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Khan AW, Garg V, Sun S, Gupta S, Dudchenko O, Roorkiwal M, Chitikineni A, Bayer PE, Shi C, Upadhyaya HD, Bohra A, Bharadwaj C, Mir RR, Baruch K, Yang B, Coyne CJ, Bansal KC, Nguyen HT, Ronen G, Aiden EL, Veneklaas E, Siddique KHM, Liu X, Edwards D, Varshney RK. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 2024:10.1038/s41588-024-01760-4. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
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Affiliation(s)
- Aamir W Khan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Saurabh Gupta
- Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Olga Dudchenko
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Hari D Upadhyaya
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Abhishek Bohra
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India
| | | | | | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Erik Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Xin Liu
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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2
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Cortés AJ. Abiotic Stress Tolerance Boosted by Genetic Diversity in Plants. Int J Mol Sci 2024; 25:5367. [PMID: 38791404 PMCID: PMC11121514 DOI: 10.3390/ijms25105367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 05/26/2024] Open
Abstract
Plant breeding [...].
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia;
- Facultad de Ciencias Agrarias—de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 23436, Sweden
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3
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Hualpa-Ramirez E, Carrasco-Lozano EC, Madrid-Espinoza J, Tejos R, Ruiz-Lara S, Stange C, Norambuena L. Stress salinity in plants: New strategies to cope with in the foreseeable scenario. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108507. [PMID: 38467083 DOI: 10.1016/j.plaphy.2024.108507] [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: 10/03/2023] [Revised: 02/12/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The excess of salts in soils causes stress in most plants, except for some halophytes that can tolerate higher levels of salinity. The excess of Na+ generates an ionic imbalance, reducing the K+ content and altering cellular metabolism, thus impacting in plant growth and development. Additionally, salinity in soil induces water stress due to osmotic effects and increments the production of reactive oxygen species (ROS) that affect the cellular structure, damaging membranes and proteins, and altering the electrochemical potential of H+, which directly affects nutrient absorption by membrane transporters. However, plants possess mechanisms to overcome the toxicity of the sodium ions, such as internalization into the vacuole or exclusion from the cell, synthesis of enzymes or protective compounds against ROS, and the synthesis of metabolites that help to regulate the osmotic potential of plants. Physiologic and molecular mechanisms of salinity tolerance in plants will be addressed in this review. Furthermore, a revision of strategies taken by researchers to confer salt stress tolerance on agriculturally important species are discussed. These strategies include conventional breeding and genetic engineering as transgenesis and genome editing by CRISPR/Cas9.
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Affiliation(s)
- Efrain Hualpa-Ramirez
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | | | | | - Ricardo Tejos
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Simón Ruiz-Lara
- Instituto de Ciencias Biológicas. Universidad de Talca, Talca, Chile
| | - Claudia Stange
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile.
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4
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Jennings S, Challinor A, Smith P, Macdiarmid JI, Pope E, Chapman S, Bradshaw C, Clark H, Vetter S, Fitton N, King R, Mwamakamba S, Madzivhandila T, Mashingaidze I, Chomba C, Nawiko M, Nyhodo B, Mazibuko N, Yeki P, Kuwali P, Kambwiri A, Kazi V, Kiama A, Songole A, Coskeran H, Quinn C, Sallu S, Dougill A, Whitfield S, Kunin B, Meebelo N, Jamali A, Kantande D, Makundi P, Mbungu W, Kayula F, Walker S, Zimba S, Galani Yamdeu JH, Kapulu N, Galdos MV, Eze S, Tripathi H, Sait S, Kepinski S, Likoya E, Greathead H, Smith HE, Mahop MT, Harwatt H, Muzammil M, Horgan G, Benton T. Stakeholder-driven transformative adaptation is needed for climate-smart nutrition security in sub-Saharan Africa. NATURE FOOD 2024; 5:37-47. [PMID: 38168785 PMCID: PMC10810754 DOI: 10.1038/s43016-023-00901-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Improving nutrition security in sub-Saharan Africa under increasing climate risks and population growth requires a strong and contextualized evidence base. Yet, to date, few studies have assessed climate-smart agriculture and nutrition security simultaneously. Here we use an integrated assessment framework (iFEED) to explore stakeholder-driven scenarios of food system transformation towards climate-smart nutrition security in Malawi, South Africa, Tanzania and Zambia. iFEED translates climate-food-emissions modelling into policy-relevant information using model output implication statements. Results show that diversifying agricultural production towards more micronutrient-rich foods is necessary to achieve an adequate population-level nutrient supply by mid-century. Agricultural areas must expand unless unprecedented rapid yield improvements are achieved. While these transformations are challenging to accomplish and often associated with increased greenhouse gas emissions, the alternative for a nutrition-secure future is to rely increasingly on imports, which would outsource emissions and be economically and politically challenging given the large import increases required.
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Affiliation(s)
- Stewart Jennings
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom.
| | - Andrew Challinor
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Jennie I Macdiarmid
- The Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Edward Pope
- Hadley Centre, Met Office, Exeter, United Kingdom
| | - Sarah Chapman
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Catherine Bradshaw
- Hadley Centre, Met Office, Exeter, United Kingdom
- The Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Heather Clark
- Institute of Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Sylvia Vetter
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Nuala Fitton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Richard King
- Chatham House, The Royal Institute of International Affairs, London, United Kingdom
| | - Sithembile Mwamakamba
- Food, Agriculture and Natural Resources Policy Analysis Network, Pretoria, South Africa
| | | | - Ian Mashingaidze
- Food, Agriculture and Natural Resources Policy Analysis Network, Pretoria, South Africa
| | | | | | - Bonani Nyhodo
- National Agricultural Marketing Council, Pretoria, South Africa
| | | | - Precious Yeki
- National Agricultural Marketing Council, Pretoria, South Africa
| | | | | | - Vivian Kazi
- Economic and Social Research Foundation, Dar es Salaam, Tanzania
| | - Agatha Kiama
- Economic and Social Research Foundation, Dar es Salaam, Tanzania
| | - Abel Songole
- Economic and Social Research Foundation, Dar es Salaam, Tanzania
| | - Helen Coskeran
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Claire Quinn
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Susannah Sallu
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Andrew Dougill
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Stephen Whitfield
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Bill Kunin
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nalishebo Meebelo
- Regional Network of Agricultural Policy Research Institutes, Lusaka, Zambia
| | - Andrew Jamali
- Malawi National Planning Commission, Lilongwe, Malawi
| | | | - Prosper Makundi
- Environmental Management Unit, Ministry of Agriculture, Dodoma, Tanzania
| | | | | | - Sue Walker
- Agricultural Research Council, Pretoria, South Africa
- University of the Free State, Bloemfontein, South Africa
| | - Sibongile Zimba
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Joseph Hubert Galani Yamdeu
- School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
- Section of Natural and Applied Sciences, School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Ndashe Kapulu
- School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
| | - Marcelo Valadares Galdos
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - Samuel Eze
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
- Department of Agriculture and Environment, Harper Adams University, Newport, United Kingdom
| | - Hemant Tripathi
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- UN Environment Programme, World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, United Kingdom
| | - Steven Sait
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Stefan Kepinski
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Emmanuel Likoya
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Henry Greathead
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Harriet Elizabeth Smith
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Marcelin Tonye Mahop
- Sustainability Research Institute, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
- USAID West Africa Biodiversity and Low Emissions Development (WABiLED) Programme, Accra, Ghana
| | - Helen Harwatt
- Chatham House, The Royal Institute of International Affairs, London, United Kingdom
| | - Maliha Muzammil
- Chatham House, The Royal Institute of International Affairs, London, United Kingdom
| | - Graham Horgan
- Biomathematics and Statistics Scotland, Aberdeen, United Kingdom
| | - Tim Benton
- Chatham House, The Royal Institute of International Affairs, London, United Kingdom
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5
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Xu X, Sun D, Ni Z, Zou X, Xu X, Sun M, Cao Q, Tong J, Ding F, Zhang Y, Wang F, Dong Y, Zhang L, Wang J, Xia X, He Z, Hao Y. Molecular identification and validation of four stable QTL for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:232. [PMID: 37875655 DOI: 10.1007/s00122-023-04481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15 K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22 Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8 cM genetic intervals spanning 13.6 Mb (76.0-89.6 Mb) and 1.7 cM and 4.9 Mb (659.9-664.8 Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR.
