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Mude LN, Mondam M, Gujjula V, Jinka S, Pinjari OB, Yellodu Adi Reddy N, Patan SSVK. Morpho-physiological and biochemical changes in finger millet [ Eleusine coracana (L.) Gaertn.] under drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2151-2171. [PMID: 33268920 PMCID: PMC7688855 DOI: 10.1007/s12298-020-00909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/02/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Finger millet (Eleusine coracana L. Gaertn.) is a nutritious and climate-resilient crop with a C4 type carbon fixation pathway. The present study was aimed to assess the drought tolerance capacities of four finger millet genotypes based on their physiological and biochemical characteristics at three different phenological stages. Finger millet genotypes RAU 8, GPU 67, GPU 28 and MS 9272 were subjected to two water regimes, regular irrigation (control) and suspended irrigation (drought stress). During water regimes, morpho-physiological [biomass accumulation, leaf relative water content, and photosynthetic pigments] and biochemical changes [proline content, water soluble carbohydrates, antioxidant enzymes, and malondialdehyde content] were studied during seedling (18th day), vegetative (49th day) and early flowering stages (73rd day). The maintenance of growth especially root growth, biomass accumulation, the differential response in the concentration and changes of pigments, accumulation of proline, water-soluble carbohydrates and increased levels of antioxidant enzymes under drought stress play a major role in differential tolerance in finger millet genotypes that is conferred by the biplot analysis. The genotype RAU 8 is the most drought-tolerant genotype at all the three different phenological stages. Whereas the genotype GPU 67 was identified as sensitive at the seedling stage and its tolerance level was improved at vegetative and early flowering stages. The genotypes GPU 28 and MS 9272 were considered as drought sensitive at all three different phenological stages. Our results provide inputs to the breeders to select genotypes as parents and to design effective strategies in crop improvement programs.
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Affiliation(s)
| | - Muniraja Mondam
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh 516005 India
| | | | - Sivakumar Jinka
- Department of Genetics and Genomics, Yogi Vemana University, Kadapa, Andhra Pradesh 516005 India
| | - Osman Basha Pinjari
- Department of Genetics and Genomics, Yogi Vemana University, Kadapa, Andhra Pradesh 516005 India
| | - Nanja Yellodu Adi Reddy
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
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Martín‐Forés I, Magro S, Bravo‐Oviedo A, Alfaro‐Sánchez R, Espelta JM, Frei T, Valdés‐Correcher E, Rodríguez Fernández‐Blanco C, Winkel G, Gerzabek G, González‐Martínez SC, Hampe A, Valladares F. Spontaneous forest regrowth in South‐West Europe: Consequences for nature's contributions to people. PEOPLE AND NATURE 2020. [DOI: 10.1002/pan3.10161] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Irene Martín‐Forés
- Department of Biogeography and Global Change National Museum of Natural SciencesMNCN‐CSIC Madrid Spain
- School of Biological Sciences The University of Adelaide Adelaide SA Australia
| | | | - Andrés Bravo‐Oviedo
- Department of Biogeography and Global Change National Museum of Natural SciencesMNCN‐CSIC Madrid Spain
| | - Raquel Alfaro‐Sánchez
- CREAFCentre de Recerca Ecològica i Aplicacions Forestals Bellaterra Catalonia Spain
- Wilfrid Laurier University Waterloo ON Canada
| | - Josep M. Espelta
- CREAFCentre de Recerca Ecològica i Aplicacions Forestals Bellaterra Catalonia Spain
| | - Theresa Frei
- European Forest Institute. Governance Programme Bonn Germany
| | | | - Carmen Rodríguez Fernández‐Blanco
- European Forest Institute. Governance Programme Bonn Germany
- EFIMED. European Forest Institute – Mediterranean Facility Barcelona Spain
| | - Georg Winkel
- European Forest Institute. Governance Programme Bonn Germany
| | - Gabriel Gerzabek
- INRAEUniv. BordeauxBIOGECO Cestas France
- Institue of Landscape and Plant Ecology University of Hohenheim Stuttgart Germany
| | | | | | - Fernando Valladares
- Department of Biogeography and Global Change National Museum of Natural SciencesMNCN‐CSIC Madrid Spain
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Madrid Spain
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Crop climate suitability mapping on the cloud: a geovisualization application for sustainable agriculture. Sci Rep 2020; 10:15487. [PMID: 32968122 PMCID: PMC7511951 DOI: 10.1038/s41598-020-72384-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/26/2020] [Indexed: 11/17/2022] Open
Abstract
