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Amelework AB, Bairu MW. Advances in Genetic Analysis and Breeding of Cassava ( Manihot esculenta Crantz): A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11121617. [PMID: 35736768 PMCID: PMC9228751 DOI: 10.3390/plants11121617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 05/30/2023]
Abstract
Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds' largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. This necessitated the establishment of a multi-disciplinary research program at the Agricultural Research Council of South Africa. The objective of this review is to highlight progress made in cassava breeding and genetic analysis. This review highlights the progress of cassava research worldwide and discusses research findings on yield, quality, and adaptability traits in cassava. It also discusses the limitations and the prospects of the cassava R&D program towards development of the cassava industry in South Africa.
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Affiliation(s)
- Assefa B. Amelework
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa;
| | - Michael W. Bairu
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa;
- Faculty of Natural & Agricultural Sciences, School of Agricultural Sciences, Food Security and Safety Focus Area, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
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2
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Díaz-Tatis PA, Ochoa JC, Rico EM, Rodríguez C, Medina A, Szurek B, Chavarriaga P, López CE. RXam2, a NLR from cassava (Manihot esculenta) contributes partially to the quantitative resistance to Xanthomonas phaseoli pv. manihotis. PLANT MOLECULAR BIOLOGY 2022; 109:313-324. [PMID: 34757519 DOI: 10.1007/s11103-021-01211-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The overexpression of RXam2, a cassava NLR (nucleotide-binding leucine-rich repeat) gene, by stable transformation and gene expression induction mediated by dTALEs, reduce cassava bacterial blight symptoms. Cassava (Manihot esculenta) is a tropical root crop affected by different pathogens including Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of cassava bacterial blight (CBB). Previous studies have reported resistance to CBB as a quantitative and polygenic character. This study sought to validate the functional role of a NLR (nucleotide-binding leucine-rich repeat) associated with a QTL to Xpm strain CIO151 called RXam2. Transgenic cassava plants overexpressing RXam2 were generated and analyzed. Plants overexpressing RXam2 showed a reduction in bacterial growth to Xpm strains CIO151, 232 and 226. In addition, designer TALEs (dTALEs) were developed to specifically bind to the RXam2 promoter region. The Xpm strain transformed with dTALEs allowed the induction of the RXam2 gene expression after inoculation in cassava plants and was associated with a diminution in CBB symptoms. These findings suggest that RXam2 contributes to the understanding of the molecular basis of quantitative disease resistance.
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Affiliation(s)
- Paula A Díaz-Tatis
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Grupo de Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Cra1 #47a15, Bogotá D.C., Colombia
| | - Juan C Ochoa
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Department of Integrative Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Edgar M Rico
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
| | - Catalina Rodríguez
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Ludwig Maximilian University of Munich, Biozentrum Martinsried, Grosshaderner Strasse 4, Martinsried, Germany
| | - Adriana Medina
- Transformation Platform, Centro Internacional de Agricultura Tropical (CIAT), Km17 Cali-Palmira, Palmira, Colombia
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME), IRD-CIRAD-Université, Montpellier, France
| | - Paul Chavarriaga
- Transformation Platform, Centro Internacional de Agricultura Tropical (CIAT), Km17 Cali-Palmira, Palmira, Colombia
| | - Camilo E López
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia.
