leaves, stems and petals, as well as in the anthers, pollen and the epidermal layers of roots and root initials, but not in root hairs. Cotton is an allotetraploid with two very similar GhMYB25 genes that were silenced by a single RNAi construct. GhMYB25-silenced cotton showed alterations in the timing of rapid fibre elongation, resulting in short fibres, dramatic reductions in trichomes on other parts of the plant, and reductions in seed production. Reciprocal crosses between transgenic and non-transgenic plants indicated that pollen and ovule viability per se were not disrupted. Ectopic over-expression of GhMYB25 had more subtle impacts, with increases in cotton fibre initiation and leaf trichome number. High expression appeared to adversely affect fertility. Our results provide convincing evidence for a role of GhMYB25, like other MIXTA-like MYBS, in regulating specialized outgrowths of epidermal cells, including, in this case, cotton fibres.
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Affiliation(s)
- Adriane Machado
- CSIRO Plant Industry, PO Box 1600, Canberra ACT 2601, Australia
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Al-Ghazi Y, Bourot S, Arioli T, Dennis ES, Llewellyn DJ. Transcript profiling during fiber development identifies pathways in secondary metabolism and cell wall structure that may contribute to cotton fiber quality. Plant Cell Physiol 2009; 50:1364-1381. [PMID: 19520671 DOI: 10.1093/pcp/pcp084] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A global gene expression profiling study at different stages of fiber development was undertaken on two cotton species cultivated for fiber, Gossypium hirsutum (L.) and G. barbadense (L.). A large proportion of the genome was expressed during both fiber elongation and subsequent secondary cell wall thickening. There was a major shift in abundance of transcripts for gene regulation, cell organization and metabolism between fiber elongation and fiber thickening that was fundamentally similar in both species. Each stage had its own distinctive features represented by specific metabolic and regulatory genes, a number of which have been noted previously. Many of the genes expressed in the fibers were of a similar type and developmental expression to those seen in other fiber-producing plants, indicating a conservation of mechanisms of cell elongation and wall thickening across diverse plant genera. Secondary metabolism and pectin synthesis and modification genes were amongst the most statistically significant differentially expressed categories between the two species during fiber elongation. The gene profiles of the fiber thickening stage, however, were almost identical between the two species, suggesting that their different final fiber quality properties may be established at earlier stages of fiber development. Expression levels of representative phenylpropanoid and pectin modification genes showed high correlations with specific fiber properties in an inter-specific cotton recombinant inbred line (RIL) population, supporting a role in determining fiber quality.
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Christianson JA, Wilson IW, Llewellyn DJ, Dennis ES. The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. Plant Physiol 2009; 149:1724-38. [PMID: 19176720 PMCID: PMC2663757 DOI: 10.1104/pp.108.131912] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 01/23/2009] [Indexed: 05/18/2023]
Abstract
Low-oxygen stress imposed by field waterlogging is a serious impediment to plant germination and growth. Plants respond to waterlogging with a complex set of physiological responses regulated at the transcriptional, cellular, and tissue levels. The Arabidopsis (Arabidopsis thaliana) NAC domain-containing gene ANAC102 was shown to be induced under 0.1% oxygen within 30 min in both roots and shoots as well as in 0.1% oxygen-treated germinating seeds. Overexpression of ANAC102 altered the expression of a number of genes, including many previously identified as being low-oxygen responsive. Decreasing ANAC102 expression had no effect on global gene transcription in plants but did alter expression patterns in low-oxygen-stressed seeds. Increasing or decreasing the expression of ANAC102 did not affect adult plant survival of low-oxygen stress. Decreased ANAC102 expression significantly decreased germination efficiency following a 0.1% oxygen treatment, but increased expression had no effect on germination. This protective role during germination appeared to be specific to low-oxygen stress, implicating ANAC102 as an important regulator of seed germination under flooding.
