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de Oliveira AC, Vanavichit A. Editorial: Generating useful genetic variation in crops by induced mutation, volume III. Front Plant Sci 2023; 14:1301977. [PMID: 37920718 PMCID: PMC10619748 DOI: 10.3389/fpls.2023.1301977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023]
Affiliation(s)
- Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Elieu Maciel School of Agronomy, Federal University of Pelotas, Capão do Leão, Brazil
| | - Apichart Vanavichit
- Rice Science Center and Rice Gene Discovery, National Center for Genetic Engineering and Biotechnology and Agronomy Department, Faculty of Agriculture, Kasetsart University, Kamphangsaen, Nakhonpathom, Thailand
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Felipez W, Villavicencio J, Nizolli VO, Pegoraro C, da Maia L, Costa de Oliveira A. Genome-Wide Identification of Bilberry WRKY Transcription Factors: Go Wild and Duplicate. Plants (Basel) 2023; 12:3176. [PMID: 37765340 PMCID: PMC10535657 DOI: 10.3390/plants12183176] [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] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 09/29/2023]
Abstract
WRKY transcription factor genes compose an important family of transcriptional regulators that are present in several plant species. According to previous studies, these genes can also perform important roles in bilberry (Vaccinium myrtillus L.) metabolism, making it essential to deepen our understanding of fruit ripening regulation and anthocyanin biosynthesis. In this context, the detailed characterization of these proteins will provide a comprehensive view of the functional features of VmWRKY genes in different plant organs and in response to different intensities of light. In this study, the investigation of the complete genome of the bilberry identified 76 VmWRKY genes that were evaluated and distributed in all twelve chromosomes. The proteins encoded by these genes were classified into four groups (I, II, III, and IV) based on their conserved domains and zinc finger domain types. Fifteen pairs of VmWRKY genes in segmental duplication and four pairs in tandem duplication were detected. A cis element analysis showed that all promoters of the VmWRKY genes contain at least one potential cis stress-response element. Differential expression analysis of RNA-seq data revealed that VmWRKY genes from bilberry show preferential or specific expression in samples. These findings provide an overview of the functional characterization of these proteins in bilberry.
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Affiliation(s)
- Winder Felipez
- Instituto de Agroecología y Seguridad Alimentaria, Facultad de Ciências Agrárias, Universidad San Francisco Xavier de Chuquisaca—USFX, Casilla, Correo Central, Sucre 1046, Bolivia;
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Jennifer Villavicencio
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
- Carrera de Ingeniería Agroforestal, Facultad de Ciencias Ambientales, Universidad Cientifica del Sur—UCSUR, Antigua Panamericana Sur km 19 Villa el Salvador, Lima CP 150142, Peru
| | - Valeria Oliveira Nizolli
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Camila Pegoraro
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Luciano da Maia
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
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Alsantely A, Gutaker R, Navarrete Rodríguez ME, Arrieta-Espinoza G, Fuchs EJ, Costa de Oliveira A, Tohme J, Zuccolo A, Wing RA, Fornasiero A. The International Oryza Map Alignment Project (IOMAP): the Americas-past achievements and future directions. J Exp Bot 2023; 74:1331-1342. [PMID: 36527431 PMCID: PMC10010607 DOI: 10.1093/jxb/erac490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary, and functional characterization of the wild relatives of rice, facilitating the cloning of >600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following in the footsteps of the original project, the goal of 'IOMAP: the Americas' is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas.
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Affiliation(s)
- Aseel Alsantely
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Rafal Gutaker
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey TW9 3AE, UK
| | - María E Navarrete Rodríguez
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Griselda Arrieta-Espinoza
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Ciudad de la Investigación-C.P., San José 11501-2050, Costa Rica
| | - Eric J Fuchs
- Escuela de Biología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Crop Science Research Center, Sant’Anna School of Advanced Studies, Pisa 56127, Italy
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Nizolli VO, Viana VE, Pegoraro C, Maia LCD, Oliveira ACD. Wheat blast: The last enemy of hunger fighters. Genet Mol Biol 2023; 46:e20220002. [PMID: 37017705 PMCID: PMC10077833 DOI: 10.1590/1678-4685-gmb-2022-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 12/09/2022] [Indexed: 04/06/2023] Open
Abstract
Effective strategies for disease control are crucial for sustaining world food production and ensuring food security for the population. Wheat blast, a disease caused by the pathogen Magnaporthe oryzae pathotype Triticum, has been a concern for cereal producers and researchers due to its aggressiveness and rapid expansion. To solve this problem, the development of resistant varieties with durable resistance is an effective, economical and sustainable way to control the disease. Conventional breeding can be aided by several molecular tools to facilitate the mining of many sources of resistance, such as R genes and QTLs. The identification of new sources of resistance, whether in the wheat crop or in other cereals are an opportunity for efficient wheat breeding through the application of different techniques. Since this disease is still poorly studied in wheat, knowledge of the rice Magnaporthe pathotype may be adapted to control wheat blast. Thus, genetic mapping, molecular markers, transgenic approaches, and genomic editing are valuable technologies to fight wheat blast. This review aimed to compile the biotechnological alternatives available to accelerate the development of improved cultivars for resistance to wheat blast.
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Affiliation(s)
- Valeria Oliveira Nizolli
- Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Centro de Genômica e Fitomelhoramento, Pelotas, RS, Brazil
| | - Vívian Ebeling Viana
- Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitossanidade, Pelotas, RS, Brazil
| | - Camila Pegoraro
- Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Centro de Genômica e Fitomelhoramento, Pelotas, RS, Brazil
| | - Luciano Carlos da Maia
- Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Centro de Genômica e Fitomelhoramento, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Centro de Genômica e Fitomelhoramento, Pelotas, RS, Brazil
- Universidade Federal de Pelotas, Centro de Desenvolvimento Tecnológico, Pelotas, RS, Brazil
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Di Marzo M, Babolin N, Viana VE, de Oliveira AC, Gugi B, Caporali E, Herrera-Ubaldo H, Martínez-Estrada E, Driouich A, de Folter S, Colombo L, Ezquer I. The Genetic Control of SEEDSTICK and LEUNIG-HOMOLOG in Seed and Fruit Development: New Insights into Cell Wall Control. Plants (Basel) 2022; 11:3146. [PMID: 36432874 PMCID: PMC9698089 DOI: 10.3390/plants11223146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Although much is known about seed and fruit development at the molecular level, many gaps remain in our understanding of how cell wall modifications can impact developmental processes in plants, as well as how biomechanical alterations influence seed and fruit growth. Mutants of Arabidopsis thaliana constitute an excellent tool to study the function of gene families devoted to cell wall biogenesis. We have characterized a collection of lines carrying mutations in representative cell wall-related genes for seed and fruit size developmental defects, as well as altered germination rates. We have linked these studies to cell wall composition and structure. Interestingly, we have found that disruption of genes involved in pectin maturation and hemicellulose deposition strongly influence germination dynamics. Finally, we focused on two transcriptional regulators, SEEDSTICK (STK) and LEUNIG-HOMOLOG (LUH), which positively regulate seed growth. Herein, we demonstrate that these factors regulate specific aspects of cell wall properties such as pectin distribution. We propose a model wherein changes in seed coat structure due to alterations in the xyloglucan-cellulose matrix deposition and pectin maturation are critical for organ growth and germination. The results demonstrate the importance of cell wall properties and remodeling of polysaccharides as major factors responsible for seed development.