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Tripathi L, Dhugga KS, Ntui VO, Runo S, Syombua ED, Muiruri S, Wen Z, Tripathi JN. Genome Editing for Sustainable Agriculture in Africa. Front Genome Ed 2022; 4:876697. [PMID: 35647578 PMCID: PMC9133388 DOI: 10.3389/fgeed.2022.876697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- *Correspondence: Leena Tripathi,
| | | | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Easter D. Syombua
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Kenyatta University, Nairobi, Kenya
| | - Zhengyu Wen
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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4
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Fathima AA, Sanitha M, Tripathi L, Muiruri S. Cassava (
Manihot esculenta
) dual use for food and bioenergy: A review. Food Energy Secur 2022. [DOI: 10.1002/fes3.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Anwar Aliya Fathima
- Department of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Chennai India
| | - Mary Sanitha
- Department of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Chennai India
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
- Department of Plant Sciences Kenyatta University Nairobi Kenya
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5
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Zárate‐Chaves CA, Gómez de la Cruz D, Verdier V, López CE, Bernal A, Szurek B. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae. MOLECULAR PLANT PATHOLOGY 2021; 22:1520-1537. [PMID: 34227737 PMCID: PMC8578842 DOI: 10.1111/mpp.13094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
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Affiliation(s)
| | | | - Valérie Verdier
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
| | - Camilo E. López
- Manihot Biotec, Departamento de BiologíaUniversidad Nacional de ColombiaBogotáColombia
| | - Adriana Bernal
- Laboratorio de Interacciones Moleculares de Microorganismos AgrícolasDepartamento de Ciencias BásicasUniversidad de los AndesBogotáColombia
| | - Boris Szurek
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
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6
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Ewa F, Asiwe JNA, Okogbenin E, Ogbonna AC, Egesi C. KASPar SNP genetic map of cassava for QTL discovery of productivity traits in moderate drought stress environment in Africa. Sci Rep 2021; 11:11268. [PMID: 34050196 PMCID: PMC8163807 DOI: 10.1038/s41598-021-90131-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
Cassava is an important staple in Sub-Sahara Africa. While its production has rapidly expanded to the dry savannahs of the continent, productivity is low in this ecology due to drought by farmers, extending the growth cycle from 12 months to 18, and sometimes 24 months to ensure better harvests. Yield is a complex trait and often difficult to manipulate for genetic gain in conventional breeding. Unfortunately, the dearth of molecular tools for decades has hampered molecular breeding (MB) to improve cassava productivity. This study was conducted to explore KASpar SNPs to generate more molecular tools to enhance genetic dissection of elite African germplasm for improved cassava productivity in dry environments of Africa where molecular resources are highly limited for crop improvement. To aid molecular genetic analysis of traits, a linkage map covering 1582.8 cM with an average resolution of 3.69 cM was constructed using 505 polymorphic SNP markers distributed over 21 linkage groups. Composite interval mapping using 267 F1 progeny in initial QTL mapping identified 27 QTLs for productivity traits in the dry savannah of Nigeria. The availability of KASPar SNPs are anticipated to improve the implementation of MB for the development of high performing drought-tolerant cassava varieties in Africa.
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Affiliation(s)
- Favour Ewa
- Department of Plant Production, Soil Science and Agricultural Engineering, School of Agriculture and Environmental Sciences, University of Limpopo, Sovenga, South Africa.
| | - Joseph N A Asiwe
- Department of Plant Production, Soil Science and Agricultural Engineering, School of Agriculture and Environmental Sciences, University of Limpopo, Sovenga, South Africa
| | | | - Alex C Ogbonna
- Department of Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Chiedozie Egesi
- Cassava Breeding Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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7
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Malik AI, Kongsil P, Nguyễn VA, Ou W, Sholihin, Srean P, Sheela MN, Becerra López-Lavalle LA, Utsumi Y, Lu C, Kittipadakul P, Nguyễn HH, Ceballos H, Nguyễn TH, Selvaraj Gomez M, Aiemnaka P, Labarta R, Chen S, Amawan S, Sok S, Youabee L, Seki M, Tokunaga H, Wang W, Li K, Nguyễn HA, Nguyễn VĐ, Hàm LH, Ishitani M. Cassava breeding and agronomy in Asia: 50 years of history and future directions. BREEDING SCIENCE 2020; 70:145-166. [PMID: 32523397 PMCID: PMC7272245 DOI: 10.1270/jsbbs.18180] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/29/2019] [Indexed: 09/29/2023]
Abstract
In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.