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Affiliation(s)
- Jed A Christianson
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia
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Abstract
The purpose of the present study was to assess the relationship between pre-performance psychological states and expert performance in non-traditional sport competition. Nineteen elite male sport climbers (M=24.6, SD=4.0 years of age) completed the Competitive State Anxiety Inventory-2 and the Positive and Negative Affect Schedule before an international rock climbing competition. Climbing performances were video-recorded to calculate movement fluency (entropy) and obtain ascent times. Official route scores were also obtained. Successful climbers reported higher pre-performance levels of somatic anxiety and climbed the most difficult part of the route more slowly than their unsuccessful counterparts. The psychological states preceding elite climbing competition appeared to be an important factor in determining success, even when differences in baseline ability were taken into account.
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Affiliation(s)
- X Sanchez
- Department of Sport and Exercise Sciences, University of Chester, Chester, UK.
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35
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Ruan YL, Llewellyn DJ, Liu Q, Xu SM, Wu LM, Wang L, Furbank RT. Expression of sucrose synthase in the developing endosperm is essential for early seed development in cotton. Funct Plant Biol 2008; 35:382-393. [PMID: 32688795 DOI: 10.1071/fp08017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 05/01/2008] [Indexed: 06/11/2023]
Abstract
Successful seed development requires coordinated interaction of the endosperm and embryo. In most dicotyledonous seeds, the endosperm is crushed and absorbed by the expanding embryo in the later stages of seed development. Little is known about the metabolic interaction between the two filial tissues early in seed development. We examined the potential role of sucrose synthase (Sus) in the endosperm development of cotton. Sus was immunologically localised in the cellularising endosperm, but not in the heart-stage embryo at 10 days after anthesis. The activities of Sus and acid invertase were significantly higher in the endosperm than in the young embryos, which corresponded to a steep concentration difference in hexoses between the endosperm and the embryo. This observation indicates a role for the endosperm in generating hexoses for the development of the two filial tissues. Interestingly, Sus expression and starch deposition were spatially separated in the seeds. Silencing the expression of Sus in the endosperm using an RNAi approach led to the arrest of early seed development. Histochemical analyses revealed a significant reduction in cellulose and callose in the deformed endosperm cells of the Sus-suppressed seed. The data indicate a critical role of Sus in early seed development through regulation of endosperm formation.
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Affiliation(s)
- Yong-Ling Ruan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | | | - Qing Liu
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Shou-Min Xu
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Li-Min Wu
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Lu Wang
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Robert T Furbank
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
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36
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Wu Y, Llewellyn DJ, White R, Ruggiero K, Al-Ghazi Y, Dennis ES. Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules. Planta 2007; 226:1475-90. [PMID: 17636323 DOI: 10.1007/s00425-007-0580-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 06/25/2007] [Indexed: 05/12/2023]
Abstract
Cotton (Gossypium hirsutum L.) fibre initial cells undergo a rapid cellular re-programming around anthesis to form the long cellulose fibres prized for textile manufacture. On the day of anthesis the cotton fibre initial cells balloon out from the ovule surface and so are clearly distinguished from adjacent epidermal pavement cells. To enhance our understanding of the molecular processes that determine which cells become fibres and why adjacent epidermal cells remain in a different developmental state we studied the expression profiles of the two respective cell types. Using laser-capture microdissection, coupled with an in vitro RNA amplification system, we used cDNA microarray slides to profile the gene expression in expanding fibre initials compared to the non-expanding epidermal cells at an early stage just after the fibre initials are discernable. Except for a few regulatory genes, the genes that are up-regulated in the cotton fibre initials relative to epidermal cells predominantly encode proteins involved in generating the components for the extra cell membrane and primary cell wall needed for the rapid cell expansion of the initials. This includes synthesis of enzymes and cell wall proteins, carbohydrates, and lipids. An analysis of single channel fluorescence levels confirmed that these classes of genes were also the most highly expressed genes in fibre initials. Genes involved in DNA metabolism were also well represented in the expanding fibre cell, consistent with the limited endoreduplication we previously reported to occur in fibre initial cells.