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Affiliation(s)
- Maurizio Di Marzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Nicola Babolin
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Vívian Ebeling Viana
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
- Plant Genomics and Breeding Center, Federal University of Pelotas, Capão do Leão 96010-610, RS, Brazil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Federal University of Pelotas, Capão do Leão 96010-610, RS, Brazil
| | - Bruno Gugi
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale EA4358, UNIROUEN—Universitè de Rouen Normandie, 76000 Rouen, France
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico
| | - Eduardo Martínez-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico
| | - Azeddine Driouich
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale EA4358, UNIROUEN—Universitè de Rouen Normandie, 76000 Rouen, France
- Fédération de Recherche “NORVEGE”-FED 4277, 76000 Rouen, France
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Viana VE, Maltzahn LE, Costa de Oliveira A, Pegoraro C. Genetic Approaches for Iron and Zinc Biofortification and Arsenic Decrease in Oryza sativa L. Grains. Biol Trace Elem Res 2022; 200:4505-4523. [PMID: 34773578 DOI: 10.1007/s12011-021-03018-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/04/2021] [Indexed: 12/29/2022]
Abstract
Rice is the staple diet to half of the world's population, being a major source of carbohydrates, vitamins, and some essential elements. However, rice naturally contains low amounts of essential minerals such as iron (Fe) and zinc (Zn), which are drastically decreased after milling. Thus, populations that consume mostly rice may have micronutrient deficiency, which is associated with different diseases. On the other hand, rice irrigated by flooding has a high ability to accumulate arsenic (As) in the grain. Therefore, when rice is grown in areas with contaminated soil or irrigation water, it represents a risk factor for consumers, since As is associated with cancer and other diseases. Different strategies have been used to mitigate micronutrient deficiencies such as Fe and Zn and to prevent As from entering the food chain. Each strategy has its positive and its negative sides. The development of genetically biofortified rice plants with Fe and Zn and with low As accumulation is one of the most promising strategies, since it does not represent an additional cost for farmers, and gives benefits to consumers as well. Considering the importance of genetic improvement (traditional or molecular) to decrease the impact of micronutrient deficiencies such as Fe and Zn and contamination with As, this review aimed to summarize the major efforts, advances, and challenges for genetic biofortification of Fe and Zn and decrease in As content in rice grains.
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Affiliation(s)
- Vívian Ebeling Viana
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Latóia Eduarda Maltzahn
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Camila Pegoraro
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil.
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de Oliveira VF, Busanello C, Viana VE, Stafen CF, Pedrolo AM, Paniz FP, Pedron T, Pereira RM, Rosa SA, de Magalhães Junior AM, Costa de Oliveira A, Batista BL, Pegoraro C. Assessing mineral and toxic elements content in rice grains grown in southern Brazil. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Maltzahn LE, Zenker SG, Lopes JL, Pereira RM, Verdi CA, Rother V, Busanello C, Viana VE, Batista BL, de Oliveira AC, Pegoraro C. Brazilian Genetic Diversity for Desirable and Undesirable Elements in the Wheat Grain. Biol Trace Elem Res 2021; 199:2351-2365. [PMID: 32797369 DOI: 10.1007/s12011-020-02338-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/06/2020] [Indexed: 11/30/2022]
Abstract
Micronutrient deficiency affects billions of people, especially in countries where the diet is low in diversity with inadequate consumption of fruits, vegetables, and animal-source foods, and higher consumption of staple food, i.e., cereals, that have low concentrations of micronutrients. Genetic biofortification is a strategy to mitigate this problem and ensure nutritional security. Wheat is a target of genetic biofortification since it contributes significantly to the caloric requirement. The biofortification process involves a screening related to the presence of genetic variability for grain mineral content. Also, the accumulation of toxic elements must be considered to ensure food safety, because if ingested above the allowed concentrations, it represents health risks. In this sense, this study aimed to quantify the micronutrients iron, zinc, copper, selenium, and manganese and toxic elements arsenic and cadmium in a Brazilian wheat panel grown in Southern Brazil. The presence of genetic variability for the accumulation of micronutrients in the grain was detected; however, we observed that only the copper and manganese accumulation meet the human daily requirements. Iron, zinc, and selenium were detected in insufficient concentration to meet the daily demand. Arsenic and cadmium accumulation were not detected in wheat grain. The wheat genotypes grown in Brazil displayed a similar profile to that found in other countries which may be due to common high-yield breeding goals and the narrowing of the genetic variability, observed worldwide. Thus, the wheat genetic biofortification success in Brazil depends on the introduction of foreign genotypes, landraces, and wild relatives.
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Affiliation(s)
- Latóia Eduarda Maltzahn
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Stefânia Garcia Zenker
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Jennifer Luz Lopes
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Rodrigo Mendes Pereira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Campus Santo André, Santo André, SP, 09210-580, Brazil
| | - Cezar Augusto Verdi
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Vianei Rother
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Carlos Busanello
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Vívian Ebeling Viana
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Bruno Lemos Batista
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Campus Santo André, Santo André, SP, 09210-580, Brazil
| | - Antonio Costa de Oliveira
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Camila Pegoraro
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil.
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de Freitas KEJ, dos Santos RS, Busanello C, de Carvalho Victoria F, Lopes JL, Wing RA, de Oliveira AC. Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza. Plants 2021; 10:plants10061057. [PMID: 34070565 PMCID: PMC8229393 DOI: 10.3390/plants10061057] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/18/2022]
Abstract
Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar’s genetics, but the way in which their genes express different phenotypes is not well understood. Further analysis of variation of grain quality genes using new information obtained from the wild relatives of rice should provide important insights into the evolution and potential use of these genetic resources. All analyses were conducted using bioinformatics approaches. The analysis of the protein sequences of grain quality genes across the Oryza suggest that the deletion/mutation of amino acids in active sites result in variations that can negatively affect specific steps of starch biosynthesis in the endosperm. On the other hand, the complete deletion of some genes in the wild species may not affect the amylose content. Here we present new insights for Starch Synthesis-Related Genes (SSRGs) evolution from starch-specific rice phenotypes.
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Affiliation(s)
- Karine E. Janner de Freitas
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | | | - Carlos Busanello
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Filipe de Carvalho Victoria
- Núcleo de Estudos da Vegetação Antártica—NEVA, Campus São Gabriel Federal do Pampa (UNIPAMPA), São Gabriel 97030, Brazil;
| | - Jennifer Luz Lopes
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Rod A. Wing
- The School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, AZ 97030, USA;
- Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal 23955, Saudi Arabia
| | - Antonio Costa de Oliveira
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
- Correspondence:
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de Oliveira Maximino JV, Barros LM, Pereira RM, de Santi II, Aranha BC, Busanello C, Viana VE, Freitag RA, Batista BL, Costa de Oliveira A, Pegoraro C. Mineral and Fatty Acid Content Variation in White Oat Genotypes Grown in Brazil. Biol Trace Elem Res 2021; 199:1194-1206. [PMID: 32537719 DOI: 10.1007/s12011-020-02229-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/30/2020] [Indexed: 11/29/2022]
Abstract
A healthy diet is directly associated with a nutrient-rich and toxic contaminant poor intake. A diet poor in diversity can lead to micronutrient deficiency. The intake of functional foods can provide benefits in the prevention and treatment of diseases. Oats are a functional food; are a source of soluble fiber, lipids, proteins, vitamins, minerals, and polyphenols; and are low in carbohydrate content. Thus, in this study, we characterize mineral accumulation, fatty acid composition, and the absence of contaminants in oat genotypes to evaluate the potential of this cereal as food to minimize the effects of micronutrient deficiency. Most of the oat genotypes showed higher mineral levels than other cereals such as wheat, rice, and maize. FAEM 5 Chiarasul, Barbarasul, UPFA Ouro, URS Altiva, URS Brava, and URS Taura showed higher iron concentration while URS Brava showed the highest zinc concentration. The oat genotypes did not show significant arsenic, strontium, and cadmium accumulation. Considering the accumulation of trace elements in the grain, little genetic diversity among the analyzed oat accessions was detected, dividing into two groups. Regarding fatty acid composition, IPR Afrodite, FAEM 4 Carlasul, FAEM 5 Chiarasul, URS Taura, Barbarasul, and URS 21 showed higher essential fatty acid concentrations. These genotypes can be used in crosses with URS Brava, which displayed a higher Fe and Zn accumulation and is genetically distant from the other cultivars. Oat is a functional food showing ability for the accumulation of minerals and also essential fatty acids.
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Affiliation(s)
- Josiane Vargas de Oliveira Maximino
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Lílian Moreira Barros
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Rodrigo Mendes Pereira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Campus Santo André, Santo Andre, SP, 09210-580, Brazil
| | - Ivandra Ignes de Santi
- Centro de Ciências Químicas, Farmacêuticas e de Alimentos, Departamento de Química Orgânica, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Bianca Camargo Aranha
- Faculdade de Agronomia Eliseu Maciel, Departamento de Ciência e Tecnologia Agroindustrial, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Carlos Busanello
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Vívian Ebeling Viana
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Rogério Antonio Freitag
- Centro de Ciências Químicas, Farmacêuticas e de Alimentos, Departamento de Química Orgânica, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Bruno Lemos Batista
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Campus Santo André, Santo Andre, SP, 09210-580, Brazil
| | - Antonio Costa de Oliveira
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil
| | - Camila Pegoraro
- Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Pelotas, RS, 96010-610, Brazil.