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Affiliation(s)
- Al Imran Malik
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Pasajee Kongsil
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Vũ Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Wenjun Ou
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Sholihin
- Indonesian Legume and Tuber Crops Research Institute, Kendalpayak Km 8, PO BOX 66, Malang 65101, Indonesia
| | - Pao Srean
- Faculty of Agriculture & Food Processing, University of Battambang, Battambang, Cambodia
| | - MN Sheela
- Central Tuber Crops Research Institute Sreekariyam, Thiruvananthapuram-605 017, Kerala, India
| | | | - Yoshinori Utsumi
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Cheng Lu
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Piya Kittipadakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Hữu Hỷ Nguyễn
- Hung Loc Agricultural Research Center, Institute for Agriculture in Southern Vietnam, 121 Nguyen Binh Khiem, District 1, HCM City, Vietnam
| | - Hernan Ceballos
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Trọng Hiển Nguyễn
- Root and Tuber Crop Research and Development Center, Food and Field Crop Research Institute, Vinh Quynh, Thanh Tri, Hanoi, Vietnam
| | - Michael Selvaraj Gomez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Pornsak Aiemnaka
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Ricardo Labarta
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Songbi Chen
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Suwaluk Amawan
- Rayong Field Crops Research Center, Sukumvit Rd, Huaypong, Meang, Rayong 21150, Thailand
| | - Sophearith Sok
- International Center for Tropical Agriculture (CIAT-Asia), Phnom Penh, Cambodia
| | - Laothao Youabee
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Motoaki Seki
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Tokunaga
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Wenquan Wang
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Kaimian Li
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Hai Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Văn Đồng Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Lê Huy Hàm
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
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8
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Tappiban P, Sraphet S, Srisawad N, Smith DR, Triwitayakorn K. Identification and expression of genes in response to cassava bacterial blight infection. J Appl Genet 2018; 59:391-403. [DOI: 10.1007/s13353-018-0457-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022]
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Sen S, Dehury B, Sahu J, Rathi S, Yadav RNS. Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family. Mol Biol Rep 2018; 45:453-468. [PMID: 29626317 DOI: 10.1007/s11033-018-4181-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR-ESTs could be assigned a significant match to the protein database. 3037 unique SSR-FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.
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Affiliation(s)
- Surojit Sen
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India.
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Jagajjit Sahu
- Distributed Information Center, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sunayana Rathi
- Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat, Assam, 785013, India
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10
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Díaz Tatis PA, Herrera Corzo M, Ochoa Cabezas JC, Medina Cipagauta A, Prías MA, Verdier V, Chavarriaga Aguirre P, López Carrascal CE. The overexpression of RXam1, a cassava gene coding for an RLK, confers disease resistance to Xanthomonas axonopodis pv. manihotis. PLANTA 2018; 247:1031-1042. [PMID: 29453662 DOI: 10.1007/s00425-018-2863-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/24/2018] [Indexed: 05/27/2023]
Abstract
The overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136, suggesting that RXam1 might be implicated in strain-specific resistance. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) is a prevalent disease in all regions, where cassava is cultivated. CBB is a foliar and vascular disease usually controlled through host resistance. Previous studies have found QTLs explaining resistance to several Xam strains. Interestingly, one QTL called XM5 that explained 13% of resistance to XamCIO136 was associated with a similar fragment of the rice Xa21-resistance gene called PCR250. In this study, we aimed to further identify and characterize this fragment and its role in resistance to CBB. Screening and hybridization of a BAC library using the molecular marker PCR250 as a probe led to the identification of a receptor-like kinase similar to Xa21 and were called RXam1 (Resistance to Xam 1). Here, we report the functional characterization of susceptible cassava plants overexpressing RXam1. Our results indicated that the overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136. This suggests that RXAM1 might be implicated in strain-specific resistance to XamCIO136.
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Affiliation(s)
- Paula A Díaz Tatis
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia
- Grupo de Ciencias Biológicas y Químicas, Departamento de Biología, Universidad Antonio Nariño, Cra1 #47a15, Bogotá, Colombia
| | - Mariana Herrera Corzo
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia
- Programa de Biología y Mejoramiento de la Palma de Aceite, Cenipalma, Dir: Km 137 via Pto Araujo-La lizama, Bogotá, Colombia
| | - Juan C Ochoa Cabezas
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia
- Department of Integrative Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Adriana Medina Cipagauta
- Plataforma de Transformación Genética, Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, Palmira, Colombia
| | - Mónica A Prías
- Plataforma de Transformación Genética, Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, Palmira, Colombia
| | - Valerie Verdier
- Institute de Recherche pour le Développement (IRD), CIRAD, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Paul Chavarriaga Aguirre
- Plataforma de Transformación Genética, Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, Palmira, Colombia
| | - Camilo E López Carrascal
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia.