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Affiliation(s)
- Yingru Wu
- CSIRO Plant Industry, P.O. Box 1600, Canberra, ACT 2601, Australia
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37
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Townsend BJ, Llewellyn DJ. Reduced terpene levels in cottonseed add food to fiber. Trends Biotechnol 2007; 25:239-41. [PMID: 17433845 DOI: 10.1016/j.tibtech.2007.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 03/06/2007] [Accepted: 03/29/2007] [Indexed: 11/28/2022]
Abstract
Using RNA interference (RNAi) technology, the levels of a toxic phytoprotectant have recently been reduced specifically in the seeds of cotton to generate a novel dual-purpose crop. By engineering an endogenous terpene pathway, there is now the exciting potential for an added-value, genetically modified crop with the cash value of the fiber supported by the improved nutritional value and expanded food and feed use for the cottonseed, which is normally a low-value by-product.
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Charles GW, Constable GA, Llewellyn DJ, Hickman MA. Tolerance of cotton expressing a 2,4-D detoxification gene to 2,4-D applied in the field. ACTA ACUST UNITED AC 2007. [DOI: 10.1071/ar06375] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The tolerance to 2,4-dichlorophenoxy acetic acid (2,4-D) of a genetically modified (transgenic) cotton (Gossypium hirsutum) expressing a 2,4-D detoxification gene was compared with conventional (non-transgenic) cotton over 2 seasons. The 2,4-D was applied over-the-top of cotton in the field at 7–17 nodes of crop growth at rates of 0.004–1.12 kg a.i./ha. The transgenic cotton displayed better tolerance to 2,4-D than conventional cotton at all growth stages and herbicide rates. Some damage was apparent on both types of cotton at 2,4-D rates of 0.07 kg/ha and above, with damage most pronounced when the plants were exposed at 7 nodes. The transgenic cotton also had some tolerance to MCPA. Commercial use of transgenic, 2,4-D-tolerant cotton has the potential to greatly reduce problems of 2,4-D damage in cotton from accidental spray drift and herbicide residues in spraying equipment, where plants are predominantly exposed to low rates of 2,4-D.
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39
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Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, Taliercio E, Turley R, McFadden H, Payton P, Klueva N, Allen R, Zhang D, Haigler C, Wilkerson C, Suo J, Schulze SR, Pierce ML, Essenberg M, Kim H, Llewellyn DJ, Dennis ES, Kudrna D, Wing R, Paterson AH, Soderlund C, Wendel JF. A global assembly of cotton ESTs. Genome Res 2006; 16:441-50. [PMID: 16478941 PMCID: PMC1415220 DOI: 10.1101/gr.4602906] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [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: 01/24/2023]
Abstract
Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D(T) genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.
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Affiliation(s)
- Joshua A Udall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
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40
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Wu Y, Machado AC, White RG, Llewellyn DJ, Dennis ES. Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant Cell Physiol 2006; 47:107-27. [PMID: 16278222 DOI: 10.1093/pcp/pci228] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cotton fibres are a subset of single epidermal cells that elongate from the seed coat to produce the long cellulose strands or lint used for spinning into yarn. To identify genes that might regulate lint fibre initiation, expression profiles of 0 days post-anthesis (dpa) whole ovules from six reduced fibre or fibreless mutants were compared with wild-type linted cotton using cDNA microarrays. Numerous clones were differentially expressed, but when only those genes that are normally expressed in the ovule outer integument (where fibres develop) were considered, just 13 different cDNA clones were down-regulated in some or all of the mutants. These included: a Myb transcription factor (GhMyb25) similar to the Antirrhinum Myb AmMIXTA, a putative homeodomain protein (related to Arabidopsis ATML1), a cyclin D gene, some previously identified fibre-expressed structural and metabolic genes, such as lipid transfer protein, alpha-expansin and sucrose synthase, as well as some unknown genes. Laser capture microdissection and reverse transcription-PCR were used to show that both the GhMyb25 and the homeodomain gene were predominantly ovule specific and were up-regulated on the day of anthesis in fibre initials relative to adjacent non-fibre ovule epidermal cells. Their spatial and temporal expression pattern therefore coincided with the time and location of fibre initiation. Constitutive overexpression of GhMyb25 in transgenic tobacco resulted in an increase in branched long-stalked leaf trichomes. The involvement of cell cycle genes prompted DNA content measurements that indicated that fibre initials, like leaf trichomes, undergo DNA endoreduplication. Cotton fibre initiation therefore has some parallels with leaf trichome development, although the detailed molecular mechanisms are clearly different.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cotton Fiber