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11
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Basso MF, Lourenço-Tessutti IT, Busanello C, Pinto CEM, de Oliveira Freitas E, Ribeiro TP, de Almeida Engler J, de Oliveira AC, Morgante CV, Alves-Ferreira M, Grossi-de-Sa MF. Insights obtained using different modules of the cotton uceA1.7 promoter. Planta 2020; 251:56. [PMID: 32006110 DOI: 10.1007/s00425-020-03348-8] [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: 10/28/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The structure of the cotton uceA1.7 promoter and its modules was analyzed; the potential of their key sequences has been confirmed in different tissues, proving to be a good candidate for the development of new biotechnological tools. Transcriptional promoters are among the primary genetic engineering elements used to control genes of interest (GOIs) associated with agronomic traits. Cotton uceA1.7 was previously characterized as a constitutive promoter with activity higher than that of the constitutive promoter from the Cauliflower mosaic virus (CaMV) 35S gene in various plant tissues. In this study, we generated Arabidopsis thaliana homozygous events stably overexpressing the gfp reporter gene driven by different modules of the uceA1.7 promoter. The expression level of the reporter gene in different plant tissues and the transcriptional stability of these modules was determined compared to its full-length promoter and the 35S promoter. The full-length uceA1.7 promoter exhibited higher activity in different plant tissues compared to the 35S promoter. Two modules of the promoter produced a low and unstable transcription level compared to the other promoters. The other two modules rich in cis-regulatory elements showed similar activity levels to full-length uceA1.7 and 35S promoters but were less stable. This result suggests the location of a minimal portion of the promoter that is required to initiate transcription properly (the core promoter). Additionally, the full-length uceA1.7 promoter containing the 5'-untranslated region (UTR) is essential for higher transcriptional stability in various plant tissues. These findings confirm the potential use of the full-length uceA1.7 promoter for the development of new biotechnological tools (NBTs) to achieve higher expression levels of GOIs in, for example, the root or flower bud for the efficient control of phytonematodes and pest-insects, respectively, in important crops.
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Affiliation(s)
- Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
| | | | - Carlos Busanello
- Federal University of Pelotas, Capão Do Leão, RS, 96160-000, Brazil
| | - Clidia Eduarda Moreira Pinto
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Elínea de Oliveira Freitas
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Thuanne Pires Ribeiro
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
| | | | | | - Carolina Vianna Morgante
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Embrapa Semi Arid, Petrolina, PE, 56302-970, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
- Catholic University of Brasília, Brasília, DF, 71966-700, Brazil.
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12
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Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. Front Plant Sci 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
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Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
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13
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Bresolin APS, Dos Santos RS, Wolter RCD, de Sousa RO, da Maia LC, Costa de Oliveira A. Iron tolerance in rice: an efficient method for performing quick early genotype screening. BMC Res Notes 2019; 12:361. [PMID: 31238948 PMCID: PMC6593560 DOI: 10.1186/s13104-019-4362-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/05/2019] [Indexed: 11/25/2022] Open
Abstract
Objectives This study was conducted to establish a method for early, quick and cheap screening of iron excess tolerance in rice (Oryza sativa L.) cultivars. Results Based on the experiments, iron excess leads to reduction in shoot length (SL) and this can be a useful characteristic for adequate screening of tolerant genotypes. The sensitive genotypes Nipponbare and BR-IRGA 409 indicated higher accumulation of iron in their tissues while BRS-Agrisul and Epagri 108 also accumulated iron, but at lower concentrations. BR-IRGA 410 displayed an intermediate phenotype regarding iron accumulation. No changes in shoot Cu content can be observed when comparing treatments. On the other hand, an increase was seen for Zn and Mn when shoots are subjected to Fe2+ excess. Fe stress at a lower concentration than 7 mM increased Zn but decreased Mn contents in shoots of BR-IRGA 409. Strong positive correlations were found here for Fe × Zn (0.93); Fe × Mn (0.97) and Zn × Mn (0.92), probably due to the Fe-induced activation of bivalent cation transporters. Results show that genotypes scored as sensitive present higher concentration of Fe in shoots and this is an efficient method to characterize rice cultivars regarding iron response. Electronic supplementary material The online version of this article (10.1186/s13104-019-4362-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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14
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Venske E, dos Santos RS, Busanello C, Gustafson P, Costa de Oliveira A. Bread wheat: a role model for plant domestication and breeding. Hereditas 2019; 156:16. [PMID: 31160891 PMCID: PMC6542105 DOI: 10.1186/s41065-019-0093-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/20/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Bread wheat is one of the most important crops in the world. Its domestication coincides with the beginning of agriculture and since then, it has been constantly under selection by humans. Its breeding has followed millennia of cultivation, sometimes with unintended selection on adaptive traits, and later by applying intentional but empirical selective pressures. For more than one century, wheat breeding has been based on science, and has been constantly evolving due to on farm agronomy and breeding program improvements. The aim of this work is to briefly review wheat breeding, with emphasis on the current advances. DISCUSSION Improving yield potential, resistance/tolerance to biotic and abiotic stresses, and baking quality, have been priorities for breeding this cereal, however, new objectives are arising, such as biofortification enhancement. The narrow genetic diversity and complexity of its genome have hampered the breeding progress and the application of biotechnology. Old approaches, such as the introgression from relative species, mutagenesis, and hybrid breeding are strongly reappearing, motivated by an accumulation of knowledge and new technologies. A revolution has taken place regarding the use of molecular markers whereby thousands of plants can be routinely genotyped for thousands of loci. After 13 years, the wheat reference genome sequence and annotation has finally been completed, and is currently available to the scientific community. Transgenics, an unusual approach for wheat improvement, still represents a potential tool, however it is being replaced by gene editing, whose technology along with genomic selection, speed breeding, and high-throughput phenotyping make up the most recent frontiers for future wheat improvement. FINAL CONSIDERATION Agriculture and plant breeding are constantly evolving, wheat has played a major role in these processes and will continue through decades to come.
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Affiliation(s)
- Eduardo Venske
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Railson Schreinert dos Santos
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Carlos Busanello
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Perry Gustafson
- Plant Sciences Division, 1–32 Agriculture, University of Missouri, Columbia, MO 65211 USA
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
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15
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Venske E, dos Santos RS, Farias DDR, Rother V, da Maia LC, Pegoraro C, Costa de Oliveira A. Meta-Analysis of the QTLome of Fusarium Head Blight Resistance in Bread Wheat: Refining the Current Puzzle. Front Plant Sci 2019; 10:727. [PMID: 31263469 PMCID: PMC6585393 DOI: 10.3389/fpls.2019.00727] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Background: Fusarium Head Blight (FHB) is a worldwide devastating disease of bread wheat (Triticum aestivum L.). Genetic resistance is the most effective way to control FHB and many QTL related to this trait have been mapped on the wheat genetic map. This information, however, must be refined to be more efficiently used in breeding programs and for the advance of the basic research. The objective of the present study was to in-depth analyze the QTLome of FHB resistance in bread wheat, further integrating genetic, genomic, and transcriptomic data, aiming to find candidate genes. Methods: An exhaustive bibliographic review on 76 scientific papers was carried out collecting information about QTL related to FHB resistance mapped on bread wheat. A dense genetic consensus map with 572,862 loci was generated for QTL projection. Meta-analysis could be performed on 323 QTL. Candidate gene mining was carried out within the most refined loci, containing genes that were cross-validated with publicly available transcriptional expression data of wheat under Fusarium infection. Most highlighted genes were investigated for protein evidence. Results: A total of 556 QTL were found in the literature, distributed on all sub-genomes and chromosomes of wheat. Meta-analysis generated 65 meta-QTL, and this refinement allows one to find markers more tightly linked to these regions. Candidate gene mining within the most refined meta-QTL, meta-QTL 1/chr. 3B, harvested 324 genes and transcriptional data cross-validated 10 of these genes, as responsive to FHB. One is of these genes encodes a Glycosiltransferase and the other encodes for a Cytochrome P450, and these such proteins have already been verified as being responsible for FHB resistance, but the remaining eight genes still have to be further studied, as promising loci for breeding. Conclusions: The QTLome of FHB resistance in wheat was successfully assembled and a refinement in terms of number and length of loci was obtained. The integration of the QTLome with genomic and transcriptomic data has allowed for the discovery of promising candidate genes for use in breeding programs.