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Affiliation(s)
- Xiaowan Xu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Zhongqiu Ni
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaoting Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiang Cao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Fugong Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Shijiazhuang, 050035, Hebei, China
| | - Fengju Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Luyan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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6
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Soriano B, Hafez AI, Naya-Català F, Moroni F, Moldovan RA, Toxqui-Rodríguez S, Piazzon MC, Arnau V, Llorens C, Pérez-Sánchez J. SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach. Genes (Basel) 2023; 14:1650. [PMID: 37628701 PMCID: PMC10454057 DOI: 10.3390/genes14081650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to (i) infer information of how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and (ii) predict how the diversity and functional profile of that microbiome would change under other variable conditions. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of Bayesian network scenarios created by SAMBA using data from a microbial synthetic community, and the pan-microbiome of gilthead sea bream (Sparus aurata) in different feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems as it can be used for modelling microbiome-host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem.
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Affiliation(s)
- Beatriz Soriano
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia and CSIC (UVEG-CSIC), 46980 Paterna, Spain;
| | - Ahmed Ibrahem Hafez
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
| | - Fernando Naya-Català
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - Federico Moroni
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - Roxana Andreea Moldovan
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain
| | - Socorro Toxqui-Rodríguez
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - María Carla Piazzon
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - Vicente Arnau
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia and CSIC (UVEG-CSIC), 46980 Paterna, Spain;
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
| | - Carlos Llorens
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
| | - Jaume Pérez-Sánchez
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
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7
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Marla S, Felderhoff T, Hayes C, Perumal R, Wang X, Poland J, Morris GP. Genomics and phenomics enabled prebreeding improved early-season chilling tolerance in Sorghum. G3 (BETHESDA, MD.) 2023; 13:jkad116. [PMID: 37232400 PMCID: PMC10411554 DOI: 10.1093/g3journal/jkad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, chilling sensitivity of sorghum, a tropical-origin cereal crop, limits early planting, and over 50 years of conventional breeding has been stymied by coinheritance of chilling tolerance (CT) loci with undesirable tannin and dwarfing alleles. In this study, phenomics and genomics-enabled approaches were used for prebreeding of sorghum early-season CT. Uncrewed aircraft systems (UAS) high-throughput phenotyping platform tested for improving scalability showed moderate correlation between manual and UAS phenotyping. UAS normalized difference vegetation index values from the chilling nested association mapping population detected CT quantitative trait locus (QTL) that colocalized with manual phenotyping CT QTL. Two of the 4 first-generation Kompetitive Allele Specific PCR (KASP) molecular markers, generated using the peak QTL single nucleotide polymorphisms (SNPs), failed to function in an independent breeding program as the CT allele was common in diverse breeding lines. Population genomic fixation index analysis identified SNP CT alleles that were globally rare but common to the CT donors. Second-generation markers, generated using population genomics, were successful in tracking the donor CT allele in diverse breeding lines from 2 independent sorghum breeding programs. Marker-assisted breeding, effective in introgressing CT allele from Chinese sorghums into chilling-sensitive US elite sorghums, improved early-planted seedling performance ratings in lines with CT alleles by up to 13-24% compared to the negative control under natural chilling stress. These findings directly demonstrate the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.
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Affiliation(s)
- Sandeep Marla
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Terry Felderhoff
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Chad Hayes
- USDA-ARS, Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, Lubbock, TX 79415, USA
| | - Ramasamy Perumal
- Western Kansas Agricultural Research Center, Kansas State University, Hays, KS 67601, USA
| | - Xu Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Department of Agricultural and Biological Engineering, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33598, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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8
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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9
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Drapal M, Enfissi EMA, Almeida J, Rapacz E, Nogueira M, Fraser PD. The potential of metabolomics in assessing global compositional changes resulting from the application of CRISPR/Cas9 technologies. Transgenic Res 2023; 32:265-278. [PMID: 37166587 DOI: 10.1007/s11248-023-00347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
Exhaustive analysis of genetically modified crops over multiple decades has increased societal confidence in the technology. New Plant Breeding Techniques are now emerging with improved precision and the ability to generate products containing no foreign DNA and mimic/replicate conventionally bred varieties. In the present study, metabolomic analysis was used to compare (i) tobacco genotypes with and without the CRISPR associated protein 9 (Cas9), (ii) tobacco lines with the edited and non-edited DE-ETIOLATED-1 gene without phenotype and (iii) leaf and fruit tissue from stable non-edited tomato progeny with and without the Cas9. In all cases, multivariate analysis based on the difference test using LC-HRMS/MS and GC-MS data indicated no significant difference in their metabolomes. The variations in metabolome composition that were evident could be associated with the processes of tissue culture regeneration and/or transformation (e.g. interaction with Agrobacterium). Metabolites responsible for the variance included quantitative changes of abundant, well characterised metabolites such as phenolics (e.g. chlorogenic acid) and several common sugars such as fructose. This study provides fundamental data on the characterisation of gene edited crops, that are important for the evaluation of the technology and its assessment. The approach also suggests that metabolomics could contribute to routine product-based analysis of crops/foods generated from New Plant Breeding approaches.
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Affiliation(s)
- Margit Drapal
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Eugenia M A Enfissi
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Elzbieta Rapacz
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Marilise Nogueira
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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10
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Kalamartzis I, Papakaloudis P, Dordas C. Basil ( Ocimum basilicum) Landraces Can Be Used in a Water-Limited Environment. PLANTS (BASEL, SWITZERLAND) 2023; 12:2425. [PMID: 37446986 DOI: 10.3390/plants12132425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Basil (Ocimum basilicum L.) is a member of the Labiatae family and is one of the most widely consumed aromatic and medicinal plants in many countries due to its numerous properties and uses. The objective of the study was to determine whether landraces are better adapted to water-limited environments compared to commercial cultivars. Irrigation levels and genotypes affected plant height and leaf area index, with 25% and 33% higher values observed under complete irrigation, respectively. Additionally, limited water availability resulted in a 20% reduction in dry matter yield and a 21% reduction in essential oil yield over the three years in all of the genotypes tested, specifically in the lower irrigation treatment (d40), compared to the control treatment (d100). The landraces that performed the best under limited water supply were Athos white spike (AWS) and Gigas white spike (GWS), indicating their suitability for environments with limited water resources. The results demonstrate that there are landraces that can be utilized in dryland climates with appropriate water management, enabling water conservation and utilization of fields in water-scarce areas for irrigation purposes.
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Affiliation(s)
- Iakovos Kalamartzis
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paschalis Papakaloudis
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos Dordas
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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11
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Bubolz J, Sleboda P, Lehrman A, Hansson SO, Johan Lagerkvist C, Andersson B, Lenman M, Resjö S, Ghislain M, Zahid MA, Kieu NP, Andreasson E. Genetically modified (GM) late blight-resistant potato and consumer attitudes before and after a field visit. GM CROPS & FOOD 2022; 13:290-298. [PMID: 36263889 PMCID: PMC9586588 DOI: 10.1080/21645698.2022.2133396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Late blight, caused by Phytophthora infestans, is the most devastating disease in potato production. Here, we show full late blight resistance in a location with a genetically diverse pathogen population with the use of GM potato stacked with three resistance (R) genes over three seasons. In addition, using this field trials, we demonstrate that in-the-field intervention among consumers led to change for more favorable attitude generally toward GM crops.