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11
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Medina CA, Reyes PA, Trujillo CA, Gonzalez JL, Bejarano DA, Montenegro NA, Jacobs JM, Joe A, Restrepo S, Alfano JR, Bernal A. The role of type III effectors from Xanthomonas axonopodis pv. manihotis in virulence and suppression of plant immunity. MOLECULAR PLANT PATHOLOGY 2018; 19:593-606. [PMID: 28218447 PMCID: PMC6638086 DOI: 10.1111/mpp.12545] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 01/25/2017] [Accepted: 02/15/2017] [Indexed: 05/29/2023]
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) causes cassava bacterial blight, the most important bacterial disease of cassava. Xam, like other Xanthomonas species, requires type III effectors (T3Es) for maximal virulence. Xam strain CIO151 possesses 17 predicted T3Es belonging to the Xanthomonas outer protein (Xop) class. This work aimed to characterize nine Xop effectors present in Xam CIO151 for their role in virulence and modulation of plant immunity. Our findings demonstrate the importance of XopZ, XopX, XopAO1 and AvrBs2 for full virulence, as well as a redundant function in virulence between XopN and XopQ in susceptible cassava plants. We tested their role in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) using heterologous systems. AvrBs2, XopR and XopAO1 are capable of suppressing PTI. ETI suppression activity was only detected for XopE4 and XopAO1. These results demonstrate the overall importance and diversity in functions of major virulence effectors AvrBs2 and XopAO1 in Xam during cassava infection.
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Affiliation(s)
- Cesar Augusto Medina
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Paola Andrea Reyes
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Cesar Augusto Trujillo
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Juan Luis Gonzalez
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - David Alejandro Bejarano
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Nathaly Andrea Montenegro
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Jonathan M. Jacobs
- Institut de Recherche pour le De´veloppement (IRD), CiradUniversite´ Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394MontpellierFrance
| | - Anna Joe
- Center for Plant Science InnovationUniversity of NebraskaLincolnNE68588‐0660USA
- Department of Plant PathologyUniversity of NebraskaLincolnNE68588‐0722USA
- Present address:
Department of Plant Pathology and the Genome CenterUniversity of California, Davis, CA 95616, USA, and Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Silvia Restrepo
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - James R. Alfano
- Center for Plant Science InnovationUniversity of NebraskaLincolnNE68588‐0660USA
- Department of Plant PathologyUniversity of NebraskaLincolnNE68588‐0722USA
| | - Adriana Bernal
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
- Present address:
Novozymes, Inc., DavisCA95618USA
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12
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McCallum EJ, Anjanappa RB, Gruissem W. Tackling agriculturally relevant diseases in the staple crop cassava (Manihot esculenta). CURRENT OPINION IN PLANT BIOLOGY 2017; 38:50-58. [PMID: 28477536 DOI: 10.1016/j.pbi.2017.04.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
Cassava is an important staple food crop for millions of people in tropical regions across Africa, South America and Asia. Viral, bacterial and fungal diseases impact cassava yield in all three regions. The viruses causing cassava mosaic disease and cassava brown streak disease have been particularly devastating to cassava production in Africa. Improved farming practices and disease monitoring can reduce the impact of cassava diseases in the field. The availability of disease resistant cassava varieties developed through breeding or genetic engineering is key to tackling disease incidence and severity.
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Affiliation(s)
- Emily J McCallum
- Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Ravi B Anjanappa
- Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092 Zurich, Switzerland.
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13
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Soto Sedano JC, Mora Moreno RE, Mathew B, Léon J, Gómez Cano FA, Ballvora A, López Carrascal CE. Major Novel QTL for Resistance to Cassava Bacterial Blight Identified through a Multi-Environmental Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:1169. [PMID: 28725234 PMCID: PMC5496946 DOI: 10.3389/fpls.2017.01169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/19/2017] [Indexed: 05/31/2023]
Abstract
Cassava, Manihot esculenta Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB. An F1 mapping population of 117 full sibs was tested for resistance to two Xam strains (Xam318 and Xam681) at two locations in Colombia: La Vega, Cundinamarca and Arauca. The evaluation was conducted in rainy and dry seasons and additional tests were carried out under controlled greenhouse conditions. The phenotypic evaluation of the response to Xam revealed continuous variation. Based on composite interval mapping analysis, 5 strain-specific QTL for resistance to Xam explaining between 15.8 and 22.1% of phenotypic variance, were detected and localized on a high resolution SNP-based genetic map of cassava. Four of them show stability among the two evaluated seasons. Genotype by environment analysis detected three QTL by environment interactions and the broad sense heritability for Xam318 and Xam681 were 20 and 53%, respectively. DNA sequence analysis of the QTL intervals revealed 29 candidate defense-related genes (CDRGs), and two of them contain domains related to plant immunity proteins, such as NB-ARC-LRR and WRKY.