- Crosses, Genetic
- DNA, Plant/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genes, Homeobox
- Genes, Plant
- Gossypium/genetics
- Gossypium/growth & development
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Mutation
- Phenotype
- Phylogeny
- Plant Proteins/genetics
- Plants, Genetically Modified
- Sequence Homology, Amino Acid
- Nicotiana/genetics
- Nicotiana/growth & development
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Affiliation(s)
- Yingru Wu
- CSIRO Plant Industry, Canberra, ACT, Australia
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41
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Wu Y, Rozenfeld S, Defferrard A, Ruggiero K, Udall JA, Kim H, Llewellyn DJ, Dennis ES. Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling. Mol Genet Genomics 2005; 274:477-93. [PMID: 16208490 DOI: 10.1007/s00438-005-0049-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Accepted: 08/19/2005] [Indexed: 10/25/2022]
Abstract
Fibres of cotton (Gossypium hirsutum L.) are single elongated epidermal cells that start to develop on the outer surface of cotton ovules on the day of anthesis. Little is known about the control of fibre initiation and development. As a first step towards discovering important genes involved in fibre initiation and development using a genomics approach, we report technical advances aimed at reducing redundancy and increasing coverage for anonymous cDNA microarrays in this study. Cotton ovule cDNA libraries (both normalised and un-normalised) from around the time of fibre initial formation have been prepared and partially characterised by sequencing. Re-association-based normalisation partially reduced library redundancy and increased representation of novel sequences. However, another library generated from in vitro cultured cotton ovules treated with the protein synthesis inhibitor, cycloheximide, showed a significantly altered gene representation including a greater proportion of protein phosphorylation genes, transport genes and transcription factors and a much reduced proportion of protein synthesis genes than were identified in the conventional types of libraries. Over 10,000 expressed sequence tag (EST) clones randomly selected from the three libraries were printed on microarray slides and used to assess gene expression in tissue cultured ovules with and without cycloheximide treatment. The microarray results showed that cycloheximide had a dramatic effect in modifying the pattern of the gene expression in cultured ovules, affecting the same types of genes identified in the preliminary analysis on relative EST abundance in the different ovule cDNA libraries. Cycloheximide clearly provided a simple and useful method for enriching novel gene sequences for genomic studies.
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Affiliation(s)
- Yingru Wu
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia
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42
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Townsend BJ, Poole A, Blake CJ, Llewellyn DJ. Antisense suppression of a (+)-delta-cadinene synthase gene in cotton prevents the induction of this defense response gene during bacterial blight infection but not its constitutive expression. Plant Physiol 2005; 138:516-28. [PMID: 15849309 PMCID: PMC1104203 DOI: 10.1104/pp.104.056010] [Citation(s) in RCA: 43] [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: 11/03/2004] [Revised: 02/15/2005] [Accepted: 03/02/2005] [Indexed: 05/18/2023]
Abstract
In cotton (Gossypium hirsutum) the enzyme (+)-delta-cadinene synthase (CDNS) catalyzes the first committed step in the biosynthesis of cadinane-type sesquiterpenes, such as gossypol, that provide constitutive and inducible protection against pests and diseases. A cotton cDNA clone encoding CDNS (cdn1-C4) was isolated from developing embryos and functionally characterized. Southern analysis showed that CDNS genes belong to a large multigene family, of which five genomic clones were studied, including three pseudogenes and one gene that may represent another subfamily of CDNS. CDNS expression was shown to be induced in cotton infected with either the bacterial blight or verticillium wilt pathogens. Constructs for the constitutive or seed-specific antisense suppression of cdn1-C4 were introduced into cotton by Agrobacterium-mediated transformation. Gossypol levels were not reduced in the seeds of transformants with either construct, nor was the induction of CDNS expression affected in stems of the constitutive antisense plants infected with Verticillium dahliae Kleb. However, the induction of CDNS mRNA and protein in response to bacterial blight infection of cotyledons was completely blocked in the constitutive antisense plants. These results suggest that cdn1-C4 may be involved specifically in the bacterial blight response and that the CDNS multigene family comprises a complex set of genes differing in their temporal and spatial regulation and responsible for different branches of the cotton sesquiterpene pathway.