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Affiliation(s)
- Jéssica Bubolz
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp Campus, Sweden
| | - Patrycja Sleboda
- Deparment of Economics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Lehrman
- Department of crop prodction ecology, Swedish University of Agricultural Sciences, Uppsala, Swedan
| | - Sven-Ove Hansson
- Department of crop prodction ecology, Swedish University of Agricultural Sciences, Uppsala, Swedan
| | - Carl Johan Lagerkvist
- Deparment of Economics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Andersson
- Department of forest mycology and plant pathology, Swedish University of Agricultural Sciences
| | - Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp Campus, Sweden
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp Campus, Sweden
| | | | - Muhammad Awais Zahid
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp Campus, Sweden
| | - Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp Campus, Sweden,Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp Campus, Sweden,CONTACT Erik Andreasson Professor Resistance Biology Unit, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190,SE-234 22, Lomma, Sweden
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12
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Relevance of the Exocyst in Arabidopsis exo70e2 Mutant for Cellular Homeostasis under Stress. Int J Mol Sci 2022; 24:ijms24010424. [PMID: 36613868 PMCID: PMC9820329 DOI: 10.3390/ijms24010424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Plants must adapt to cope with adverse environmental conditions that affect their growth and development. To overcome these constraints, they can alter their developmental patterns by modulating cellular processes and activating stress-responsive signals. Alongside the activation of the antioxidant (AOX) system, a high number of genes are expressed, and proteins must be distributed to the correct locations within the cell. The endomembrane system and associated vesicles thus play an important role. Several pathways have been associated with adverse environmental conditions, which is the case for the exocyst-positive organelle-EXPO. The present work, using Arabidopsis mutants with T-DNA insertions in the gene EXO70, essential for EXPO vesicles formation, was designed to characterise the anatomical (morphology and root length), biochemical (quantification of stress markers and antioxidant system components), and molecular responses (gene expression) to abiotic stresses (saline, drought, oxidative, and metal-induced toxicity). The results obtained showed that mutant plants behave differently from the wild type (WT) plants. Therefore, in the exo70 mutant, morphological changes were more noticeable in plants under stress, and the non-enzymatic component of the antioxidant system was activated, with no alterations to the enzymatic component. Furthermore, other defence strategies, such as autophagy, did not show important changes. These results confirmed the EXPO as an important structure for tolerance/adaptation to stress.
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13
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Bhandari N, Walambe R, Kotecha K, Khare SP. A comprehensive survey on computational learning methods for analysis of gene expression data. Front Mol Biosci 2022; 9:907150. [PMID: 36458095 PMCID: PMC9706412 DOI: 10.3389/fmolb.2022.907150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/28/2022] [Indexed: 09/19/2023] Open
Abstract
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous amounts of data. Traditionally, statistical methods are used for comparative analysis of gene expression data. However, more complex analysis for classification of sample observations, or discovery of feature genes requires sophisticated computational approaches. In this review, we compile various statistical and computational tools used in analysis of expression microarray data. Even though the methods are discussed in the context of expression microarrays, they can also be applied for the analysis of RNA sequencing and quantitative proteomics datasets. We discuss the types of missing values, and the methods and approaches usually employed in their imputation. We also discuss methods of data normalization, feature selection, and feature extraction. Lastly, methods of classification and class discovery along with their evaluation parameters are described in detail. We believe that this detailed review will help the users to select appropriate methods for preprocessing and analysis of their data based on the expected outcome.
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Affiliation(s)
- Nikita Bhandari
- Computer Science Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, India
| | - Rahee Walambe
- Electronics and Telecommunication Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, India
- Symbiosis Center for Applied AI (SCAAI), Symbiosis International (Deemed University), Pune, India
| | - Ketan Kotecha
- Computer Science Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, India
- Symbiosis Center for Applied AI (SCAAI), Symbiosis International (Deemed University), Pune, India
| | - Satyajeet P. Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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14
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Hirabayashi K, Murch SJ, Erland LAE. Predicted impacts of climate change on wild and commercial berry habitats will have food security, conservation and agricultural implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157341. [PMID: 35842164 DOI: 10.1016/j.scitotenv.2022.157341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Climate change is now a reality and is altering ecosystems, with Canada experiencing 2-4 times the global average rate of warming. This will have a critical impact on berry cultivation and horticulture. Enhancing our understanding of how wild and cultivated berries will perform under changing climates will be essential to mitigating impacts on ecosystems, culture and food security. Our objective was to predict the impact of climate change on habitat suitability of four berry producing Vaccinium species: two species with primarily northern distributions (V. uliginosum, V. vitis-idaea), one species with a primarily southern distribution (V. oxycoccos), and the commercially cultivated V. macrocarpon. We used the maximum entropy (Maxent) model and the CMIP6 shared socioeconomic pathways (SSPs) 126 and 585 projected to 2041-2060 and 2061-2080. Wild species showed a uniform northward progression and expansion of suitable habitat. Our modeling predicts that suitable growing regions for commercial cranberries are also likely to shift with some farms becoming unsuitable for the current varieties and other regions becoming more suitable for cranberry farms. Both V. macrocarpon and V. oxycoccos showed a high dependence on precipitation-associated variables. Vaccinium vitis-idaea and V. uliginosum had a greater number of variables with smaller contributions which may improve their resilience to individual climactic events. Future competition between commercial cranberry farms and wild berries in protected areas could lead to conflicts between agriculture and conservation priorities. New varieties of commercial berries are required to maintain current commercial berry farms.
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Affiliation(s)
- Kaede Hirabayashi
- Chemistry, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada; Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Susan J Murch
- Chemistry, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Lauren A E Erland
- Chemistry, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada; Agriculture, University of the Fraser Valley, Chilliwack, BC, V2R 0N9, Canada.
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15
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Macfarlane NB, Adams J, Bennett EL, Brooks TM, Delborne JA, Eggermont H, Endy D, Esvelt KM, Kolodziejczyk B, Kuiken T, Oliva MJ, Peña Moreno S, Slobodian L, Smith RB, Thizy D, Tompkins DM, Wei W, Redford KH. Direct and indirect impacts of synthetic biology on biodiversity conservation. iScience 2022; 25:105423. [DOI: 10.1016/j.isci.2022.105423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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16
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Mei F, Chen B, Du L, Li S, Zhu D, Chen N, Zhang Y, Li F, Wang Z, Cheng X, Ding L, Kang Z, Mao H. A gain-of-function allele of a DREB transcription factor gene ameliorates drought tolerance in wheat. THE PLANT CELL 2022; 34:4472-4494. [PMID: 35959993 PMCID: PMC9614454 DOI: 10.1093/plcell/koac248] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/04/2022] [Indexed: 05/13/2023]
Abstract
Drought is a major environmental factor limiting wheat production worldwide. However, the genetic components underlying wheat drought tolerance are largely unknown. Here, we identify a DREB transcription factor gene (TaDTG6-B) by genome-wide association study that is tightly associated with drought tolerance in wheat. Candidate gene association analysis revealed that a 26-bp deletion in the TaDTG6-B coding region induces a gain-of-function for TaDTG6-BDel574, which exhibits stronger transcriptional activation, protein interactions, and binding activity to dehydration-responsive elements (DRE)/CRT cis-elements than the TaDTG6-BIn574 encoded by the allele lacking the deletion, thus conferring greater drought tolerance in wheat seedlings harboring this variant. Knockdown of TaDTG6-BDel574 transcripts attenuated drought tolerance in transgenic wheat, whereas its overexpression resulted in enhanced drought tolerance without accompanying phenotypic abnormalities. Furthermore, the introgression of the TaDTG6-BDel574 elite allele into drought-sensitive cultivars improved their drought tolerance, thus providing a valuable genetic resource for wheat breeding. We also identified 268 putative target genes that are directly bound and transcriptionally regulated by TaDTG6-BDel574. Further analysis showed that TaDTG6-BDel574 positively regulates TaPIF1 transcription to enhance wheat drought tolerance. These results describe the genetic basis and accompanying mechanism driving phenotypic variation in wheat drought tolerance, and provide a novel genetic resource for crop breeding programs.
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Affiliation(s)
- Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dehe Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Pioneering Innovation Center for Wheat Stress Tolerance Improvement, Yangling, Shaanxi 712100, China
- Yangling Seed Industry Innovation Center, Yangling, Shaanxi 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Pioneering Innovation Center for Wheat Stress Tolerance Improvement, Yangling, Shaanxi 712100, China
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17
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Zerriffi H, Reyes R, Maloney A. Pathways to sustainable land use and food systems in Canada. SUSTAINABILITY SCIENCE 2022; 18:389-406. [PMID: 36275780 PMCID: PMC9575642 DOI: 10.1007/s11625-022-01213-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Meeting global sustainability targets under the United Nations Sustainable Development Goals and the Paris Agreement requires paying attention to major land-use sectors such as forestry and agriculture. These sectors play a large role in national emissions, biodiversity conservation, and human well-being. There are numerous possible pathways to sustainability in these sectors and potential synergies and trade-offs along those pathways. This paper reports on the use of a model for Canada's land use to 2050 to assess three different pathways (one based on current trends and two with differing levels of ambition for meeting sustainability targets). This was done as part of a large international consortium, Food, Agriculture, Biodiversity, Land and Energy (FABLE), which allows for incorporating international trade in meeting both national and global sustainability targets. The results show not only the importance of increasingly stringent policies in meeting the targets, but also the role that population and consumption (e.g., diets) play in meeting the targets. Both the medium and high ambition sustainability pathways can drastically reduce greenhouse gas emissions while protecting forestland. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11625-022-01213-z.