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Affiliation(s)
- Johana C. Soto Sedano
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de ColombiaBogotá, Colombia
| | - Rubén E. Mora Moreno
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de ColombiaBogotá, Colombia
| | - Boby Mathew
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
| | - Fabio A. Gómez Cano
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de ColombiaBogotá, Colombia
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
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14
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Li S, Cui Y, Zhou Y, Luo Z, Liu J, Zhao M. The industrial applications of cassava: current status, opportunities and prospects. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2282-2290. [PMID: 28233322 DOI: 10.1002/jsfa.8287] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 05/27/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a drought-tolerant, staple food crop that is grown in tropical and subtropical areas. As an important raw material, cassava is a valuable food source in developing countries and is also extensively employed for producing starch, bioethanol and other bio-based products (e.g. feed, medicine, cosmetics and biopolymers). These cassava-based industries also generate large quantities of wastes/residues rich in organic matter and suspended solids, providing great potential for conversion into value-added products through biorefinery. However, the community of cassava researchers is relatively small and there is very limited information on cassava. Therefore this review summarizes current knowledge on the system biology, economic value, nutritional quality and industrial applications of cassava and its wastes in an attempt to accelerate understanding of the basic biology of cassava. The review also discusses future perspectives with respect to integrating and utilizing cassava information resources for increasing the economic and environmental sustainability of cassava industries. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Yanyan Cui
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Yuan Zhou
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Zhiting Luo
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Jidong Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Mouming Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
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15
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Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS One 2017; 12:e0177456. [PMID: 28493955 PMCID: PMC5426748 DOI: 10.1371/journal.pone.0177456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.
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Affiliation(s)
- Bin Wang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xin Guo
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Pingjuan Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Mengbin Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaoling Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Liangping Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiling Yang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiao Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Deli Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Jixiang Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiwei Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Chunji Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xue Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaolin Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- * E-mail:
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16
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Soto Sedano C, Mora Moreno RE, Calle F, López Carrascal CE. QTL identification for cassava bacterial blight resistance under natural infection conditions. ACTA BIOLÓGICA COLOMBIANA 2017. [DOI: 10.15446/abc.v22n1.57951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
La yuca, Manihot esculenta Crantz, representa la principal fuente de alimento para cerca de 1000 millones de personas. La producción de yuca se ve afectada por diversas enfermedades, una de las más serias es la bacteriosis vascular (CBB) causada por Xanthomonas axonopodis pv. manihotis (Xam). En este estudio se realizó un análisis de loci de rasgos cuantitativos (QTL) para la resistencia a CBB en condiciones naturales de infección, usando una población de mapeo constituida por 99 genotipos de hermanos completos segregantes y un mapa genético altamente denso basado en SNPs. La evaluación fenotípica se llevó a cabo en Puerto López (Meta), Colombia, durante la época de lluvias durante el segundo semestre de 2015. En la población de mapeo fueron detectados individuos con una segregación transgresiva tanto resistentes como susceptibles. A través de un análisis no paramétrico de intervalo simple, se detectaron dos QTL que explican el 10,9 y el 12,6 % de la varianza fenotípica de la resistencia en campo a CBB. Mediante análisis bioinformáticos se identificaron cuatro genes candidatos presentes en los intervalos de los QTL. Este trabajo representa un esfuerzo por dilucidar los mecanismos moleculares implicados en la resistencia de yuca a CBB.
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17
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Quesada-Ocampo LM, Vargas AM, Naegele RP, Francis DM, Hausbeck MK. Resistance to Crown and Root Rot Caused by Phytophthora capsici in a Tomato Advanced Backcross of Solanum habrochaites and Solanum lycopersicum. PLANT DISEASE 2016; 100:829-835. [PMID: 30688608 DOI: 10.1094/pdis-08-15-0888-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora capsici causes devastating disease on many vegetable crops, including tomato and other solanaceous species. Solanum habrochaites accession LA407, a wild relative of cultivated tomato, has shown complete resistance to four P. capsici isolates from Michigan cucurbitaceous and solanaceous crops in a previous study. Greenhouse experiments were conducted to evaluate 62 lines of a tomato inbred backcross population between LA407 and the cultivated tomato 'Hunt 100' and 'Peto 95-43' for resistance to two highly virulent P. capsici isolates. Roots of 6-week-old seedlings were inoculated with each of two P. capsici isolates and maintained in the greenhouse. Plants were evaluated for wilting and plant death three times per week for 5 weeks. Significant differences were observed in disease response among the inbred tomato lines. Most lines evaluated were susceptible to P. capsici isolate 12889 but resistant to isolate OP97; 24 tomato lines were resistant to both isolates. Heritability of Phytophthora root rot resistance was high in this population. Polymorphic molecular markers located in genes related to resistance and defense responses were identified and added to a genetic map previously generated for the population. Resistant lines and polymorphic markers identified in this study are a valuable resource for development of tomato varieties resistant to P. capsici.