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Affiliation(s)
- Belinda J Townsend
- Commonwealth Scientific and Industrial Research Organisation-Plant Industry, Canberra, Australian Capital Territory 2601, Australia
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43
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Ruan YL, Llewellyn DJ, Furbank RT, Chourey PS. The delayed initiation and slow elongation of fuzz-like short fibre cells in relation to altered patterns of sucrose synthase expression and plasmodesmata gating in a lintless mutant of cotton. J Exp Bot 2005; 56:977-984. [PMID: 15710635 DOI: 10.1093/jxb/eri091] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cotton (Gossypium hirsutum L.) seed develops single-celled long fibres (lint) from the seed-coat epidermis at anthesis. Previous studies have shown that the initiation and rapid elongation of these fibres requires the expression of sucrose synthase (Sus) and, potentially, a transient closure of plasmodesmata. This study extends the previous work to examine the patterns of Sus expression and plasmodesmata gating in fuzz-like short fibres of a mutant that shows delayed initiation and much slower and reduced elongation of the fibre cells. Immunolocalization studies revealed delayed expression of Sus in the mutant seed-coat epidermis that correlates temporally and spatially with the initiation of the fibre cells. Anatomically, these short fibres differed from the normal lint in that their basal ends enlarged immediately after initiation, while the majority of the normal lint on wild-type seed did not show this enlargement until the end of elongation. Suppression of Sus expression in the seed-coat epidermis of the transgenic plants reduced the length of both lint and short fuzz fibres at maturity, suggesting that the growth of short fibres also requires high levels of Sus expression. Confocal imaging of the membrane-impermeant fluorescent solute carboxyfluorescein (CF) revealed no closure of plasmodesmata during the entire elongation period of short fibres from the mutant seed. These results show (i) the delayed initiation of fuzz-like short fibres from the mutant seed correlates with delayed or insufficient expression of Sus in a subset of seed-coat epidermal cells destined to become fibres and (ii) the much shortened elongation of the fibres from the mutant may be related to their inability to close plasmodesmata.
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Affiliation(s)
- Yong-Ling Ruan
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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44
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Schünmann PHD, Llewellyn DJ, Surin B, Boevink P, Feyter RCD, Waterhouse PM. A suite of novel promoters and terminators for plant biotechnology. Funct Plant Biol 2003; 30:453-460. [PMID: 32689029 DOI: 10.1071/fp02167] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The gene regulation signals from subterranean clover stunt virus (SCSV) were investigated for their expression in dicot plants. The SCSV genome has at least eight circular DNA molecules. Each circular DNA component contains a promoter element, a single open reading frame and a terminator. The promoters from seven of the segments were examined for their strength and tissue specificity in transgenic tobacco (Nicotiana tabacum L.), potato (Solanum tuberosum L.) and cotton (Gossypium hirsutum L.) using a GUS reporter gene assay system. While the promoters of many of the segments were poorly expressed, promoters derived from segments 4 and 7 were shown to direct high levels of expression in various plant tissues and organs. The segment 1 promoter directs predominantly callus-specific expression and, when used to control a selectable marker gene, facilitated the transformation of all three species (tobacco, potato and cotton). From the results, a suite of plant expression vectors (pPLEX) derived from the SCSV genome were constructed and used here to produce herbicide- and insect-resistant cotton, demonstrating their utility in the expression of foreign genes in dicot crop species and their potential for use in agricultural biotechnology.