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Affiliation(s)
- Hisham Zerriffi
- Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4 Canada
| | - Rene Reyes
- Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4 Canada
- Instituto Forestal, Fundo Teja Norte sin número, Valdivia, Chile
| | - Avery Maloney
- Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4 Canada
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18
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Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
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19
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Pangenomics and Crop Genome Adaptation in a Changing Climate. PLANTS 2022; 11:plants11151949. [PMID: 35956427 PMCID: PMC9370458 DOI: 10.3390/plants11151949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/15/2022]
Abstract
During crop domestication and breeding, wild plant species have been shaped into modern high-yield crops and adapted to the main agro-ecological regions. However, climate change will impact crop productivity in these regions, and agriculture needs to adapt to support future food production. On a global scale, crop wild relatives grow in more diverse environments than crop species, and so may host genes that could support the adaptation of crops to new and variable environments. Through identification of individuals with increased climate resilience we may gain a greater understanding of the genomic basis for this resilience and transfer this to crops. Pangenome analysis can help to identify the genes underlying stress responses in individuals harbouring untapped genomic diversity in crop wild relatives. The information gained from the analysis of these pangenomes can then be applied towards breeding climate resilience into existing crops or to re-domesticating crops, combining environmental adaptation traits with crop productivity.
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20
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Gill M, Anderson R, Hu H, Bennamoun M, Petereit J, Valliyodan B, Nguyen HT, Batley J, Bayer PE, Edwards D. Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction. BMC PLANT BIOLOGY 2022; 22:180. [PMID: 35395721 PMCID: PMC8991976 DOI: 10.1186/s12870-022-03559-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/21/2022] [Indexed: 05/26/2023]
Abstract
Recent growth in crop genomic and trait data have opened opportunities for the application of novel approaches to accelerate crop improvement. Machine learning and deep learning are at the forefront of prediction-based data analysis. However, few approaches for genotype to phenotype prediction compare machine learning with deep learning and further interpret the models that support the predictions. This study uses genome wide molecular markers and traits across 1110 soybean individuals to develop accurate prediction models. For 13/14 sets of predictions, XGBoost or random forest outperformed deep learning models in prediction performance. Top ranked SNPs by F-score were identified from XGBoost, and with further investigation found overlap with significantly associated loci identified from GWAS and previous literature. Feature importance rankings were used to reduce marker input by up to 90%, and subsequent models maintained or improved their prediction performance. These findings support interpretable machine learning as an approach for genomic based prediction of traits in soybean and other crops.
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Affiliation(s)
- Mitchell Gill
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Robyn Anderson
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Mohammed Bennamoun
- Department of Computer Science and Software Engineering, The University of Western Australia, Perth, WA, Australia
| | - Jakob Petereit
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia.
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21
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Wu PY, Stich B, Weisweiler M, Shrestha A, Erban A, Westhoff P, Inghelandt DV. Improvement of prediction ability by integrating multi-omic datasets in barley. BMC Genomics 2022; 23:200. [PMID: 35279073 PMCID: PMC8917753 DOI: 10.1186/s12864-022-08337-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genomic prediction (GP) based on single nucleotide polymorphisms (SNP) has become a broadly used tool to increase the gain of selection in plant breeding. However, using predictors that are biologically closer to the phenotypes such as transcriptome and metabolome may increase the prediction ability in GP. The objectives of this study were to (i) assess the prediction ability for three yield-related phenotypic traits using different omic datasets as single predictors compared to a SNP array, where these omic datasets included different types of sequence variants (full-SV, deleterious-dSV, and tolerant-tSV), different types of transcriptome (expression presence/absence variation-ePAV, gene expression-GE, and transcript expression-TE) sampled from two tissues, leaf and seedling, and metabolites (M); (ii) investigate the improvement in prediction ability when combining multiple omic datasets information to predict phenotypic variation in barley breeding programs; (iii) explore the predictive performance when using SV, GE, and ePAV from simulated 3’end mRNA sequencing of different lengths as predictors. Results The prediction ability from genomic best linear unbiased prediction (GBLUP) for the three traits using dSV information was higher than when using tSV, all SV information, or the SNP array. Any predictors from the transcriptome (GE, TE, as well as ePAV) and metabolome provided higher prediction abilities compared to the SNP array and SV on average across the three traits. In addition, some (di)-similarity existed between different omic datasets, and therefore provided complementary biological perspectives to phenotypic variation. Optimal combining the information of dSV, TE, ePAV, as well as metabolites into GP models could improve the prediction ability over that of the single predictors alone. Conclusions The use of integrated omic datasets in GP model is highly recommended. Furthermore, we evaluated a cost-effective approach generating 3’end mRNA sequencing with transcriptome data extracted from seedling without losing prediction ability in comparison to the full-length mRNA sequencing, paving the path for the use of such prediction methods in commercial breeding programs. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08337-7).
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22
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Tailored communication changes consumers’ attitudes and product preferences for genetically modified food. Food Qual Prefer 2022. [DOI: 10.1016/j.foodqual.2021.104419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Marsh JI, Petereit J, Bayer PE, Batley J, Edwards D. Expanding Gene-Editing Potential in Crop Improvement with Pangenomes. Int J Mol Sci 2022; 23:ijms23042276. [PMID: 35216392 PMCID: PMC8879065 DOI: 10.3390/ijms23042276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.
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González Guzmán M, Cellini F, Fotopoulos V, Balestrini R, Arbona V. New approaches to improve crop tolerance to biotic and abiotic stresses. PHYSIOLOGIA PLANTARUM 2022; 174:e13547. [PMID: 34480798 PMCID: PMC9290814 DOI: 10.1111/ppl.13547] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 05/24/2023]
Abstract
During the last years, a great effort has been dedicated at the development and employment of diverse approaches for achieving more stress-tolerant and climate-flexible crops and sustainable yield increases to meet the food and energy demands of the future. The ongoing climate change is in fact leading to more frequent extreme events with a negative impact on food production, such as increased temperatures, drought, and soil salinization as well as invasive arthropod pests and diseases. In this review, diverse "green strategies" (e.g., chemical priming, root-associated microorganisms), and advanced technologies (e.g., genome editing, high-throughput phenotyping) are described on the basis of the most recent research evidence. Particularly, attention has been focused on the potential use in a context of sustainable and climate-smart agriculture (the so called "next agriculture generation") to improve plant tolerance and resilience to abiotic and biotic stresses. In addition, the gap between the results obtained in controlled experiments and those from application of these technologies in real field conditions (lab to field step) is also discussed.
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Affiliation(s)
- Miguel González Guzmán
- Departament de Ciències Agràries i del Medi NaturalUniversitat Jaume ICastelló de la PlanaSpain
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
| | - Francesco Cellini
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (ALSIA)MetapontoItaly
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante (CNR, IPSP)TorinoItaly
| | - Vasileios Fotopoulos
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Department of Agricultural Sciences, Biotechnology & Food ScienceCyprus University of TechnologyLemesosCyprus
| | - Raffaella Balestrini
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante (CNR, IPSP)TorinoItaly
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi NaturalUniversitat Jaume ICastelló de la PlanaSpain
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
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25
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Jiang X, Zhang W, Fernie AR, Wen W. Combining novel technologies with interdisciplinary basic research to enhance horticultural crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:35-46. [PMID: 34699639 DOI: 10.1111/tpj.15553] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/17/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.