Climate change, food security, and environmental sustainability are pressing issues faced by today’s global population. As production demands increase and climate threatens crop productivity, agricultural research develops innovative technologies to meet these challenges. Strategies include biodiverse cropping arrangements, new crop introductions, and genetic modification of crop varieties that are resilient to climatic and environmental stressors. Geography in particular is equipped to address a critical question in this pursuit—when and where can crop system innovations be introduced? This manuscript presents a case study of the geographic scaling potential utilizing common bean, delivers an open access Google Earth Engine geovisualization application for mapping the fundamental climate niche of any crop, and discusses food security and legume biodiversity in Sub-Saharan Africa. The application is temporally agile, allowing variable growing season selections and the production of ‘living maps’ that are continually producible as new data become available. This is an essential communication tool for the future, as practitioners can evaluate the potential geographic range for newly-developed, experimental, and underrepresented crop varieties for facilitating sustainable and innovative agroecological solutions.
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Roda FA, Marques I, Batista-Santos P, Esquível MG, Ndayiragije A, Lidon FC, Swamy BPM, Ramalho JC, Ribeiro-Barros AI. Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves. Front Genet 2020; 11:543. [PMID: 32733530 PMCID: PMC7359728 DOI: 10.3389/fgene.2020.00543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 11/13/2022] Open
Abstract
Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha-1), Se (500 g ha-1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.
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Affiliation(s)
- Faustino Adriano Roda
- Ministério de Agricultura e Segurança Alimentar, Instituto de Investigação Agrária de Moçambique, Centro Zonal Noroeste, Lichinga, Mozambique
- Universidade Eduardo Mondlane-Centro de Biotechnologia, Maputo, Mozambique
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Marques
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Batista-Santos
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Glória Esquível
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Alexis Ndayiragije
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - Fernando Cebola Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - B. P. Mallikarjuna Swamy
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - José Cochicho Ramalho
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Cao S, Xu D, Hanif M, Xia X, He Z. Genetic architecture underpinning yield component traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1811-1823. [PMID: 32062676 DOI: 10.1007/s00122-020-03562-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mamoona Hanif
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
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56
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Leisner CP. Review: Climate change impacts on food security- focus on perennial cropping systems and nutritional value. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110412. [PMID: 32081261 DOI: 10.1016/j.plantsci.2020.110412] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/09/2019] [Accepted: 01/08/2020] [Indexed: 05/18/2023]
Abstract
Anthropogenic increases in fossil fuel emissions have been a primary driver of increased concentrations of atmospheric carbon dioxide ([CO2]) and other greenhouse gases resulting in warmer temperatures, alterations in precipitation patterns, and increased occurrence of extreme weather events in terrestrial areas across the globe. In agricultural growing regions, alterations in climate can challenge plant productivity in ways that impact the ability of the world to sustain adequate food production for a growing and increasingly affluent population with shifting access to affordable and nutritious food. While the knowledge gap that exists regarding potential climate change impacts is large across agriculture, it is especially large in specialty cropping systems. This includes fruit and vegetable crops, and perennial cropping systems which also contribute (along with row crops) to our global diet. In order to obtain a comprehensive view of the true impact of climate change on our global food supply, we must expand our narrow focus from improving yield and plant productivity to include the impact of climate change on the nutritional value of these crops. In order to address these questions, we need a multi-faceted approach that integrates physiology and genomics tools and conducts comprehensive experiments under realistic depictions of future projected climate. This review describes gaps in our knowledge in relation to these responses, and future questions and actions that are needed to develop a sustainable future food supply in light of global climate change.