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Affiliation(s)
- Petra H D Schünmann
- Corresponding author; CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Brian Surin
- CRC for Plant Science, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia
| | - Petra Boevink
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Peter M Waterhouse
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia. CRC for Plant Science, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia
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45
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Schünmann PHD, Llewellyn DJ, Surin B, Boevink P, Feyter RCD, Waterhouse PM. A suite of novel promoters and terminators for plant biotechnology. Funct Plant Biol 2003; 30:443-452. [PMID: 32689029 DOI: 10.1071/fp02166] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The gene regulation signals from subterranean clover stunt virus (SCSV) were investigated for their expression in dicot plants. The SCSV genome has at least eight circular DNA molecules. Each circular DNA component contains a promoter element, a single open reading frame and a terminator. The promoters from seven of the segments were examined for their strength and tissue specificity in transgenic tobacco (Nicotiana tabacum L.), potato (Solanum tuberosum L.) and cotton (Gossypium hirsutum L.) using a GUS reporter gene assay system. While the promoters of many of the segments were poorly expressed, promoters derived from segments 4 and 7 were shown to direct high levels of expression in various plant tissues and organs. The segment 1 promoter directs predominantly callus-specific expression and, when used to control a selectable marker gene, facilitated the transformation of all three species (tobacco, potato and cotton). From the results, a suite of plant expression vectors (pPLEX) derived from the SCSV genome were constructed and used here to produce herbicide- and insect-resistant cotton, demonstrating their utility in the expression of foreign genes in dicot crop species and their potential for use in agricultural biotechnology.
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Affiliation(s)
- Petra H D Schünmann
- Corresponding author; CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Brian Surin
- CRC for Plant Science, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia
| | - Petra Boevink
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | | | - Peter M Waterhouse
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia. CRC for Plant Science, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia
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46
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Ruan YL, Llewellyn DJ, Furbank RT. Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development. Plant Cell 2003; 15:952-64. [PMID: 12671090 PMCID: PMC152341 DOI: 10.1105/tpc.010108] [Citation(s) in RCA: 278] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2002] [Accepted: 02/07/2003] [Indexed: 05/18/2023]
Abstract
Cotton is the most important textile crop as a result of its long cellulose-enriched mature fibers. These single-celled hairs initiate at anthesis from the ovule epidermis. To date, genes proven to be critical for fiber development have not been identified. Here, we examined the role of the sucrose synthase gene (Sus) in cotton fiber and seed by transforming cotton with Sus suppression constructs. We focused our analysis on 0 to 3 days after anthesis (DAA) for early fiber development and 25 DAA, when the fiber and seed are maximal in size. Suppression of Sus activity by 70% or more in the ovule epidermis led to a fiberless phenotype. The fiber initials in those ovules were fewer and shrunken or collapsed. The level of Sus suppression correlated strongly with the degree of inhibition of fiber initiation and elongation, probably as a result of the reduction of hexoses. By 25 DAA, a portion of the seeds in the fruit showed Sus suppression only in the seed coat fibers and transfer cells but not in the endosperm and embryo. These transgenic seeds were identical to wild-type seeds except for much reduced fiber growth. However, the remaining seeds in the fruit showed Sus suppression both in the seed coat and in the endosperm and embryo. These seeds were shrunken with loss of the transfer cells and were <5% of wild-type seed weight. These results demonstrate that Sus plays a rate-limiting role in the initiation and elongation of the single-celled fibers. These analyses also show that suppression of Sus only in the maternal seed tissue represses fiber development without affecting embryo development and seed size. Additional suppression in the endosperm and embryo inhibits their own development, which blocks the formation of adjacent seed coat transfer cells and arrests seed development entirely.
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Affiliation(s)
- Yong-Ling Ruan
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, ACT 2601, Australia.