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Affiliation(s)
- Eduardo Venske
- Crop Science Department, Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, Brazil
| | | | - Daniel da Rosa Farias
- Instituto Federal de Educação, Ciência e Tecnologia Catarinense (IFC), Araquari, Brazil
| | - Vianei Rother
- Crop Science Department, Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, Brazil
| | - Luciano Carlos da Maia
- Crop Science Department, Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, Brazil
| | - Camila Pegoraro
- Crop Science Department, Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, Brazil
| | - Antonio Costa de Oliveira
- Crop Science Department, Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, Brazil
- *Correspondence: Antonio Costa de Oliveira
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16
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Venske E, Stafen CF, de Oliveira VF, da Maia LC, de Magalhães Junior AM, McNally KL, Costa de Oliveira A, Pegoraro C. Genetic diversity, linkage disequilibrium, and population structure in a panel of Brazilian rice accessions. J Appl Genet 2018; 60:27-31. [PMID: 30353473 DOI: 10.1007/s13353-018-0475-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 02/01/2023]
Abstract
Narrowing of genetic diversity and the quantitative nature of most agronomic traits is a challenge for rice breeding. Genome-wide association studies have a great potential to identify important variation in loci underlying quantitative and complex traits; however, before performing the analysis, it is important to assess parameters of the genotypic data and population under study, to improve the accuracy of the genotype-phenotype associations. The aim of this study was to access the genetic diversity, linkage disequilibrium, and population structure of a working panel of Brazilian and several introduced rice accessions, which are currently being phenotyped for a vast number of traits to undergo association mapping. Ninety-four accessions were genotyped with 7098 SNPs, and after filtering for higher call rates and removing rare variants, 93 accessions and 4973 high-quality SNPs remained for subsequent analyses and association studies. The overall mean of the polymorphic information content, heterozygosity, and gene diversity of the SNPs was comparable to other rice panels. The r2 measure of linkage disequilibrium decayed to 0.25 in approximately 150 kb, a slow decay, explained by the autogamous nature of rice and the small size of the panel. Regarding population structure, eight groups were formed according to Bayesian clustering. Principle components and neighbor-joining analyses were able to distinguish part of the groups formed, mainly regarding the sub-species indica and japonica. Our results demonstrate that the population and SNPs are of high quality for association mapping.
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Affiliation(s)
- Eduardo Venske
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Universidade Federal de Pelotas, Campus Universitário do Capão do Leão, PO Box 354, Pelotas, Rio Grande do Sul, 96010-900, Brazil
| | - Cássia Fernanda Stafen
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Universidade Federal de Pelotas, Campus Universitário do Capão do Leão, PO Box 354, Pelotas, Rio Grande do Sul, 96010-900, Brazil
| | - Victoria Freitas de Oliveira
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Universidade Federal de Pelotas, Campus Universitário do Capão do Leão, PO Box 354, Pelotas, Rio Grande do Sul, 96010-900, Brazil
| | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Universidade Federal de Pelotas, Campus Universitário do Capão do Leão, PO Box 354, Pelotas, Rio Grande do Sul, 96010-900, Brazil
| | | | - Kenneth L McNally
- International Rice Research Institute, Te-Tzu Chang Genetic Resources Center, 4031, Los Baños, Laguna, Philippines
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Universidade Federal de Pelotas, Campus Universitário do Capão do Leão, PO Box 354, Pelotas, Rio Grande do Sul, 96010-900, Brazil.
| | - Camila Pegoraro
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Universidade Federal de Pelotas, Campus Universitário do Capão do Leão, PO Box 354, Pelotas, Rio Grande do Sul, 96010-900, Brazil
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17
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Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, da Rosa Farias D, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YIC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 2018; 50:1618. [PMID: 30291357 DOI: 10.1038/s41588-018-0261-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.
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Affiliation(s)
- Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Phyzen Genomics Institute, Phyzen, Inc., Seoul, South Korea
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,International Rice Research Institute, Los Baños, Philippines
| | - Derrick J Zwickl
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Li Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Chengjun Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Aiko Iwata
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Jose Luis Goicoechea
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Yi Liao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Julie Jacquemin
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Crop Biodiversity and Breeding Informatics Group, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Claude Becker
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Carlos E M Londono
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Xiang Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Paul Sanchez
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Rice Experiment Station, Biggs, CA, USA
| | - Andrea Zuccolo
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jetty S S Ammiraju
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,DuPont-Pioneer, Johnston, IA, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ann Danowitz
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Luis F Rivera
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,BIOS-Parque Los Yarumos, Manizales, Colombia
| | - Andrea R Gschwend
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Institute of Botany, National Taiwan University, Taipei, Taiwan
| | - Shu-Min Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jhih-Wun Zeng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan
| | - Qiang Zhao
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
| | - Qi Feng
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Richard Cooke
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Daniel da Rosa Farias
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | - Railson S Dos Santos
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Kevin G Nyberg
- Department of Biology, University of Maryland, College Park, MD, USA
| | | | - Ramil Mauleon
- International Rice Research Institute, Los Baños, Philippines
| | | | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Dave Flowers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kshirod K Jena
- International Rice Research Institute, Los Baños, Philippines
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bin Han
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Nori Kurata
- National Institute of Genetics, Mishima, Japan
| | | | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Robert W. Holley Center for Agriculture and Health, US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA. .,International Rice Research Institute, Los Baños, Philippines. .,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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18
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Viana VE, Busanello C, da Maia LC, Pegoraro C, Costa de Oliveira A. Activation of rice WRKY transcription factors: an army of stress fighting soldiers? Curr Opin Plant Biol 2018; 45:268-275. [PMID: 30060992 DOI: 10.1016/j.pbi.2018.07.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 05/04/2023]
Abstract
Rice WRKYs comprise a large family of transcription factors and present remarkable structure features and a unique DNA binding site. Their importance in plants goes beyond the response to stressful stimuli, since they participate in hormonal pathways and developmental processes. Indeed, the majority of WRKYs present an independent activation since they are able to perform self-transcriptional regulation. However, some WRKY activation depends on epigenetic and transcript regulation by micro RNAs. Their protein function depends, almost always, on the posttranslational changes. Taking to account its properties of auto-activation, all these regulators process are extremely important for complete WRKY regulation. In this sense, here we provide an overview of transcriptional activation and posttranscriptional and posttranslational regulation of rice WRKY genes under stresses.
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Affiliation(s)
- Vívian Ebeling Viana
- Graduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas-RS, Brazil; Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Carlos Busanello
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Camila Pegoraro
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Antonio Costa de Oliveira
- Graduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas-RS, Brazil; Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil.
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19
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Finatto T, Viana VE, Woyann LG, Busanello C, da Maia LC, de Oliveira AC. Can WRKY transcription factors help plants to overcome environmental challenges? Genet Mol Biol 2018; 41:533-544. [PMID: 30235398 PMCID: PMC6136380 DOI: 10.1590/1678-4685-gmb-2017-0232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
WRKY transcription factors (TFs) are responsible for the regulation of genes responsive to many plant growth and developmental cues, as well as to biotic and abiotic stresses. The modulation of gene expression by WRKY proteins primarily occurs by DNA binding at specific cis-regulatory elements, the W-box elements, which are short sequences located in the promoter region of certain genes. In addition, their action can occur through interaction with other TFs and the cellular transcription machinery. The current genome sequences available reveal a relatively large number of WRKY genes, reaching hundreds of copies. Recently, functional genomics studies in model plants have enabled the identification of function and mechanism of action of several WRKY TFs in plants. This review addresses the more recent studies in plants regarding the function of WRKY TFs in both model and crop plants for coping with environmental challenges, including a wide variety of abiotic and biotic stresses.
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Affiliation(s)
- Taciane Finatto
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vívian Ebeling Viana
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Leomar Guilherme Woyann
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carlos Busanello
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano Carlos da Maia
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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20
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dos Santos FIDC, Marini N, dos Santos RS, Hoffman BSF, Alves-Ferreira M, de Oliveira AC. Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity. PLoS One 2018; 13:e0193418. [PMID: 29494624 PMCID: PMC5832244 DOI: 10.1371/journal.pone.0193418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/09/2018] [Indexed: 11/18/2022] Open
Abstract
Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here.