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Affiliation(s)
- Xiaohui Jiang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Tea Research Institute, Guangdong Provincial Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Chettry U, Chrungoo NK. Beyond the Cereal Box: Breeding Buckwheat as a Strategic Crop for Human Nutrition. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2021; 76:399-409. [PMID: 34652552 DOI: 10.1007/s11130-021-00930-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 04/24/2023]
Abstract
While intensification of farming systems is essential for achieving the Millennium Development Goal of "Zero hunger", issues such as availability of nutritious foods would demand increased attention if any long-term form of food security is to be achieved. Since wheat, rice and maize have reached near to 80 percent of their yield potential and reliance on these crops alone would not be sufficient to close the gap between demand and supply, there is a need to bring other climate-resilient and nutritionally dense crops into agricultural portfolio. Buckwheat (Fagopyrum spp.) has attracted considerable interest amongst global scientific community due to its nutritional and pharmaceutical properties. The gluten free nature of buckwheat, nutritionally balanced amino acid composition of its grain protein, and high levels of anti-oxidants, such as rutin, makes buckwheat an important crop with immense nutraceutical benefits. However, a key challenge in buckwheat cultivation is the variation in yield between years, which impacts the entire value chain. Current information on buckwheat indicates existence of significant phenotypic variation for agronomic and nutritional traits. However, genetic bottlenecks in conventional breeding restrict effective utilization of the existing diversity in mainstreaming buckwheat cultivation. Availability of high density buckwheat genome map for both the cultivated species viz. F. esculentum and F. tataricum would add to our understanding of genetic basis of their agronomic traits. The review examines the potential of buckwheat as a strategic crop for human nutrition and prospects of effective exploitation genomic information of common and Tartary buckwheat for genome assisted breeding.
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Affiliation(s)
- Upasna Chettry
- Department of Botany, North-Eastern Hill University, Shillong, 793022, India
| | - Nikhil K Chrungoo
- Department of Botany, North-Eastern Hill University, Shillong, 793022, India.
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Genetic and Proteomic Basis of Sclerotinia Stem Rot Resistance in Indian Mustard [ Brassica juncea (L.) Czern & Coss.]. Genes (Basel) 2021; 12:genes12111784. [PMID: 34828391 PMCID: PMC8621386 DOI: 10.3390/genes12111784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Sclerotinia stem rot is one of the utmost important disease of mustard, causing considerable losses in seed yield and oil quality. The study of the genetic and proteomic basis of resistance to this disease is imperative for its effective utilization in developing resistant cultivars. Therefore, the genetic pattern of Sclerotinia stem rot resistance in Indian mustard was studied using six generations (P1, P2, F1, F2, BC1P1, and BC1P2) developed from the crossing of one resistant (RH 1222-28) and two susceptible (EC 766300 and EC 766123) genotypes. Genetic analysis revealed that resistance was governed by duplicate epistasis. Comparative proteome analysis of resistant and susceptible genotypes indicated that peptidyl-prolyl cis-trans isomerase (A0A078IDN6 PPIase) showed high expression in resistant genotype at the early infection stage while its expression was delayed in susceptible genotypes. This study provides important insight to mustard breeders for designing effective breeding programs to develop resistant cultivars against this devastating disease.
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28
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Razzaq A, Wani SH, Saleem F, Yu M, Zhou M, Shabala S. Rewilding crops for climate resilience: economic analysis and de novo domestication strategies. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6123-6139. [PMID: 34114599 DOI: 10.1093/jxb/erab276] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/09/2021] [Indexed: 05/08/2023]
Abstract
To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year-1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisald 38040,Pakistan
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, J&K,India
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisald 38040,Pakistan
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000,China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas 7001,Australia
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000,China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas 7001,Australia
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29
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Khan MN, Li Y, Khan Z, Chen L, Liu J, Hu J, Wu H, Li Z. Nanoceria seed priming enhanced salt tolerance in rapeseed through modulating ROS homeostasis and α-amylase activities. J Nanobiotechnology 2021; 19:276. [PMID: 34530815 PMCID: PMC8444428 DOI: 10.1186/s12951-021-01026-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/03/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Salinity is a big threat to agriculture by limiting crop production. Nanopriming (seed priming with nanomaterials) is an emerged approach to improve plant stress tolerance; however, our knowledge about the underlying mechanisms is limited. RESULTS Herein, we used cerium oxide nanoparticles (nanoceria) to prime rapeseeds and investigated the possible mechanisms behind nanoceria improved rapeseed salt tolerance. We synthesized and characterized polyacrylic acid coated nanoceria (PNC, 8.5 ± 0.2 nm, -43.3 ± 6.3 mV) and monitored its distribution in different tissues of the seed during the imbibition period (1, 3, 8 h priming). Our results showed that compared with the no nanoparticle control, PNC nanopriming improved germination rate (12%) and biomass (41%) in rapeseeds (Brassica napus) under salt stress (200 mM NaCl). During the priming hours, PNC were located mostly in the seed coat, nevertheless the intensity of PNC in cotyledon and radicle was increased alongside with the increase of priming hours. During the priming hours, the amount of the absorbed water (52%, 14%, 12% increase at 1, 3, 8 h priming, respectively) and the activities of α-amylase were significantly higher (175%, 309%, 295% increase at 1, 3, 8 h priming, respectively) in PNC treatment than the control. PNC primed rapeseeds showed significantly lower content of MDA, H2O2, and •O2- in both shoot and root than the control under salt stress. Also, under salt stress, PNC nanopriming enabled significantly higher K+ retention (29%) and significantly lower Na+ accumulation (18.5%) and Na+/K+ ratio (37%) than the control. CONCLUSIONS Our results suggested that besides the more absorbed water and higher α-amylase activities, PNC nanopriming improves salt tolerance in rapeseeds through alleviating oxidative damage and maintaining Na+/K+ ratio. It adds more knowledge regarding the mechanisms underlying nanopriming improved plant salt tolerance.
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Affiliation(s)
- Mohammad Nauman Khan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanhui Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zaid Khan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linlin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiahao Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin Hu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Wu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Zhaohu Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- School of Agriculture and Technology, China Agricultural University, Beijing, 100083, China.
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Razzaq A, Saleem F, Wani SH, Abdelmohsen SAM, Alyousef HA, Abdelbacki AMM, Alkallas FH, Tamam N, Elansary HO. De-novo Domestication for Improving Salt Tolerance in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:681367. [PMID: 34603347 PMCID: PMC8481614 DOI: 10.3389/fpls.2021.681367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/12/2021] [Indexed: 05/21/2023]
Abstract
Global agriculture production is under serious threat from rapidly increasing population and adverse climate changes. Food security is currently a huge challenge to feed 10 billion people by 2050. Crop domestication through conventional approaches is not good enough to meet the food demands and unable to fast-track the crop yields. Also, intensive breeding and rigorous selection of superior traits causes genetic erosion and eliminates stress-responsive genes, which makes crops more prone to abiotic stresses. Salt stress is one of the most prevailing abiotic stresses that poses severe damages to crop yield around the globe. Recent innovations in state-of-the-art genomics and transcriptomics technologies have paved the way to develop salinity tolerant crops. De novo domestication is one of the promising strategies to produce superior new crop genotypes through exploiting the genetic diversity of crop wild relatives (CWRs). Next-generation sequencing (NGS) technologies open new avenues to identifying the unique salt-tolerant genes from the CWRs. It has also led to the assembly of highly annotated crop pan-genomes to snapshot the full landscape of genetic diversity and recapture the huge gene repertoire of a species. The identification of novel genes alongside the emergence of cutting-edge genome editing tools for targeted manipulation renders de novo domestication a way forward for developing salt-tolerance crops. However, some risk associated with gene-edited crops causes hurdles for its adoption worldwide. Halophytes-led breeding for salinity tolerance provides an alternative strategy to identify extremely salt tolerant varieties that can be used to develop new crops to mitigate salinity stress.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Division of Genetics and Plant Breeding, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Shaimaa A. M. Abdelmohsen
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Haifa A. Alyousef
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Fatemah H. Alkallas
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nissren Tamam
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
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Vitoriano CB, Calixto CPG. Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress. PLANTS 2021; 10:plants10081647. [PMID: 34451692 PMCID: PMC8400768 DOI: 10.3390/plants10081647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Rice (Oryza sativa L.) is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of thermotolerance must be understood. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses. Alternative splicing (AS), in particular, is a widespread mechanism impacting the stress defence in plants but it has been completely overlooked in rice genome-wide heat stress studies. In this context, we carried out a robust data mining of publicly available RNA-seq datasets to investigate the extension of heat-induced AS in rice leaves. For this, datasets of interest were subjected to filtering and quality control, followed by accurate transcript-specific quantifications. Powerful differential gene expression (DE) and differential AS (DAS) identified 17,143 and 2162 heat response genes, respectively, many of which are novel. Detailed analysis of DAS genes coding for key regulators of gene expression suggests that AS helps shape transcriptome and proteome diversity in response to heat. The knowledge resulting from this study confirmed a widespread transcriptional and post-transcriptional response to heat stress in plants, and it provided novel candidates for rapidly advancing rice breeding in response to climate change.