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Affiliation(s)
- Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn AL 36849 USA.
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57
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Hazzouri KM, Flowers JM, Nelson D, Lemansour A, Masmoudi K, Amiri KMA. Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era. FRONTIERS IN PLANT SCIENCE 2020; 11:293. [PMID: 32256513 PMCID: PMC7090123 DOI: 10.3389/fpls.2020.00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/26/2020] [Indexed: 05/05/2023]
Abstract
Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.
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Affiliation(s)
- Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - David Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Khaled Masmoudi
- College of Food and Agriculture, Department of Integrative Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- College of Science, Department of Biology, United Arab Emirates University, Al Ain, United Arab Emirates
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58
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Matsubara K. How Hybrid Breakdown Can Be Handled in Rice Crossbreeding? FRONTIERS IN PLANT SCIENCE 2020; 11:575412. [PMID: 33193514 PMCID: PMC7641626 DOI: 10.3389/fpls.2020.575412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 05/16/2023]
Abstract
In crosses between genetically divergent parents, traits such as weakness and sterility often segregate in later generations. This hybrid breakdown functions as a reproductive barrier and reduces selection efficiency in crossbreeding. Here, I provide an overview of hybrid breakdown in rice crosses and discuss ways to avoid and mitigate the effects of hybrid breakdown on rice crossbreeding, including genomics-assisted breeding.
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59
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Kumari R, Wankhede DP, Bajpai A, Maurya A, Prasad K, Gautam D, Rangan P, Latha M, John K. J, A. S, Bhat KV, Gaikwad AB. Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications. PLoS One 2019; 14:e0226002. [PMID: 31834893 PMCID: PMC6910694 DOI: 10.1371/journal.pone.0226002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 11/18/2019] [Indexed: 11/23/2022] Open
Abstract
Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species.
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Affiliation(s)
- Ratna Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Akansha Bajpai
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Avantika Maurya
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kartikay Prasad
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dikshant Gautam
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. Latha
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Joseph John K.
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Suma A.
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kangila V. Bhat
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ambika B. Gaikwad
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- * E-mail:
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Davis SC, Simpson J, Gil-Vega KDC, Niechayev NA, van Tongerlo E, Castano NH, Dever LV, Búrquez A. Undervalued potential of crassulacean acid metabolism for current and future agricultural production. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6521-6537. [PMID: 31087091 PMCID: PMC6883259 DOI: 10.1093/jxb/erz223] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/03/2019] [Indexed: 05/11/2023]
Abstract
The potential for crassulacean acid metabolism (CAM) to support resilient crops that meet demands for food, fiber, fuel, and pharmaceutical products far exceeds current production levels. This review provides background on five families of plants that express CAM, including examples of many species within these families that have potential agricultural uses. We summarize traditional uses, current developments, management practices, environmental tolerance ranges, and economic values of CAM species with potential commercial applications. The primary benefit of CAM in agriculture is high water use efficiency that allows for reliable crop yields even in drought conditions. Agave species, for example, grow in arid conditions and have been exploited for agricultural products in North and South America for centuries. Yet, there has been very little investment in agricultural improvement for most useful Agave varieties. Other CAM species that are already traded globally include Ananas comosus (pineapple), Aloe spp., Vanilla spp., and Opuntia spp., but there are far more with agronomic uses that are less well known and not yet developed commercially. Recent advances in technology and genomic resources provide tools to understand and realize the tremendous potential for using CAM crops to produce climate-resilient agricultural commodities in the future.