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21
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dos Santos RS, Farias DDR, Pegoraro C, Rombaldi CV, Fukao T, Wing RA, de Oliveira AC. Evolutionary analysis of the SUB1 locus across the Oryza genomes. Rice (N Y) 2017; 10:4. [PMID: 28176282 PMCID: PMC5296262 DOI: 10.1186/s12284-016-0140-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/20/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Tolerance to complete submergence is recognized in a limited number of Asian rice (Oryza sativa L.) varieties, most of which contain submergence-inducible SUB1A on the polygenic SUBMERGENCE-1 (SUB1) locus. It has been shown that the SUB1 locus encodes two Ethylene-Responsive Factor (ERF) genes, SUB1B and SUB1C, in all O. sativa varieties. These genes were also found in O rufipogon and O nivara, wild relatives of O. sativa. However, detailed analysis of the polygenic locus in other Oryza species has not yet been made. FINDINGS Chromosomal location, phylogenetic, and gene structure analyses have revealed that the SUB1 locus is conserved in the long arm of chromosome 9 in most Oryza species. We also show that the SUB1A-like gene of O. nivara is on chromosome 1 and that Leersia perrieri, a grass-tolerant to deep-flooding, presents three ERF genes in the SUB1 locus. CONCLUSION We provide here a deeper insight into the evolutionary origin and variation of the SUB1 locus and raise the possibility that an association of these genes with flooding tolerance in L. perrieri may exist.
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Affiliation(s)
- Railson Schreinert dos Santos
- Technology Development Center (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Daniel da Rosa Farias
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Camila Pegoraro
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Cesar Valmor Rombaldi
- Technology Development Center (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Takeshi Fukao
- Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, USA
| | - Rod A. Wing
- The School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, USA
| | - Antonio Costa de Oliveira
- Technology Development Center (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
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22
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da Maia LC, Cadore PRB, Benitez LC, Danielowski R, Braga EJB, Fagundes PRR, Magalhães AM, Costa de Oliveira A. Transcriptome profiling of rice seedlings under cold stress. Funct Plant Biol 2017; 44:419-429. [PMID: 32480575 DOI: 10.1071/fp16239] [Citation(s) in RCA: 15] [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: 07/10/2016] [Accepted: 11/11/2016] [Indexed: 05/27/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important species for food production worldwide, besides being an excellent genetic model among the grasses. Cold is one of the major abiotic factors reducing rice yield, primarily affecting germination and reproduction phases. Currently, the RNAseq technique allows the identification of differential expressed genes in response to a given treatment, such as cold stress. In the present work, a transcriptome (RNAseq) analysis was performed in the V3 phase for contrasting genotypes Oro (tolerant) and Tio Taka (sensitive), in response to cold (13°C). A total of 241 and 244M readings were obtained, resulting in the alignment of 25.703 and 26.963 genes in genotypes Oro and Tio Taka respectively. The analyses revealed 259 and 5579 differential expressed genes in response to cold in the genotypes Oro and Tio Taka respectively. Ontology classes with larger changes were metabolic process ~27%, cellular process ~21%, binding ~30% and catalytic activity ~22%. In the genotype Oro, 141 unique genes were identified, 118 were common between Oro and Tio Taka and 5461 were unique to Tio Taka. Genes involved in metabolic routes of signal transduction, phytohormones, antioxidant system and biotic stress were identified. These results provide an understanding that breeding for a quantitative trait, such as cold tolerance at germination, several gene loci must be simultaneously selected. In general, few genes were identified, but it was not possible to associate only one gene function as responsible for the cultivar tolerance; since different genes from different metabolic routes were identified. The genes described in the present work will be useful for future investigations and for the detailed validation in marker assisted selection projects for cold tolerance in the germination of rice.
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Affiliation(s)
- Luciano C da Maia
- Universidade Federal de Pelotas, Department of Plant Sciences, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil
| | - Pablo R B Cadore
- Universidade Federal de Pelotas, Department of Plant Sciences, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil
| | - Leticia C Benitez
- Universidade Federal de Pelotas, Department of Botany, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil
| | - Rodrigo Danielowski
- Universidade Federal de Pelotas, Department of Plant Sciences, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil
| | - Eugenia J B Braga
- Universidade Federal de Pelotas, Department of Botany, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil
| | - Paulo R R Fagundes
- EMBRAPA - Brazilian Agricultural Research Corporation, BR-392 Road, Km 78, 9° Distrito, Monte Bonito, Pelotas/RS - Brazil
| | - Ariano M Magalhães
- EMBRAPA - Brazilian Agricultural Research Corporation, BR-392 Road, Km 78, 9° Distrito, Monte Bonito, Pelotas/RS - Brazil
| | - Antonio Costa de Oliveira
- Universidade Federal de Pelotas, Department of Plant Sciences, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil
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23
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dos Santos RS, de Araujo AT, Pegoraro C, de Oliveira AC. Dealing with iron metabolism in rice: from breeding for stress tolerance to biofortification. Genet Mol Biol 2017; 40:312-325. [PMID: 28304072 PMCID: PMC5452141 DOI: 10.1590/1678-4685-gmb-2016-0036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 02/18/2016] [Accepted: 09/22/2016] [Indexed: 12/23/2022] Open
Abstract
Iron is a well-known metal. Used by humankind since ancient times in many different ways, this element is present in all living organisms, where, unfortunately, it represents a two-way problem. Being an essential block in the composition of different proteins and metabolic pathways, iron is a vital component for animals and plants. That is why iron deficiency has a severe impact on the lives of different organisms, including humans, becoming a major concern, especially in developing countries where access to adequate nutrition is still difficult. On the other hand, this metal is also capable of causing damage when present in excess, becoming toxic to cells and affecting the whole organism. Because of its importance, iron absorption, transport and storage mechanisms have been extensively investigated in order to design alternatives that may solve this problem. As the understanding of the strategies that plants use to control iron homeostasis is an important step in the generation of improved plants that meet both human agricultural and nutritional needs, here we discuss some of the most important points about this topic.
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Affiliation(s)
- Railson Schreinert dos Santos
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
- Technology Development Center (CDTec), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
| | | | - Camila Pegoraro
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
- Technology Development Center (CDTec), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
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24
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Ferrari M, Baldin MM, Schutze IX, Garcia C, Possebon B, Fialho GS, Botton M, Oliveira ACD, Maia LCD. POTENCIAL FISIOLÓGICO DE ESPÉCIES OLERÍCOLAS SUBMETIDAS A DIFERENTES ESPECTROS DE LUZ. RevistaUnivap 2016. [DOI: 10.18066/revistaunivap.v22i40.1020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
O objetivo do trabalho foi avaliar o efeito de diferentes espectros de luz sobre o potencial fisiológico de espécies olerícolas. O experimento foi conduzido em delineamento inteiramente casualizado, no esquema fatorial três por cinco, com quatro repetições. As três espécies testadas foram alface (Lactuca sativa L.), rúcula (Eruca sativa Mill.) e couve chinesa (Brassica rapa var. pekinensis). Os cinco espectros de luz utilizados foram: vermelho, azul, amarelo, branco e ausência de luz. O teste de germinação foi conduzido em germinador tipo BOD, com temperatura constante de 25°C. Para a alface o espectro azul revela efeito negativo sobre as variáveis primeira contagem, percentual de germinação e comprimento de radícula. Para espécies de rúcula e couve chinesa, o espectro de luz vermelha e amarela apresentaram os melhores resultados para as variáveis estudadas.
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25
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Ezquer I, Mizzotti C, Nguema-Ona E, Gotté M, Beauzamy L, Viana VE, Dubrulle N, Costa de Oliveira A, Caporali E, Koroney AS, Boudaoud A, Driouich A, Colombo L. The Developmental Regulator SEEDSTICK Controls Structural and Mechanical Properties of the Arabidopsis Seed Coat. Plant Cell 2016; 28:2478-2492. [PMID: 27624758 PMCID: PMC5134981 DOI: 10.1105/tpc.16.00454] [Citation(s) in RCA: 59] [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: 06/13/2016] [Revised: 08/22/2016] [Accepted: 09/09/2016] [Indexed: 05/10/2023]
Abstract
Although many transcription factors involved in cell wall morphogenesis have been identified and studied, it is still unknown how genetic and molecular regulation of cell wall biosynthesis is integrated into developmental programs. We demonstrate by molecular genetic studies that SEEDSTICK (STK), a transcription factor controlling ovule and seed integument identity, directly regulates PMEI6 and other genes involved in the biogenesis of the cellulose-pectin matrix of the cell wall. Based on atomic force microscopy, immunocytochemistry, and chemical analyses, we propose that structural modifications of the cell wall matrix in the stk mutant contribute to defects in mucilage release and seed germination under water-stress conditions. Our studies reveal a molecular network controlled by STK that regulates cell wall properties of the seed coat, demonstrating that developmental regulators controlling organ identity also coordinate specific aspects of cell wall characteristics.