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Razzaq A, Kaur P, Akhter N, Wani SH, Saleem F. Next-Generation Breeding Strategies for Climate-Ready Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:620420. [PMID: 34367194 PMCID: PMC8336580 DOI: 10.3389/fpls.2021.620420] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Climate change is a threat to global food security due to the reduction of crop productivity around the globe. Food security is a matter of concern for stakeholders and policymakers as the global population is predicted to bypass 10 billion in the coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations in microbiome applications, and exploiting the natural variations in underutilized crops is an excellent way forward to fulfill future food requirements. In this review, we describe the next-generation breeding tools that can be used to increase crop production by developing climate-resilient superior genotypes to cope with the future challenges of global food security. Recent innovations in genomic-assisted breeding (GAB) strategies allow the construction of highly annotated crop pan-genomes to give a snapshot of the full landscape of genetic diversity (GD) and recapture the lost gene repertoire of a species. Pan-genomes provide new platforms to exploit these unique genes or genetic variation for optimizing breeding programs. The advent of next-generation clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such as prime editing, base editing, and de nova domestication, has institutionalized the idea that genome editing is revamped for crop improvement. Also, the availability of versatile Cas orthologs, including Cas9, Cas12, Cas13, and Cas14, improved the editing efficiency. Now, the CRISPR/Cas systems have numerous applications in crop research and successfully edit the major crop to develop resistance against abiotic and biotic stress. By adopting high-throughput phenotyping approaches and big data analytics tools like artificial intelligence (AI) and machine learning (ML), agriculture is heading toward automation or digitalization. The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs. In addition, the integration of next-generation multidisciplinary breeding platforms can open exciting avenues to develop climate-ready crops toward global food security.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Naheed Akhter
- College of Allied Health Professional, Faculty of Medical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
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Johnson N, Boatwright JL, Bridges W, Thavarajah P, Kumar S, Shipe E, Thavarajah D. Genome-wide association mapping of lentil (Lens culinaris Medikus) prebiotic carbohydrates toward improved human health and crop stress tolerance. Sci Rep 2021; 11:13926. [PMID: 34230595 PMCID: PMC8260633 DOI: 10.1038/s41598-021-93475-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Lentil, a cool-season food legume, is rich in protein and micronutrients with a range of prebiotic carbohydrates, such as raffinose-family oligosaccharides (RFOs), fructooligosaccharides (FOSs), sugar alcohols (SAs), and resistant starch (RS), which contribute to lentil's health benefits. Beneficial microorganisms ferment prebiotic carbohydrates in the colon, which impart health benefits to the consumer. In addition, these carbohydrates are vital to lentil plant health associated with carbon transport, storage, and abiotic stress tolerance. Thus, lentil prebiotic carbohydrates are a potential nutritional breeding target for increasing crop resilience to climate change with increased global nutritional security. This study phenotyped a total of 143 accessions for prebiotic carbohydrates. A genome-wide association study (GWAS) was then performed to identify associated variants and neighboring candidate genes. All carbohydrates analyzed had broad-sense heritability estimates (H2) ranging from 0.22 to 0.44, comparable to those reported in the literature. Concentration ranges corresponded to percent recommended daily allowances of 2-9% SAs, 7-31% RFOs, 51-111% RS, and 57-116% total prebiotic carbohydrates. Significant SNPs and associated genes were identified for numerous traits, including a galactosyltransferase (Lcu.2RBY.1g019390) known to aid in RFO synthesis. Further studies in multiple field locations are necessary. Yet, these findings suggest the potential for molecular-assisted breeding for prebiotic carbohydrates in lentil to support human health and crop resilience to increase global food security.
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Affiliation(s)
- Nathan Johnson
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - J Lucas Boatwright
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
- Advanced Plant Technology, Clemson University, Clemson, SC, 29634, USA
| | - William Bridges
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - Pushparajah Thavarajah
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - Shiv Kumar
- Biodiversity and Crop Improvement Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institute, P.O. Box 6299, Rabat, Morocco
| | - Emerson Shipe
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - Dil Thavarajah
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA.
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Liu S, Huang S, Zeng Q, Wang X, Yu R, Wang Q, Singh RP, Bhavani S, Kang Z, Wu J, Han D. Refined mapping of stripe rust resistance gene YrP10090 within a desirable haplotype for wheat improvement on chromosome 6A. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2005-2021. [PMID: 33683400 DOI: 10.1007/s00122-021-03801-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
A large genomic region spanning over 300 Mb on chromosome 6A under intense artificial selection harbors multiple loci associated with favorable traits including stripe rust resistance in wheat. The development of resistance cultivars can be an optimal strategy for controlling wheat stripe rust disease. Although loci for stripe rust resistance have been identified on chromosome 6A in previous studies, it is unclear whether these loci span a common genetic interval, and few studies have attempted to analyze the haplotype changes that have accompanied wheat improvement over the period of modern breeding. In this study, we used F2:3 families and F6:7 recombinant inbred lines (RILs) derived from a cross between a resistant CIMMYT wheat accession P10090 and the susceptible landrace Mingxian 169 to improve the resolution of the QTL on chromosome 6A. The co-located QTL, designated as YrP10090, was flanked by SNP markers AX-94460938 and AX-110585473 with a genetic interval of 3.5 cM, however, corresponding to a large physical distance of over 300 Mb in RefSeq v.1.0 (positions 107.1-446.5 Mb). More than 1,300 SNP markers in this genetic region were extracted for haplotype analysis in a panel of 1,461 worldwide common wheat accessions, and three major haplotypes (Hap1, Hap2, and Hap3) were identified. The favorable haplotype Hap1 associated with stripe rust resistance exhibited a large degree of linkage disequilibrium. Selective sweep analyses were performed between different haplotype groups, revealing specific genomic regions with strong artificial selection signals. These regions harbored multiple desirable traits associated with resilience to environmental stress, different yield components, and quality characteristics. P10090 and its derivatives that carry the desirable haplotype can provide a concrete foundation for bread wheat improvement including the genomic selection.
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Affiliation(s)
- Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, Estado de Mexico, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, Estado de Mexico, Mexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Ghazal H, Adam Y, Idrissi Azami A, Sehli S, Nyarko HN, Chaouni B, Olasehinde G, Isewon I, Adebiyi M, Ajani O, Matovu E, Obembe O, Ajamma Y, Kuzamunu G, Pandam Salifu S, Kayondo J, Benkahla A, Adebiyi E. Plant genomics in Africa: present and prospects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:21-36. [PMID: 33837593 DOI: 10.1111/tpj.15272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Plants are the world's most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population's increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.
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Affiliation(s)
- Hassan Ghazal
- National Center for Scientific and Technical Research, Rabat, Morocco
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
| | | | - Sofia Sehli
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Hannah N Nyarko
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Bouchra Chaouni
- Laboratory of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Grace Olasehinde
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Biological Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Itunuoluwa Isewon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Marion Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Computer Science, Landmark University, Kwara-State, Omu-Aran, Nigeria
| | - Olayinka Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Chemistry, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Olawole Obembe
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Biological Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Yvonne Ajamma
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
| | - Gaston Kuzamunu
- African Institute for Mathematical Sciences, Cape Town, 7945, South Africa
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa
- Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Observatory, 7925, South Africa
| | - Samson Pandam Salifu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Jonathan Kayondo
- Uganda Virus Research Institute (UVRI), Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Alia Benkahla
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), G200, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
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Westerman EL, Bowman SEJ, Davidson B, Davis MC, Larson ER, Sanford CPJ. Deploying Big Data to Crack the Genotype to Phenotype Code. Integr Comp Biol 2021; 60:385-396. [PMID: 32492136 DOI: 10.1093/icb/icaa055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mechanistically connecting genotypes to phenotypes is a longstanding and central mission of biology. Deciphering these connections will unite questions and datasets across all scales from molecules to ecosystems. Although high-throughput sequencing has provided a rich platform on which to launch this effort, tools for deciphering mechanisms further along the genome to phenome pipeline remain limited. Machine learning approaches and other emerging computational tools hold the promise of augmenting human efforts to overcome these obstacles. This vision paper is the result of a Reintegrating Biology Workshop, bringing together the perspectives of integrative and comparative biologists to survey challenges and opportunities in cracking the genotype to phenotype code and thereby generating predictive frameworks across biological scales. Key recommendations include promoting the development of minimum "best practices" for the experimental design and collection of data; fostering sustained and long-term data repositories; promoting programs that recruit, train, and retain a diversity of talent; and providing funding to effectively support these highly cross-disciplinary efforts. We follow this discussion by highlighting a few specific transformative research opportunities that will be advanced by these efforts.