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Affiliation(s)
- Sarah C Davis
- Voinovich School of Leadership and Public Affairs, Ohio University, Athens, OH, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
| | - June Simpson
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, México
| | | | - Nicholas A Niechayev
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Evelien van Tongerlo
- Horticulture and Product Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Louisa V Dever
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Alberto Búrquez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Unidad Hermosillo, Sonora, México
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61
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Conservation Genomics in a Changing Arctic. Trends Ecol Evol 2019; 35:149-162. [PMID: 31699414 DOI: 10.1016/j.tree.2019.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
Abstract
Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.
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Hendre PS, Muthemba S, Kariba R, Muchugi A, Fu Y, Chang Y, Song B, Liu H, Liu M, Liao X, Sahu SK, Wang S, Li L, Lu H, Peng S, Cheng S, Xu X, Yang H, Wang J, Liu X, Simons A, Shapiro HY, Mumm RH, Van Deynze A, Jamnadass R. African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops. PLANTA 2019; 250:989-1003. [PMID: 31073657 DOI: 10.1007/s00425-019-03156-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/01/2019] [Indexed: 05/28/2023]
Abstract
The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.
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Affiliation(s)
- Prasad S Hendre
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya.
| | - Samuel Muthemba
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Robert Kariba
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Alice Muchugi
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Yuan Fu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Min Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xuezhu Liao
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Sibo Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shufeng Peng
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shifeng Cheng
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Anthony Simons
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - Howard-Yana Shapiro
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
- University of California, 1 Shields Ave, Davis, CA, 95616, USA
| | - Rita H Mumm
- University of Illinois, Urbana, IL, 61801, USA
| | | | - Ramni Jamnadass
- African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya
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Mayes S, Ho WK, Chai HH, Gao X, Kundy AC, Mateva KI, Zahrulakmal M, Hahiree MKIM, Kendabie P, Licea LCS, Massawe F, Mabhaudhi T, Modi AT, Berchie JN, Amoah S, Faloye B, Abberton M, Olaniyi O, Azam-Ali SN. Bambara groundnut: an exemplar underutilised legume for resilience under climate change. PLANTA 2019; 250:803-820. [PMID: 31267230 DOI: 10.1007/s00425-019-03191-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/16/2019] [Indexed: 05/18/2023]
Abstract
Bambara groundnut has the potential to be used to contribute more the climate change ready agriculture. The requirement for nitrogen fixing, stress tolerant legumes is clear, particularly in low input agriculture. However, ensuring that existing negative traits are tackled and demand is stimulated through the development of markets and products still represents a challenge to making greater use of this legume. World agriculture is currently based on very limited numbers of crops, representing a significant risk to food supplies, particularly in the face of climate change which is expected to increase the frequency of extreme events. Minor and underutilised crops can help to develop a more resilient and nutritionally dense future agriculture. Bambara groundnut [Vigna subterranea (L.) Verdc.[, as a drought resistant, nitrogen-fixing, legume has a role to play. However, as with most underutilised crops, there are significant gaps in knowledge and also negative traits such as 'hard-to-cook' and 'photoperiod sensitivity to pod filling' associated with the crop which future breeding programmes and processing methods need to tackle, to allow it to make a significant contribution to the well-being of future generations. The current review assesses these factors and also considers what are the next steps towards realising the potential of this crop.