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47
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Townsend BJ, Llewellyn DJ. Spatial and temporal regulation of a soybean (Glycine max) lectin promoter in transgenic cotton (Gossypium hirsutum). Funct Plant Biol 2002; 29:835-843. [PMID: 32689531 DOI: 10.1071/pp01235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The activity of a soybean (Glycine max L. Merrill) lectin gene promoter was investigated in transgenic cotton plants (Gossypium hirsutum L.) with the view to using this promoter for the seed-specific alteration of gossypol, a secondary metabolite in cotton that has adverse effects on the nutritional value of cottonseed products like oil and protein-rich meal. Agrobacterium-mediated transformation generated stable transformants containing a construct with the lectin promoter fused to the β-glucuronidase reporter gene (pLeGUS). Fluorometric GUS assays and northern hybridization detected strong promoter activity during embryo development. GUS activity in developing embryos was detected as early as 10 d post-anthesis (dpa), peaking late in embryo maturation. Enzyme activity persisted in imbibed mature seed, and negligible activity remained detectable in the roots and cotyledons of 7-d-old seedlings. No GUS activity was detected in leaves and squares of mature plants. GUS transcripts increased during embryo development to peak about 35 dpa, declining to a low level in imbibed mature seed. No transcripts were detected in roots, cotyledons, leaves or squares. Histochemical GUS activity staining indicated promoter activity in all cells of the cotyledons, including the flattened cells of the gossypol glands, the presumed site of synthesis of gossypol. This study concluded that the soybean lectin gene promoter is a useful tool for the seed-specific expression of transgenes in cotton.
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Affiliation(s)
- Belinda J Townsend
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia. The Australian National University, Canberra ACT 0200, Australia
| | - Danny J Llewellyn
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia.Corresponding author;
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48
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Gubler F, Chandler PM, White RG, Llewellyn DJ, Jacobsen JV. Gibberellin signaling in barley aleurone cells. Control of SLN1 and GAMYB expression. Plant Physiol 2002; 129:191-200. [PMID: 12011350 PMCID: PMC155883 DOI: 10.1104/pp.010918] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2001] [Revised: 11/15/2001] [Accepted: 01/20/2002] [Indexed: 05/18/2023]
Abstract
We have previously identified GAMYB, a gibberellin (GA)-regulated transcriptional activator of alpha-amylase gene expression, in aleurone cells of barley (Hordeum vulgare). To examine the regulation of GAMYB expression, we describe the use of nuclear run-on experiments to show that GA causes a 2-fold increase in the rate of GAMYB transcription and that the effect of GA can be blocked by abscisic acid (ABA). To identify GA-signaling components that regulate GAMYB expression, we examined the role of SLN1, a negative regulator of GA signaling in barley. SLN1, which is the product of the Sln1 (Slender1) locus, is necessary for repression of GAMYB in barley aleurone cells. The activity of SLN1 in aleurone cells is regulated posttranslationally. SLN1 protein levels decline rapidly in response to GA before any increase in GAMYB levels. Green fluorescent protein-SLN1 fusion protein was targeted to the nucleus of aleurone protoplasts and disappeared in response to GA. Evidence from a dominant dwarf mutant at Sln1, and from the gse1 mutant (that affects GA "sensitivity"), indicates that GA acts by regulating SLN1 degradation and not translation. Mutation of the DELLA region of SLN1 results in increased protein stability in GA-treated layers, indicating that the DELLA region plays an important role in GA-induced degradation of SLN1. Unlike GA, ABA had no effect on SLN1 stability, confirming that ABA acts downstream of SLN1 to block GA signaling.
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Affiliation(s)
- Frank Gubler
- Commonwealth Scientific and Industrial Research Organization, Plant Industry, G.P.O. Box 1600, Canberra, Australian Capital Territory 2601, Australia.