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Affiliation(s)
- Erica L Westerman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Sarah E J Bowman
- High-Throughput Crystallization Screening Center, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.,Department of Biochemistry, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, NY 14203, USA
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Marcus C Davis
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Eric R Larson
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Christopher P J Sanford
- Department of Ecology, Evolution and Organismal Biology, Kennesaw State University, Kennesaw, GA 30144, USA
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Soares JRS, Ramos RS, da Silva RS, Neves DVC, Picanço MC. Climate change impact assessment on worldwide rain fed soybean based on species distribution models. Trop Ecol 2021. [DOI: 10.1007/s42965-021-00174-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Cortés AJ, López-Hernández F. Harnessing Crop Wild Diversity for Climate Change Adaptation. Genes (Basel) 2021; 12:783. [PMID: 34065368 PMCID: PMC8161384 DOI: 10.3390/genes12050783] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
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Bambara Groundnut (Vigna subterranea L. Verdc): A Crop for the New Millennium, Its Genetic Diversity, and Improvements to Mitigate Future Food and Nutritional Challenges. SUSTAINABILITY 2021. [DOI: 10.3390/su13105530] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The world’s food and agricultural schemes have gradually fallen into an alarming state due to challenges such as high population birth rates, diverse agro-climatic zones, a lack of measures to counter global warming, severe practices of sole-culture cultivation, and asset reduction. A very high dependency on limited staple food crops is associated with repetitious diets, deprivation of food, and shortages of trace minerals, which often causes dietary sicknesses. To ensure nutritious diets worldwide, a real-world and justifiable scheme is provided to garner extra attention towards variation in both agriculture/farming approaches and food habits. The EAT-Lancet statement emphasized an increase in agri-based diets as a way of attaining global generational health. Enlarging neglected crops with plenty of genomic stocks and potentially profitable attributes is a solution that could address food and nutritional security concerns. Bambara groundnut is one such imperative and neglected legume crop that contributes positively to improving global food and nutrient safety. As a “complete food”, this crop has recently been treated as a new millennium crop, and furthermore, it is more adjusted to poor soil and climatic conditions than other dominant crops. Bambara groundnut is a repository of vital nutrients that provides carbohydrates, crucial amino acids, proteins, and energy as well as minerals and vitamins to developed and low-income countries where animal proteins are not readily available. This review explores the potential of Bambara groundnut in ensuring food and nutrient security; its variables, production, processing, nutrient values, role in reducing the nutritional gap, and diverse uses; and attempts in improving its traits. To strengthen food production, an agricultural revolution is required for underutilized crop species to feed the ever-expanding population in the world. Henceforth, advanced plant-breeding procedures, such as next-generation breeding techniques, various molecular tools, TILLING, Eco-TILLING, proteomics, genomics, and transcriptomics (which has been used for major crops), also need to be practiced to intensify production. To boost productivity and to feed the most starved and malnourished populations of the world, it is assumed that the application of modern techniques will play a vital role in the advancement of the underutilized Bambara groundnut.
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Bayer PE, Edwards D. Machine learning in agriculture: from silos to marketplaces. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:648-650. [PMID: 33289294 PMCID: PMC8051597 DOI: 10.1111/pbi.13521] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/23/2020] [Accepted: 11/29/2020] [Indexed: 05/03/2023]
Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
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Yang N, Yan J. New genomic approaches for enhancing maize genetic improvement. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101977. [PMID: 33418269 DOI: 10.1016/j.pbi.2020.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 05/13/2023]
Abstract
Maize (Zea mays) is one of the most widely grown crops in the world, with an annual global production of over 1147 million tons. Genomics approaches are thought to be the best solution for accelerating yield improvement to meet the challenges of a growing population and global climate change. Here, we review current approaches to the exploration of novel genetic variation in genomes, DNA modifications, and transcription levels of cultivated maize, landraces, and wild relatives. We discuss applications of genetic engineering to maize yield improvement and highlight future directions for maize genomics studies.
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Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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Lyzenga WJ, Pozniak CJ, Kagale S. Advanced domestication: harnessing the precision of gene editing in crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:660-670. [PMID: 33657682 PMCID: PMC8051614 DOI: 10.1111/pbi.13576] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 05/05/2023]
Abstract
Human population growth has increased the demand for food crops, animal feed, biofuel and biomaterials, all the while climate change is impacting environmental growth conditions. There is an urgent need to develop crop varieties which tolerate adverse growth conditions while requiring fewer inputs. Plant breeding is critical to global food security and, while it has benefited from modern technologies, it remains constrained by a lack of valuable genetic diversity, linkage drag, and an effective way to combine multiple favourable alleles for complex traits. CRISPR/Cas technology has transformed genome editing across biological systems and promises to transform agriculture with its high precision, ease of design, multiplexing ability and low cost. We discuss the integration of CRISPR/Cas-based gene editing into crop breeding to advance domestication and refine inbred crop varieties for various applications and growth environments. We highlight the use of CRISPR/Cas-based gene editing to fix desirable allelic variants, generate novel alleles, break deleterious genetic linkages, support pre-breeding and for introgression of favourable loci into elite lines.
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Affiliation(s)
- Wendy J. Lyzenga
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | | | - Sateesh Kagale
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
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Hu P, Zheng Q, Luo Q, Teng W, Li H, Li B, Li Z. Genome-wide association study of yield and related traits in common wheat under salt-stress conditions. BMC PLANT BIOLOGY 2021; 21:27. [PMID: 33413113 PMCID: PMC7792188 DOI: 10.1186/s12870-020-02799-1] [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: 04/08/2020] [Accepted: 12/16/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield. RESULT In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding. CONCLUSION Utilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.
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Affiliation(s)
- Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan Teng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Wang Y, Yu C, Cheng Y, Yao F, Long L, Wu Y, Li J, Li H, Wang J, Jiang Q, Li W, Pu Z, Qi P, Ma J, Deng M, Wei Y, Chen X, Chen G, Kang H, Jiang Y, Zheng Y. Genome-wide association mapping reveals potential novel loci controlling stripe rust resistance in a Chinese wheat landrace diversity panel from the southern autumn-sown spring wheat zone. BMC Genomics 2021; 22:34. [PMID: 33413106 PMCID: PMC7791647 DOI: 10.1186/s12864-020-07331-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 12/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe rust resistance genes and cultivation of resistant cultivars are considered to be the most effective approaches to control this disease. In this study, we evaluated the infection type (IT), disease severity (DS) and area under the disease progress curve (AUDPC) of 143 Chinese wheat landrace accessions for stripe rust resistance. Assessments were undertaken in five environments at the adult-plant stage with Pst mixture races under field conditions. In addition, IT was assessed at the seedling stage with two prevalent Pst races (CYR32 and CYR34) under a controlled greenhouse environment. RESULTS Seventeen accessions showed stable high-level resistance to stripe rust across all environments in the field tests. Four accessions showed resistance to the Pst races CYR32 and CYR34 at the seedling stage. Combining phenotypic data from the field and greenhouse trials with 6404 markers that covered the entire genome, we detected 17 quantitative trait loci (QTL) on 11 chromosomes for IT associated with seedling resistance and 15 QTL on seven chromosomes for IT, final disease severity (FDS) or AUDPC associated with adult-plant resistance. Four stable QTL detected on four chromosomes, which explained 9.99-23.30% of the phenotypic variation, were simultaneously associated with seedling and adult-plant resistance. Integrating a linkage map of stripe rust resistance in wheat, 27 QTL overlapped with previously reported genes or QTL, whereas four and one QTL conferring seedling and adult-plant resistance, respectively, were mapped distantly from previously reported stripe rust resistance genes or QTL and thus may be novel resistance loci. CONCLUSIONS Our results provided an integrated overview of stripe rust resistance resources in a wheat landrace diversity panel from the southern autumn-sown spring wheat zone of China. The identified resistant accessions and resistance loci will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.