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Affiliation(s)
- Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
| | - Wai Kuan Ho
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Hui Hui Chai
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Xiuqing Gao
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Aloyce C Kundy
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Kumbirai I Mateva
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | | | | | - Presidor Kendabie
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Luis C S Licea
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Festo Massawe
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Tafadzwanashe Mabhaudhi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Albert T Modi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Joseph N Berchie
- CSIR-Crop Research Institute, P.O. Box 3785, Fumesua, Kumasi, Ghana
| | - Stephen Amoah
- CSIR-Crop Research Institute, P.O. Box 3785, Fumesua, Kumasi, Ghana
| | - Ben Faloye
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Genetic Resources Centre, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Michael Abberton
- Genetic Resources Centre, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Oyatomi Olaniyi
- Genetic Resources Centre, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Sayed N Azam-Ali
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
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Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
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Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
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Senapati N, Brown HE, Semenov MA. Raising genetic yield potential in high productive countries: Designing wheat ideotypes under climate change. AGRICULTURAL AND FOREST METEOROLOGY 2019; 271:33-45. [PMID: 31217650 PMCID: PMC6559216 DOI: 10.1016/j.agrformet.2019.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/12/2019] [Accepted: 02/17/2019] [Indexed: 05/07/2023]
Abstract
Designing crop ideotype is an important step to raise genetic yield potential in a target environment. In the present study, we designed wheat ideotypes based on the state-of-the-art knowledge in crop physiology to increase genetic yield potential for the 2050-climate, as projected by the HadGEM2 global climate model for the RCP8.5 emission scenario, in two high-wheat-productive countries, viz. the United Kingdom (UK) and New Zealand (NZ). Wheat ideotypes were optimized to maximize yield potential for both water-limited (IW2050 ) and potential (IP2050 ) conditions by using Sirius model and exploring the full range of cultivar parameters. On average, a 43-51% greater yield potential over the present winter wheat cv. Claire was achieved for IW2050 in the UK and NZ, whereas a 51-62% increase was obtained for IP2050 . Yield benefits due to the potential condition over water-limitation were small in the UK, but 13% in NZ. The yield potentials of wheat were 16% (2.6 t ha-1) and 31% (5 t ha-1) greater in NZ than in the UK under 2050-climate in water-limited and potential conditions respectively. Modelling predicts the possibility of substantial increase in genetic yield potential of winter wheat under climate change in high productive countries. Wheat ideotypes optimized for future climate could provide plant scientists and breeders with a road map for selection of the target traits and their optimal combinations for wheat improvement and genetic adaptation to raise the yield potential.
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Affiliation(s)
- Nimai Senapati
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
| | - Hamish E. Brown
- The New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, New Zealand
| | - Mikhail A. Semenov
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
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66
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Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS, Nie F. Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops. PLoS One 2019; 14:e0216299. [PMID: 31034501 PMCID: PMC6488077 DOI: 10.1371/journal.pone.0216299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/17/2019] [Indexed: 02/03/2023] Open
Abstract
Blueberry is a kind of new rising popular perennial fruit with high healthful quality. It is of utmost importance to develop new blueberry varieties for different climatic zones to satisfy the demand of people in the world. Molecular marker assisted breeding is believed to be an ideal method for the development of new blueberry varieties for its shorter breeding cycle than the conventional breeding. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers are widely used molecular tools for marker assisted breeding, which could be detected at large scale by the transcriptome sequencing. Here, we sequenced the leaves transcriptome of 19 rabbiteye (Vaccinium ashei Reade), 13 southern highbush (Vaccinium. corymbosum L × native southern Vaccinium Spp) and 22 cultivars of northern highbush blueberry (Vaccinium corymbosum L) by using next generation sequencing technologies. A total of 80.825 Gb clean data with an average of about 12.525 million reads per cultivar were obtained. We assembled 58,968, 55,973 and 53,887 unigenes by using the clean data from rabbiteye, southern highbush and northern highbush blueberry cultivars, respectively. Among these unigenes, 3599, 3495 and 3513 unigenes were detected as candidate resistance genes in three blueberry crops. Moreover, we identified more than 8756, 9020, and 9198 SSR markers from these unigenes, and 7665, 4861, 13,063 SNPs from the annotated single copy unigenes, respectively. The results will be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry, and would also offer huge number of molecular tools for the marker assisted breeding to produce blueberry cultivars with different adaptive characteristics.