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49
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Ruan YL, Llewellyn DJ, Furbank RT. The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin. Plant Cell 2001; 13:47-60. [PMID: 11158528 PMCID: PMC102212 DOI: 10.1105/tpc.13.1.47] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2000] [Accepted: 11/03/2000] [Indexed: 05/17/2023]
Abstract
Each cotton fiber is a single cell that elongates to 2.5 to 3.0 cm from the seed coat epidermis within approximately 16 days after anthesis (DAA). To elucidate the mechanisms controlling this rapid elongation, we studied the gating of fiber plasmodesmata and the expression of the cell wall-loosening gene expansin and plasma membrane transporters for sucrose and K(+), the major osmotic solutes imported into fibers. Confocal imaging of the membrane-impermeant fluorescent solute carboxyfluorescein (CF) revealed that the fiber plasmodesmata were initially permeable to CF (0 to 9 DAA), but closed at approximately 10 DAA and re-opened at 16 DAA. A developmental switch from simple to branched plasmodesmata was also observed in fibers at 10 DAA. Coincident with the transient closure of the plasmodesmata, the sucrose and K(+) transporter genes were expressed maximally in fibers at 10 DAA with sucrose transporter proteins predominately localized at the fiber base. Consequently, fiber osmotic and turgor potentials were elevated, driving the rapid phase of elongation. The level of expansin mRNA, however, was high at the early phase of elongation (6 to 8 DAA) and decreased rapidly afterwards. The fiber turgor was similar to the underlying seed coat cells at 6 to 10 DAA and after 16 DAA. These results suggest that fiber elongation is initially achieved largely by cell wall loosening and finally terminated by increased wall rigidity and loss of higher turgor. To our knowledge, this study provides an unprecedented demonstration that the gating of plasmodesmata in a given cell is developmentally reversible and is coordinated with the expression of solute transporters and the cell wall-loosening gene. This integration of plasmodesmatal gating and gene expression appears to control fiber cell elongation.
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Affiliation(s)
- Y L Ruan
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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50
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Decroocq V, Zhu X, Kauffman M, Kyozuka J, Peacock WJ, Dennis ES, Llewellyn DJ. A TM3-like MADS-box gene from Eucalyptus expressed in both vegetative and reproductive tissues. Gene X 1999; 228:155-60. [PMID: 10072768 DOI: 10.1016/s0378-1119(98)00613-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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: 11/30/2022] Open
Abstract
MADS-box genes in plants are a diverse class of transcription factors that are involved in regulating developmental processes, particularly meristem and organ identity during floral development. They are characterized by a highly conserved MADS-box domain of 59 amino acids that binds to specific DNA sequences. We report the characterization of a cDNA clone, ETL (Eucalyptus TM3 Like), from Eucalyptus globulus subspecies bicostata encoding a putative transcription factor of the MADS-box class that is strongly expressed in both vegetative and floral tissues, suggesting that it regulates processes other than floral development. The clone was isolated from a floral bud cDNA library with a probe generated from Eucalyptus genomic DNA by PCR using degenerate primers to the MADS-box of the floral regulatory gene APETALA 1. The ETL cDNA clone encodes a putative protein of 206 amino acids that contains an N-terminal MADS-box and a helical domain of approx. 60 amino acids predicted to form a coiled-coil (K-box). These structural features are characteristic of plant MADS-box proteins. The MADS-box domain contains all the signature residues of a class of MADS-box genes typified by the tomato gene TM3 and overall, ETL shows 56% amino acid identity to TM3. Like TM3, the ETL gene is expressed in both vegetative and reproductive organs, predominantly in root and shoot meristems and organ primordia, as well as in developing male and female floral organs.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA-Binding Proteins/genetics
- Eucalyptus/chemistry
- Eucalyptus/genetics
- Eucalyptus/growth & development
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- In Situ Hybridization
- MADS Domain Proteins
- Meristem/genetics
- Molecular Sequence Data
- Plant Proteins
- Plants, Medicinal
- RNA, Messenger/genetics
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription Factors/genetics
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Affiliation(s)
- V Decroocq
- CSIRO Plant Industry, P.O. Box 1600, Canberra, ACT 2601, Australia
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