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Affiliation(s)
- L M Quesada-Ocampo
- Department of Plant Pathology, North Carolina State University, Raleigh 27695
| | - A M Vargas
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
| | - R P Naegele
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
| | - D M Francis
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, Wooster 44691
| | - M K Hausbeck
- Department of Plant, Soil and Microbial Sciences, Michigan State University
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18
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Ceballos H, Kawuki RS, Gracen VE, Yencho GC, Hershey CH. Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1647-67. [PMID: 26093610 PMCID: PMC4540783 DOI: 10.1007/s00122-015-2555-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/05/2015] [Indexed: 05/19/2023]
Abstract
Consolidates relevant molecular and phenotypic information on cassava to demonstrate relevance of heterosis, and alternatives to exploit it by integrating different tools. Ideas are useful to other asexually reproduced crops. Asexually propagated crops offer the advantage that all genetic effects can be exploited in farmers' production fields. However, non-additive effects complicate selection because, while influencing the performance of the materials under evaluation, they cannot be transmitted efficiently to the following cycle of selection. Cassava can be used as a model crop for asexually propagated crops because of its diploid nature and the absence of (known) incompatibility effects. New technologies such as genomic selection (GS), use of inbred progenitors based on doubled haploids and induction of flowering can be employed for accelerating genetic gains in cassava. Available information suggests that heterosis, non-additive genetic effects and within-family variation are relatively large for complex traits such as fresh root yield, moderate for dry matter or starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.
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Affiliation(s)
- Hernán Ceballos
- International Center for Tropical Agriculture (CIAT), Apartado Aéreo, 6713, Cali, Colombia,
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Lozano R, Hamblin MT, Prochnik S, Jannink JL. Identification and distribution of the NBS-LRR gene family in the Cassava genome. BMC Genomics 2015; 16:360. [PMID: 25948536 PMCID: PMC4422547 DOI: 10.1186/s12864-015-1554-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop. RESULTS With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor. CONCLUSIONS This study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.
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Affiliation(s)
- Roberto Lozano
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.
| | - Martha T Hamblin
- Institute for Genomic Diversity, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA.
| | - Simon Prochnik
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
| | - Jean-Luc Jannink
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
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20
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Soto JC, Ortiz JF, Perlaza-Jiménez L, Vásquez AX, Lopez-Lavalle LAB, Mathew B, Léon J, Bernal AJ, Ballvora A, López CE. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics 2015; 16:190. [PMID: 25887443 PMCID: PMC4417308 DOI: 10.1186/s12864-015-1397-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/24/2015] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. RESULTS A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. CONCLUSIONS This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.
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Affiliation(s)
- Johana Carolina Soto
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Juan Felipe Ortiz
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. .,Present address Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - Laura Perlaza-Jiménez
- Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia. .,Present address Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Andrea Ximena Vásquez
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | | | - Boby Mathew
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Jens Léon
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Adriana Jimena Bernal
- Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia.
| | - Agim Ballvora
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Camilo Ernesto López
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
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In silico genome comparison and distribution analysis of simple sequences repeats in cassava. Int J Genomics 2014; 2014:471461. [PMID: 25374887 PMCID: PMC4211302 DOI: 10.1155/2014/471461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/08/2014] [Indexed: 11/17/2022] Open
Abstract
We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava's SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp) and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp). It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5' UTRs have 196,1 SSRs/Mbp, and 3' UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava's genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution.