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Affiliation(s)
- Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Hao Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit; and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
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Olanrewaju OS, Oyatomi O, Babalola OO, Abberton M. Breeding Potentials of Bambara Groundnut for Food and Nutrition Security in the Face of Climate Change. FRONTIERS IN PLANT SCIENCE 2021; 12:798993. [PMID: 35069656 PMCID: PMC8768941 DOI: 10.3389/fpls.2021.798993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/09/2021] [Indexed: 05/22/2023]
Abstract
Constant production of quality food should be a norm in any community, but climate change, increasing population, and unavailability of land for farming affect food production. As a result, food scarcity is affecting some communities, especially in the developing world. Finding a stable solution to this problem is a major cause of concern for researchers. Synergistic application of molecular marker techniques with next generation sequencing (NGS) technologies can unlock the potentials hidden in most crop genomes for improving yield and food availability. Most crops such as Bambara groundnut (BGN), Winged bean, and African yam bean are underutilized. These underutilized crops can compete with the major crops such as cowpea, soybean, maize, and rice, in areas of nutrition, ability to withstand drought stress, economic importance, and food production. One of these underutilized crops, BGN [Vigna subterranea (L.), Verdc.], is an indigenous African legume and can survive in tropical climates and marginal soils. In this review, we focus on the roles of BGN and the opportunities it possesses in tackling food insecurity and its benefits to local farmers. We will discuss BGN's potential impact on global food production and how the advances in NGS technologies can enhance its production.
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Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Genetic Resources Center (GRC), International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olaniyi Oyatomi
- Genetic Resources Center (GRC), International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Michael Abberton
- Genetic Resources Center (GRC), International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- *Correspondence: Michael Abberton,
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Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, Harliwong I, Wei H, Yang B, Ye Q, Anderson E, Mao Q, Drmanac R, Wang O, Peters BA, Xu M, Wu P, Topp B, Coin LJM, Henry RJ. Comparison of long-read methods for sequencing and assembly of a plant genome. Gigascience 2020; 9:giaa146. [PMID: 33347571 PMCID: PMC7751402 DOI: 10.1093/gigascience/giaa146] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/07/2020] [Accepted: 11/22/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. RESULTS Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. CONCLUSIONS The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
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Affiliation(s)
- Valentine Murigneux
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Subash Kumar Rai
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy J C Bruxner
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Wei Tian
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ivon Harliwong
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Hanmin Wei
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Bicheng Yang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Qianyu Ye
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ellis Anderson
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Qing Mao
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Radoje Drmanac
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Ou Wang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Brock A Peters
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Mengyang Xu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Qingdao, Building 2, No. 2 Hengyunshan Road, Qingdao 266555, China
| | - Pei Wu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Tianjin, Airport Business Park, Building E3, Airport Economics Area, Tianjin 300308, China
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lachlan J M Coin
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3004, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, Harliwong I, Wei H, Yang B, Ye Q, Anderson E, Mao Q, Drmanac R, Wang O, Peters BA, Xu M, Wu P, Topp B, Coin LJM, Henry RJ. Comparison of long-read methods for sequencing and assembly of a plant genome. Gigascience 2020; 9:6042729. [PMID: 33347571 DOI: 10.1101/2020.03.16.992933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/07/2020] [Accepted: 11/22/2020] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. RESULTS Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. CONCLUSIONS The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
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Affiliation(s)
- Valentine Murigneux
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Subash Kumar Rai
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy J C Bruxner
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Wei Tian
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ivon Harliwong
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Hanmin Wei
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Bicheng Yang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Qianyu Ye
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ellis Anderson
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Qing Mao
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Radoje Drmanac
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Ou Wang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Brock A Peters
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Mengyang Xu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Qingdao, Building 2, No. 2 Hengyunshan Road, Qingdao 266555, China
| | - Pei Wu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Tianjin, Airport Business Park, Building E3, Airport Economics Area, Tianjin 300308, China
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lachlan J M Coin
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3004, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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Henry RJ, Furtado A, Rangan P. Pathways of Photosynthesis in Non-Leaf Tissues. BIOLOGY 2020; 9:E438. [PMID: 33276443 PMCID: PMC7760132 DOI: 10.3390/biology9120438] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 01/12/2023]
Abstract
Plants have leaves as specialised organs that capture light energy by photosynthesis. However, photosynthesis is also found in other plant organs. Photosynthesis may be found in the petiole, stems, flowers, fruits, and seeds. All photosynthesis can contribute to the capture of carbon and growth of the plant. The benefit to the plant of photosynthesis in these other tissues or organs may often be associated with the need to re-capture carbon especially in storage organs that have high respiration rates. Some plants that conduct C3 photosynthesis in the leaves have been reported to use C4 photosynthesis in petioles, stems, flowers, fruits, or seeds. These pathways of non-leaf photosynthesis may be especially important in supporting plant growth under stress and may be a key contributor to plant growth and survival. Pathways of photosynthesis have directionally evolved many times in different plant lineages in response to environmental selection and may also have differentiated in specific parts of the plant. This consideration may be useful in the breeding of crop plants with enhanced performance in response to climate change.
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Affiliation(s)
- Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia; (A.F.); (P.R.)
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia; (A.F.); (P.R.)
| | - Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia; (A.F.); (P.R.)
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Galluzzi G, Seyoum A, Halewood M, López Noriega I, Welch EW. The Role of Genetic Resources in Breeding for Climate Change: The Case of Public Breeding Programmes in Eighteen Developing Countries. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091129. [PMID: 32878309 PMCID: PMC7569780 DOI: 10.3390/plants9091129] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
The role of plant breeding in adapting crops to climate changes that affect food production in developing countries is recognized as extremely important and urgent, alongside other agronomic, socio-economic and policy adaptation pathways. To enhance plant breeders' capacity to respond to climate challenges, it is acknowledged that they need to be able to access and use as much genetic diversity as they can get. Through an analysis of data from a global survey, we explore if and how public breeders in selected developing countries are responding to climate challenges through a renewed or innovative use of plant genetic resources, particularly in terms of types of material incorporated into their breeding work as well as sources of such germplasm. It also looks at the possible limitations breeders encounter in their efforts towards exploring diversity for adaptation. Breeders are clearly considering climate challenges. In general, their efforts are aimed at intensifying their breeding work on traits that they were already working on before climate change was so widely discussed. Similarly, the kinds of germplasm they use, and the sources from which they obtain it, do not appear to have changed significantly over the course of recent years. The main challenges breeders faced in accessing germplasm were linked to administrative/legal factors, particularly related to obtaining genetic resources across national borders. They also underscore technical challenges such as a lack of appropriate technologies to exploit germplasm sets such as crop wild relatives and landraces. Addressing these limitations will be crucial to fully enhance the role of public sector breeders in helping to adapt vulnerable agricultural systems to the challenges of climate change.
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Affiliation(s)
- Gea Galluzzi
- Bioversity International, Via dei Tre Denari 472/a, Maccarese (Fiumicino), 00057 Rome, Italy; (M.H.); (I.L.N.)
- Correspondence: ; Tel.: +39-348-403-0812
| | - Aseffa Seyoum
- Center for Science, Technology, and Environmental Policy Studies, School of Public Affairs, Arizona State University, 411 N Central Ave, Phoenix, AZ 85004, USA; (A.S.); (E.W.W.)
| | - Michael Halewood
- Bioversity International, Via dei Tre Denari 472/a, Maccarese (Fiumicino), 00057 Rome, Italy; (M.H.); (I.L.N.)
| | - Isabel López Noriega
- Bioversity International, Via dei Tre Denari 472/a, Maccarese (Fiumicino), 00057 Rome, Italy; (M.H.); (I.L.N.)
| | - Eric W. Welch
- Center for Science, Technology, and Environmental Policy Studies, School of Public Affairs, Arizona State University, 411 N Central Ave, Phoenix, AZ 85004, USA; (A.S.); (E.W.W.)
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