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Affiliation(s)
- Ignacio Ezquer
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, 20133 Milan, Italy
| | - Chiara Mizzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Eric Nguema-Ona
- Laboratoire Glycobiologie et Matrice Extracellulaire, Normandie Université, UNIROUEN, Végétal, Agronomie, Sol, et Innovation (VASI), 76821 Mont-Saint-Aignan, France
- Centre Mondial de l'Innovation-Laboratoire de Nutrition Végétale, 35400 Saint Malo, France
| | - Maxime Gotté
- Laboratoire Glycobiologie et Matrice Extracellulaire, Normandie Université, UNIROUEN, Végétal, Agronomie, Sol, et Innovation (VASI), 76821 Mont-Saint-Aignan, France
| | - Léna Beauzamy
- Laboratoire de Reproduction et Développement des Plantes, INRA, CNRS, ENS, UCB Lyon 1, Université de Lyon, 69364 Lyon Cedex 07, France
| | - Vivian Ebeling Viana
- Plant Genomics and Breeding Center, Technology Development Center, Federal University of Pelotas, RS 96010-900, Brazil
| | - Nelly Dubrulle
- Laboratoire de Reproduction et Développement des Plantes, INRA, CNRS, ENS, UCB Lyon 1, Université de Lyon, 69364 Lyon Cedex 07, France
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Technology Development Center, Federal University of Pelotas, RS 96010-900, Brazil
| | - Elisabetta Caporali
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Abdoul-Salam Koroney
- Laboratoire Glycobiologie et Matrice Extracellulaire, Normandie Université, UNIROUEN, Végétal, Agronomie, Sol, et Innovation (VASI), 76821 Mont-Saint-Aignan, France
| | - Arezki Boudaoud
- Laboratoire de Reproduction et Développement des Plantes, INRA, CNRS, ENS, UCB Lyon 1, Université de Lyon, 69364 Lyon Cedex 07, France
| | - Azeddine Driouich
- Laboratoire Glycobiologie et Matrice Extracellulaire, Normandie Université, UNIROUEN, Végétal, Agronomie, Sol, et Innovation (VASI), 76821 Mont-Saint-Aignan, France
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, 20133 Milan, Italy
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26
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do Amaral MN, Arge LWP, Benitez LC, Danielowski R, Silveira SFDS, Farias DDR, de Oliveira AC, da Maia LC, Braga EJB. Comparative transcriptomics of rice plants under cold, iron, and salt stresses. Funct Integr Genomics 2016; 16:567-79. [PMID: 27468828 DOI: 10.1007/s10142-016-0507-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/12/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
Abiotic stresses such as salinity, iron toxicity, and low temperatures are the main limiting factors of rice (Oryza sativa L.) yield. The elucidation of the genes involved in responses to these stresses is extremely important to understand the mechanisms that confer tolerance, as well as for the development of cultivars adapted to these conditions. In this study, the RNA-seq technique was used to compare the transcriptional profile of rice leaves (cv. BRS Querência) in stage V3, exposed to cold, iron, and salt stresses for 24 h. A range of 41 to 51 million reads was aligned, in which a total range of 88.47 to 89.21 % was mapped in the reference genome. For cold stress, 7905 differentially expressed genes (DEGs) were observed, 2092 for salt and 681 for iron stress; 370 of these were common to the three DEG stresses. Functional annotation by software MapMan demonstrated that cold stress usually promoted the greatest changes in the overall metabolism, and an enrichment analysis of overrepresented gene ontology (GO) terms showed that most of them are contained in plastids, ribosome, and chloroplasts. Saline stress induced a more complex interaction network of upregulated overrepresented GO terms with a relatively low number of genes compared with cold stress. Our study demonstrated a high number of differentially expressed genes under cold stress and a greater relationship between salt and iron stress levels. The physiological process most affected at the molecular level by the three stresses seems to be photosynthesis.
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27
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Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, de Oliveira AC, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Tuberosa R, Valliyodan B, Varshney RK, Yano M. Global agricultural intensification during climate change: a role for genomics. Plant Biotechnol J 2016; 14:1095-8. [PMID: 26360509 PMCID: PMC5049667 DOI: 10.1111/pbi.12467] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 05/25/2015] [Revised: 07/23/2015] [Accepted: 08/06/2015] [Indexed: 05/03/2023]
Abstract
Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.
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Affiliation(s)
- Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jacqueline Batley
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia
| | | | - John Bryant
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed Association, Nasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | | | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agriculture, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Leland J Cseke
- Department of Biological Sciences Huntsville, The University of Alabama in Huntsville, Huntsville, AL, USA
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - David Edwards
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | | | - Robert Henry
- The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, Australia
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Glenn Thomas Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | | | - Mike Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - David Lightfoot
- College of Agricultural Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the Future, Kuala Lumpur, Malaysia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | - Rajeev K Varshney
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Centre of Excellence in Genomics, International Crops Research Institute for the Semi- Arid Tropics (ICRISAT), Hyderabad, India
| | - Masahiro Yano
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Japan
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Pegoraro C, Tadiello A, Girardi CL, Chaves FC, Quecini V, de Oliveira AC, Trainotti L, Rombaldi CV. Transcriptional regulatory networks controlling woolliness in peach in response to preharvest gibberellin application and cold storage. BMC Plant Biol 2015; 15:279. [PMID: 26582034 PMCID: PMC4652400 DOI: 10.1186/s12870-015-0659-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/03/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Postharvest fruit conservation relies on low temperatures and manipulations of hormone metabolism to maintain sensory properties. Peaches are susceptible to chilling injuries, such as 'woolliness' that is caused by juice loss leading to a 'wooly' fruit texture. Application of gibberellic acid at the initial stages of pit hardening impairs woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcriptional profiling to investigate the effects of gibberellic acid application and cold storage on harvested peaches. RESULTS Approximately half of the investigated genes exhibited significant differential expression in response to the treatments. Cellular and developmental process gene ontologies were overrepresented among the differentially regulated genes, whereas sequences in cell death and immune response categories were underrepresented. Gene set enrichment demonstrated a predominant role of cold storage in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone responses exhibited a more complex transcriptional response, indicating an extensive network of crosstalk between hormone signaling and low temperatures. Time course transcriptional analyses demonstrate the large contribution of gene expression regulation on the biochemical changes leading to woolliness in peach. CONCLUSION Overall, our results provide insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach and suggest that hormone mediated reprogramming previous to pit hardening affects the onset of chilling injuries.
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Affiliation(s)
- Camila Pegoraro
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Campus UFPel Capão do Leão, Pelotas, RS, 96010-900, Brazil.
- Current Address: Embrapa Uva e Vinho, Rua Livramento 515, Bento Gonçalves, RS, 95700-000, Brazil.
| | - Alice Tadiello
- Department of Biology, University of Padova, Viale G. Colombo, Padova, 3, 35121, Italy.
- Current Address: Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, San Michele all'Adige, Trento, 38010, Italy.
| | - César L Girardi
- Embrapa Uva e Vinho, Rua Livramento 515, Bento Gonçalves, RS, 95700-000, Brazil.
| | - Fábio C Chaves
- Departament of Food Science and Technology, Universidade Federal de Pelotas, Campus UFPel Capão do Leão, Pelotas, RS, 96010-900, Brazil.
| | - Vera Quecini
- Embrapa Uva e Vinho, Rua Livramento 515, Bento Gonçalves, RS, 95700-000, Brazil.
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Campus UFPel Capão do Leão, Pelotas, RS, 96010-900, Brazil.
| | - Livio Trainotti
- Department of Biology, University of Padova, Viale G. Colombo, Padova, 3, 35121, Italy.
| | - Cesar Valmor Rombaldi
- Departament of Food Science and Technology, Universidade Federal de Pelotas, Campus UFPel Capão do Leão, Pelotas, RS, 96010-900, Brazil.
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015; 16:538. [PMID: 26194356 PMCID: PMC4508813 DOI: 10.1186/s12864-015-1762-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS Here we present the Rice TE database (RiTE-db)--a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.