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Affiliation(s)
- Yunsheng Wang
- College of Life and Health Science, Kaili University, Kaili City, Guizhou Province, China
- * E-mail: (YW); (FN)
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Fei Nie
- Biological Institute of Guizhou Province, Guiyang City, Guizhou Province, China
- * E-mail: (YW); (FN)
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67
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Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation. Biochem Genet 2019; 57:747-766. [PMID: 30997627 DOI: 10.1007/s10528-019-09920-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, 'Gigantes' and 'Elephantes' phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for 'Gigantes' and 'Elephantes,' respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in 'Elephantes' and 648 upregulated in 'Gigantes.' A significant upregulation of defense-related genes was observed in 'Elephantes,' among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in 'Gigantes' and 'Elephantes,' respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in 'Gigantes' and 40.1% in 'Elephantes' of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.
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68
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Alahmad S, El Hassouni K, Bassi FM, Dinglasan E, Youssef C, Quarry G, Aksoy A, Mazzucotelli E, Juhász A, Able JA, Christopher J, Voss-Fels KP, Hickey LT. A Major Root Architecture QTL Responding to Water Limitation in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:436. [PMID: 31024600 PMCID: PMC6468307 DOI: 10.3389/fpls.2019.00436] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (qSRA-6A) which also displayed high levels of pairwise LD (r 2 = 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for qSRA-6A, highlighting the opportunity to perform marker-assisted selection for the qSRA-6A locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall.
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Affiliation(s)
- Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Khaoula El Hassouni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Chvan Youssef
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Georgia Quarry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alpaslan Aksoy
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | | | - Angéla Juhász
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Jason A. Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA, Australia
| | - Jack Christopher
- Leslie Research Facility, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Kai P. Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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69
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Senapati N, Semenov MA. Assessing yield gap in high productive countries by designing wheat ideotypes. Sci Rep 2019; 9:5516. [PMID: 30940895 PMCID: PMC6445095 DOI: 10.1038/s41598-019-40981-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/27/2019] [Indexed: 01/17/2023] Open
Abstract
Designing crop ideotypes in silico is a powerful tool to explore the crop yield potential and yield gap. We defined yield gap as the difference between yield potential of a crop ideotype optimized under local environment and yield of an existing cultivar under optimal management. Wheat ideotypes were designed for the current climate using the Sirius model for both water-limited and irrigated conditions in two high wheat-productive countries viz. the United Kingdom (UK) and New Zealand (NZ) with the objective of estimating yield gap. The mean ideotype yields of 15.0-19.0 t ha-1 were achieved in water-limited conditions in the UK and NZ, whereas 15.6-19.5 t ha-1 under irrigated conditions. Substantial yield gaps were found in both water-limited, 28-31% (4-6 t ha-1), and irrigated conditions, 30-32% (5-6 t ha-1) in the UK and NZ. Both yield potential (25-27%) and yield gap (32-38%) were greater in NZ than the UK. Ideotype design is generic and could apply globally for estimating yield gap. Despite wheat breeding efforts, the considerable yield gap still potentially exists in high productive countries such as the UK and NZ. To accelerate breeding, wheat ideotypes can provide the key traits for wheat improvement and closing the yield gap.
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Affiliation(s)
- Nimai Senapati
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Herts, AL5 2JQ, United Kingdom.
| | - Mikhail A Semenov
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Herts, AL5 2JQ, United Kingdom
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70
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Jain A, Roorkiwal M, Kale S, Garg V, Yadala R, Varshney RK. InDel markers: An extended marker resource for molecular breeding in chickpea. PLoS One 2019; 14:e0213999. [PMID: 30883592 PMCID: PMC6422259 DOI: 10.1371/journal.pone.0213999] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/05/2019] [Indexed: 12/03/2022] Open
Abstract
Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.
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Affiliation(s)
- Ankit Jain
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR)
| | - Sandip Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Gatersleben, Germany
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramakrishna Yadala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR)
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Abstract
In the Midwest U.S. dominated corn-soybean landscape, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. Studies of the system-level integration of such approaches have proceeded by using the currently available cultivars and breeding selections of various tree nut and fruit species. While existing varieties and breeding selections provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. and its marginal land-types is unexplored. Thus, a second tier of research includes the genetic improvement and adaptation of tree crop selections to their respective target environments throughout the Midwest U.S. Fortunately, select tree crops of interest are amendable to systematic breeding and have wild relatives that are endemic across the region. In this paper, we discuss the value of these wild relatives for broadening the adaption of cultivated tree crop selections by using the hazelnut as an example species. We present a framework using geospatial tools to define and prioritize target environments for breeding and, in turn, exploiting wild relative germplasm.