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22
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Leal LG, Perez Á, Quintero A, Bayona Á, Ortiz JF, Gangadharan A, Mackey D, López C, López-Kleine L. Identification of immunity-related genes in Arabidopsis and cassava using genomic data. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:345-53. [PMID: 24316329 PMCID: PMC4357831 DOI: 10.1016/j.gpb.2013.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/19/2013] [Accepted: 09/22/2013] [Indexed: 11/01/2022]
Abstract
Recent advances in genomic and post-genomic technologies have provided the opportunity to generate a previously unimaginable amount of information. However, biological knowledge is still needed to improve the understanding of complex mechanisms such as plant immune responses. Better knowledge of this process could improve crop production and management. Here, we used holistic analysis to combine our own microarray and RNA-seq data with public genomic data from Arabidopsis and cassava in order to acquire biological knowledge about the relationships between proteins encoded by immunity-related genes (IRGs) and other genes. This approach was based on a kernel method adapted for the construction of gene networks. The obtained results allowed us to propose a list of new IRGs. A putative function in the immunity pathway was predicted for the new IRGs. The analysis of networks revealed that our predicted IRGs are either well documented or recognized in previous co-expression studies. In addition to robust relationships between IRGs, there is evidence suggesting that other cellular processes may be also strongly related to immunity.
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Affiliation(s)
- Luis Guillermo Leal
- Department of Statistics, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Álvaro Perez
- Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Andrés Quintero
- Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Ángela Bayona
- Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Felipe Ortiz
- Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Anju Gangadharan
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - David Mackey
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Camilo López
- Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Liliana López-Kleine
- Department of Statistics, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
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23
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Arrieta-Ortiz ML, Rodríguez-R LM, Pérez-Quintero ÁL, Poulin L, Díaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J, Boureau T, Darrasse A, David P, Dugé de Bernonville T, Fontanilla P, Gagnevin L, Guérin F, Jacques MA, Lauber E, Lefeuvre P, Medina C, Medina E, Montenegro N, Muñoz Bodnar A, Noël LD, Ortiz Quiñones JF, Osorio D, Pardo C, Patil PB, Poussier S, Pruvost O, Robène-Soustrade I, Ryan RP, Tabima J, Urrego Morales OG, Vernière C, Carrere S, Verdier V, Szurek B, Restrepo S, López C, Koebnik R, Bernal A. Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151. PLoS One 2013; 8:e79704. [PMID: 24278159 PMCID: PMC3838355 DOI: 10.1371/journal.pone.0079704] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/24/2013] [Indexed: 11/24/2022] Open
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
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Affiliation(s)
- Mario L. Arrieta-Ortiz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Luis M. Rodríguez-R
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | | | - Lucie Poulin
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Ana C. Díaz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathalia Arias Rojas
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Cesar Trujillo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | | | - Rebecca Bart
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Jens Boch
- Department of Genetics, Martin Luther University, Halle-Wittenberg, Germany
| | - Tristan Boureau
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Armelle Darrasse
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Perrine David
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Thomas Dugé de Bernonville
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Paula Fontanilla
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Lionel Gagnevin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Fabien Guérin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Marie-Agnès Jacques
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Pierre Lefeuvre
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Cesar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Edgar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathaly Montenegro
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Alejandra Muñoz Bodnar
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Juan F. Ortiz Quiñones
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniela Osorio
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Carolina Pardo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Prabhu B. Patil
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Stéphane Poussier
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
| | - Olivier Pruvost
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Isabelle Robène-Soustrade
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Robert P. Ryan
- College of Life Sciences, University of Dundee, Dundee, Scotland
| | - Javier Tabima
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Oscar G. Urrego Morales
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Christian Vernière
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Valérie Verdier
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
| | - Boris Szurek
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Camilo López
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Ralf Koebnik
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Adriana Bernal
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- * E-mail:
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24
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Osman KA, Tang B, Wang Y, Chen J, Yu F, Li L, Han X, Zhang Z, Yan J, Zheng Y, Yue B, Qiu F. Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage. PLoS One 2013; 8:e79305. [PMID: 24244474 PMCID: PMC3828346 DOI: 10.1371/journal.pone.0079305] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 09/22/2013] [Indexed: 11/19/2022] Open
Abstract
Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL), QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging), 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1) were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.
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Affiliation(s)
- Khalid A. Osman
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bin Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yaping Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Juanhua Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Feng Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xuesong Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianbin Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yonglian Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bing Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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25
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Rabbi IY, Kulembeka HP, Masumba E, Marri PR, Ferguson M. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:329-42. [PMID: 22419105 DOI: 10.1007/s00122-012-1836-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/24/2012] [Indexed: 05/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina's GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences' KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.
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Affiliation(s)
- Ismail Yusuf Rabbi
- International Institute of Tropical Agriculture, PMB 5320 Oyo Road, Ibadan, Nigeria.
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