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Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Elena Barghini
- Department of Agriculture, Food, and Environment, University of Pisa, 56124, Pisa, Italy.
| | - Rosa M Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Angelina Angelova
- School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland.
| | - Carlos E Maldonado L
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Stefan Roffler
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Hajime Ohyanagi
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101, China.
| | | | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
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Finatto T, de Oliveira AC, Chaparro C, da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O, Picault N. Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. Rice (N Y) 2015; 8:13. [PMID: 25844118 PMCID: PMC4385019 DOI: 10.1186/s12284-015-0045-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Iron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe(2+)) in the soil solution. Although the first interface of the element is in the roots, the consequences of an excessive uptake can be observed in several rice tissues. In an original attempt to find both genes and transposable elements involved in the response to an iron toxicity stress, we used a microarray approach to study the transcriptional responses of rice leaves of cv. Nipponbare (Oryza sativa L. ssp. japonica) to iron excess in nutrient solution. RESULTS A large number of genes were significantly up- or down-regulated in leaves under the treatment. We analyzed the gene ontology and metabolic pathways of genes involved in the response to this stress and the cis-regulatory elements (CREs) present in the promoter region of up-regulated genes. The majority of genes act in the pathways of lipid metabolic process, carbohydrate metabolism, biosynthesis of secondary metabolites and plant hormones. We also found genes involved in iron acquisition and mobilization, transport of cations and regulatory mechanisms for iron responses, and in oxidative stress and reactive oxygen species detoxification. Promoter regions of 27% of genes up-regulated present at least one significant occurrence of an ABA-responsive CRE. Furthermore, and for the first time, we were able to show that iron stress triggers the up-regulation of many LTR-retrotransposons. We have established a complete inventory of transposable elements transcriptionally activated under iron excess and the CREs which are present in their LTRs. CONCLUSION The short-term response of Nipponbare seedlings to iron excess, includes activation of genes involved in iron homeostasis, in particular transporters, transcription factors and ROS detoxification in the leaves, but also many transposable elements. Our data led to the identification of CREs which are associated with both genes and LTR-retrotransposons up-regulated under iron excess. Our results strengthen the idea that LTR-retrotransposons participate in the transcriptional response to stress and could thus confer an adaptive advantage for the plant.
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Affiliation(s)
- Taciane Finatto
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
- />Present address: Universidade Tecnológica Federal do Paraná, Campus Pato Branco, 85503-390 Pato Branco, PR Brazil
| | - Antonio Costa de Oliveira
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Cristian Chaparro
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
- />Present address: Laboratoire Ecologie et Evolution des Interactions, UMR 5244, F-66860, Université de Perpignan Via Domitia, Perpignan, France
| | - Luciano C da Maia
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Daniel R Farias
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Leomar G Woyann
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Claudete C Mistura
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Adriana P Soares-Bresolin
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Christel Llauro
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Olivier Panaud
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Nathalie Picault
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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Ahmadi N, Audebert A, Bennett MJ, Bishopp A, de Oliveira AC, Courtois B, Diedhiou A, Diévart A, Gantet P, Ghesquière A, Guiderdoni E, Henry A, Inukai Y, Kochian L, Laplaze L, Lucas M, Luu DT, Manneh B, Mo X, Muthurajan R, Périn C, Price A, Robin S, Sentenac H, Sine B, Uga Y, Véry AA, Wissuwa M, Wu P, Xu J. The roots of future rice harvests. Rice (N Y) 2014; 7:29. [PMID: 26224558 PMCID: PMC4884021 DOI: 10.1186/s12284-014-0029-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/12/2014] [Indexed: 05/05/2023]
Abstract
Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.
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Affiliation(s)
| | | | - Malcolm J Bennett
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | - Anthony Bishopp
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | | | | | - Abdala Diedhiou
- />Université Cheikh Anta Diop (UCAD), Département de Biologie Végétale, Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
| | - Anne Diévart
- />CIRAD, UMR AGAP, Montpellier Cedex 5, 34398 France
| | - Pascal Gantet
- />Université Montpellier 2, UMR DIADE, Montpellier, France
- />IRD, LMI RICE, USTH, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | | | | | - Yoshiaki Inukai
- />International Cooperation Center for Agricultural Education (ICCAE), Nagoya University, Furo-cho, Chikusa 464-8601 Nagoya, Japan
| | - Leon Kochian
- />Robert W. Holley Center for Agriculture and Health, USDA-ARS and Department of Plant Biology, Cornell University, Ithaca, 14853 NY USA
| | - Laurent Laplaze
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />IRD, UMR DIADE, Montpellier, France
| | | | - Doan Trung Luu
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Baboucarr Manneh
- />Africa Rice Center, AfricaRice Sahel Regional Station, B.P. 96, St Louis, Senegal
| | - Xiaorong Mo
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | | | | | - Adam Price
- />University of Aberdeen, Aberdeen, AB24 3UU UK
| | | | - Hervé Sentenac
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Bassirou Sine
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />ISRA, CERAAS, Thiès, Senegal
| | - Yusaku Uga
- />National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, 305-8602 Ibaraki, Japan
| | - Anne Aliénor Véry
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Matthias Wissuwa
- />Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, 305-8686 Japan
| | - Ping Wu
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | - Jian Xu
- />Department of Biological Sciences and NUS Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore 117543 Singapore
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Paula AO, Oliveira ACD, Rocha RF. P097: Antimicrobial usage in the treatment of patients with bloodstream infection. Antimicrob Resist Infect Control 2013. [PMCID: PMC3688517 DOI: 10.1186/2047-2994-2-s1-p97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Paiva MHRS, Oliveira ACD, Paula AOD. P304: Conducts following occupational accidents involving exposure to biological material among emergency medical services personnel. Antimicrob Resist Infect Control 2013. [PMCID: PMC3687990 DOI: 10.1186/2047-2994-2-s1-p304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Paula AO, Oliveira ACD. P140: Interventions aiming to raise healthcare workers adherence to hand hygiene: integrative review. Antimicrob Resist Infect Control 2013. [PMCID: PMC3688140 DOI: 10.1186/2047-2994-2-s1-p140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Paiva MHRS, Oliveira ACD, Paula AOD. P313: Prehospital care: analysis of serological status and vaccination coverage for Hepatitis B on injured workers. Antimicrob Resist Infect Control 2013. [PMCID: PMC3688001 DOI: 10.1186/2047-2994-2-s1-p313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Pegoraro C, Santos RSD, Krüger MM, Tiecher A, Maia LCD, Rombaldi CV, Oliveira ACD. Effects of hypoxia storage on gene transcript accumulation during tomato fruit ripening. ACTA ACUST UNITED AC 2012. [DOI: 10.1590/s1677-04202012000200007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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de Souza AWS, da Silva MD, Machado LSG, Oliveira ACD, Pinheiro FAG, Sato EI. Short-term effect of leflunomide in patients with Takayasu arteritis: an observational study. Scand J Rheumatol 2012; 41:227-30. [PMID: 22400913 DOI: 10.3109/03009742.2011.633553] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To evaluate the efficacy of leflunomide in controlling disease activity in patients with Takayasu arteritis (TA) refractory or intolerant to conventional treatment. METHODS We conducted a prospective open-label study of 15 TA patients (mean age 36.2 years) with active disease based on clinical assessment, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and magnetic resonance angiography (MRA). Patients received leflunomide 20 mg/day for at least 6 months and were followed up for a mean of 9.1 months. Adverse events attributable to leflunomide were recorded. RESULTS At baseline, 14 TA patients had active disease despite therapy with corticosteroids and immunosuppressive agents, while one patient had intolerance to current treatment. In the follow-up visit, we found a significant decrease in the frequency of patients with active TA (93% vs. 20%, p = 0.002), in the mean daily dose of prednisone (34.2 vs. 13.9 mg, p < 0.001) and in the median values of ESR (29.0 vs. 27.0 mm/h, p = 0.012) and CRP (10.3 vs. 5.3 mg/L, p = 0.012). Two patients (13.3%) developed new angiographic lesions in the follow-up MRA. Three patients (20%) experienced mild adverse events during the study and none discontinued therapy. CONCLUSIONS This is the first open-label study to demonstrate improvement in disease activity and acute phase reactants with 20 mg/day of leflunomide in TA patients who were refractory or intolerant to conventional therapy with corticosteroids and immunosuppressive agents. Leflunomide was safe and a steroid-sparing effect was observed. A double-blind controlled study is desirable to confirm this finding.
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Affiliation(s)
- A W S de Souza
- Rheumatology Division, Federal University of São Paulo-Unifesp/EPM, Brazil.
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Victoria FC, da Maia LC, de Oliveira AC. In silico comparative analysis of SSR markers in plants. BMC Plant Biol 2011; 11:15. [PMID: 21247422 PMCID: PMC3037304 DOI: 10.1186/1471-2229-11-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
BACKGROUND The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes. RESULTS In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools. CONCLUSIONS The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.
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Affiliation(s)
- Filipe C Victoria
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
- Graduate Program in Biotechnology, Universidade Federal de Pelotas, RS, Brasil
| | - Luciano C da Maia
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
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Lima MDF, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, de Oliveira AC, Hemerly AS, Ferreira PCG. Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. BMC Plant Biol 2010; 10:254. [PMID: 21087491 PMCID: PMC3095333 DOI: 10.1186/1471-2229-10-254] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 11/18/2010] [Indexed: 05/05/2023]
Abstract
BACKGROUND The orderly progression through mitosis is regulated by the Anaphase-Promoting Complex (APC), a large multiprotein E3 ubiquitin ligase that targets key cell-cycle regulators for destruction by the 26 S proteasome. The APC is composed of at least 11 subunits and associates with additional regulatory activators during mitosis and interphase cycles. Despite extensive research on APC and activator functions in the cell cycle, only a few components have been functionally characterized in plants. RESULTS Here, we describe an in-depth search for APC subunits and activator genes in the Arabidopsis, rice and poplar genomes. Also, searches in other genomes that are not completely sequenced were performed. Phylogenetic analyses indicate that some APC subunits and activator genes have experienced gene duplication events in plants, in contrast to animals. Expression patterns of paralog subunits and activators in rice could indicate that this duplication, rather than complete redundancy, could reflect initial specialization steps. The absence of subunit APC7 from the genome of some green algae species and as well as from early metazoan lineages, could mean that APC7 is not required for APC function in unicellular organisms and it may be a result of duplication of another tetratricopeptide (TPR) subunit. Analyses of TPR evolution suggest that duplications of subunits started from the central domains. CONCLUSIONS The increased complexity of the APC gene structure, tied to the diversification of expression paths, suggests that land plants developed sophisticated mechanisms of APC regulation to cope with the sedentary life style and its associated environmental exposures.
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Affiliation(s)
- Marcelo de F Lima
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
| | - Núbia B Eloy
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
| | - Camila Pegoraro
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Campus Universitário s/n - Capão do Leão, CEP 90001-970, Pelotas, RS, Brasil
| | - Rauan Sagit
- Stockholm Bioinformatics Center, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106, 91,Stockholm, Sweden
| | - Cristian Rojas
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
| | - Thiago Bretz
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
| | - Lívia Vargas
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
| | - Arne Elofsson
- Stockholm Bioinformatics Center, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106, 91,Stockholm, Sweden
| | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Campus Universitário s/n - Capão do Leão, CEP 90001-970, Pelotas, RS, Brasil
| | - Adriana S Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
| | - Paulo CG Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brasil
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da Maia LC, de Souza VQ, Kopp MM, de Carvalho FIF, de Oliveira AC. Tandem repeat distribution of gene transcripts in three plant families. Genet Mol Biol 2009; 32:822-33. [PMID: 21637460 PMCID: PMC3036893 DOI: 10.1590/s1415-47572009005000091] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 06/17/2009] [Indexed: 12/02/2022] Open
Abstract
Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size and tandem repeat fractions in expressed regions. The conservation of motifs among species and its implication on genome evolution and dynamics are discussed.
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Affiliation(s)
- Luciano Carlos da Maia
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
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da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FIF, Costa de Oliveira A. SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation. Int J Plant Genomics 2008; 2008:412696. [PMID: 18670612 PMCID: PMC2486402 DOI: 10.1155/2008/412696] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 01/29/2008] [Accepted: 05/20/2008] [Indexed: 05/18/2023]
Abstract
Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.
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Affiliation(s)
- Luciano Carlos da Maia
- Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil
| | - Dario Abel Palmieri
- Laboratory for Environmental Studies, Catholic University of Salvador, Salvador, BA, 40.220-140, Brazil
| | - Velci Queiroz de Souza
- Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil
| | - Mauricio Marini Kopp
- Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil
| | - Fernando Irajá Félix de Carvalho
- Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil
- *Antonio Costa de Oliveira:
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Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing Y, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O’Donovan C, Ohyanagi H, Okido T, OOta S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda JI, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genes Dev 2007; 17:175-83. [PMID: 17210932 PMCID: PMC1781349 DOI: 10.1101/gr.5509507] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.9] [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: 05/17/2006] [Accepted: 10/31/2006] [Indexed: 11/25/2022]
Abstract
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.
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Affiliation(s)
- Takeshi Itoh
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
| | - Tsuyoshi Tanaka
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Roberto A. Barrero
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Chisato Yamasaki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Yasuyuki Fujii
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Phillip B. Hilton
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Baltazar A. Antonio
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Hideo Aono
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Rolf Apweiler
- EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Richard Bruskiewich
- Biometrics and Bioinformatics Unit, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Thomas Bureau
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Frances Burr
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | | | - Galina Fuks
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Takuya Habara
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Georg Haberer
- Institute for Bioinformatics, GSF National Research Center for Environment and Health, D-85764 Neuherberg, Germany
| | - Bin Han
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
| | - Erimi Harada
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Aiko T. Hiraki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Hirohiko Hirochika
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Douglas Hoen
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Hiroki Hokari
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Satomi Hosokawa
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
| | - Yue Hsing
- Institute of Botany, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Hiroshi Ikawa
- Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Ibaraki 305-0032, Japan
| | - Kazuho Ikeo
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Tadashi Imanishi
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Yukiyo Ito
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
| | - Pankaj Jaiswal
- Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
| | - Masako Kanno
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Yoshihiro Kawahara
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Toshiyuki Kawamura
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroaki Kawashima
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Jitendra P. Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Shoshi Kikuchi
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Setsuko Komatsu
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Kanako O. Koyanagi
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Hiromi Kubooka
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Damien Lieberherr
- SWISS-PROT Group, Swiss Institute of Bioinformatics, CH-1211 Geneva 4, Switzerland
| | - Yao-Cheng Lin
- Institute of Botany, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - David Lonsdale
- EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Takashi Matsumoto
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Akihiro Matsuya
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | | | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Akio Miyao
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Nicola Mulder
- EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Yoshiaki Nagamura
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Jongmin Nam
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
- Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nobukazu Namiki
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
| | - Hisataka Numa
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Shin Nurimoto
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Claire O’Donovan
- EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Hajime Ohyanagi
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
- Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Ibaraki 305-0032, Japan
| | - Toshihisa Okido
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Satoshi OOta
- RIKEN BioResource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305-0074, Japan
| | - Naoki Osato
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Lance E. Palmer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11723, USA
- Department of Molecular Genetics and Microbiology, and Center for Infectious Diseases, The State University of New York at Stony Brook, Stony Brook, New York 11794, USA
| | | | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Naomi Saichi
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroaki Sakai
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Yasumichi Sakai
- Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Ibaraki 305-0032, Japan
| | - Katsumi Sakata
- Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Ibaraki 305-0032, Japan
| | - Tetsuya Sakurai
- Metabolomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Fumihiko Sato
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Yoshiharu Sato
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Heiko Schoof
- Institute for Bioinformatics, GSF National Research Center for Environment and Health, D-85764 Neuherberg, Germany
- Technische Universität München, Genome Oriented Bioinformatics, D-85354 Freising-Weihenstephan, Germany
- Plant Computational Biology, Max-Planck-Institute for Plant Breeding Research, D 50829 Cologne, Germany
| | - Motoaki Seki
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Michie Shibata
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
| | - Yuji Shimizu
- Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Ibaraki 305-0032, Japan
| | - Kazuo Shinozaki
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Yuji Shinso
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Nagendra K. Singh
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Brian Smith-White
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Jun-ichi Takeda
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Motohiko Tanino
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Supat Thongjuea
- Rice Gene Discovery Unit, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Fusano Todokoro
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Mika Tsugane
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
| | - Akhilesh K. Tyagi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Apichart Vanavichit
- Rice Gene Discovery Unit, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Aihui Wang
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Rod A. Wing
- Arizona Genomics Institute, The University of Arizona, Tucson, Arizona 85721, USA
| | - Kaori Yamaguchi
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Mayu Yamamoto
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
| | - Naoyuki Yamamoto
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Yeisoo Yu
- Arizona Genomics Institute, The University of Arizona, Tucson, Arizona 85721, USA
| | - Hao Zhang
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
| | - Qiang Zhao
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
| | - Kenichi Higo
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Bio-Oriented Technology Research Advancement Institution, Minato-ku, Tokyo 105-0001, Japan
| | - Benjamin Burr
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Takashi Gojobori
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Takuji Sasaki
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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