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72
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Nguyen KL, Grondin A, Courtois B, Gantet P. Next-Generation Sequencing Accelerates Crop Gene Discovery. TRENDS IN PLANT SCIENCE 2019; 24:263-274. [PMID: 30573308 DOI: 10.1016/j.tplants.2018.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 05/22/2023]
Abstract
The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes.
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Affiliation(s)
- Khanh Le Nguyen
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; LMI RICE 2, AGI, Km2 Pham Van Dong, Tu Liem, Hanoi, Vietnam
| | - Alexandre Grondin
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, F-34398 Montpellier, France; Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; Centre of the Region Haná for Biotechnological and Agricultural Research, Dept. of Molecular Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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73
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Raza A, Razzaq A, Mehmood SS, Zou X, Zhang X, Lv Y, Xu J. Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review. PLANTS (BASEL, SWITZERLAND) 2019; 8:E34. [PMID: 30704089 PMCID: PMC6409995 DOI: 10.3390/plants8020034] [Citation(s) in RCA: 391] [Impact Index Per Article: 78.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 11/17/2022]
Abstract
Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO₂ or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.
| | - Sundas Saher Mehmood
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Xuekun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Jinsong Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
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Mariotti R, Fornasiero A, Mousavi S, Cultrera NG, Brizioli F, Pandolfi S, Passeri V, Rossi M, Magris G, Scalabrin S, Scaglione D, Di Gaspero G, Saumitou-Laprade P, Vernet P, Alagna F, Morgante M, Baldoni L. Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker. FRONTIERS IN PLANT SCIENCE 2019; 10:1760. [PMID: 32117338 PMCID: PMC7025539 DOI: 10.3389/fpls.2019.01760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/16/2019] [Indexed: 05/20/2023]
Abstract
The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Inter-varietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), suggesting a simple Mendelian inheritance of the trait. A double digest restriction associated DNA (ddRAD) sequencing of a biparental population segregating for incompatibility groups has been performed and high-density linkage maps were constructed in order to map the SI locus and identify gene candidates and linked markers. The progeny consisted of a full-sib family of 229 individuals derived from the cross 'Leccino' (G1) × 'Dolce Agogia' (G2) varieties, segregating 1:1 (G1:G2), in accordance with a diallelic self-incompatibility (DSI) model. A total of 16,743 single nucleotide polymorphisms was identified, 7,006 in the female parent 'Leccino' and 9,737 in the male parent 'Dolce Agogia.' Each parental map consisted of 23 linkage groups and showed an unusual large size (5,680 cM in 'Leccino' and 3,538 cM in 'Dolce Agogia'). Recombination was decreased across all linkage groups in pollen mother cells of 'Dolce Agogia,' the parent with higher heterozygosity, compared to megaspore mother cells of 'Leccino,' in a context of a species that showed exceptionally high recombination rates. A subset of 109 adult plants was assigned to either incompatibility group by a stigma test and the diallelic self-incompatibility (DSI) locus was mapped to an interval of 5.4 cM on linkage group 18. This region spanned a size of approximately 300 Kb in the olive genome assembly. We developed a sequence-tagged site marker in the DSI locus and identified five haplotypes in 57 cultivars with known incompatibility group assignment. A combination of two single-nucleotide polymorphisms (SNPs) was sufficient to predict G1 or G2 phenotypes in olive cultivars, enabling early marker-assisted selection of compatible genotypes and allowing for a rapid screening of inter-compatibility among cultivars in order to guarantee effective fertilization and increase olive production. The construction of high-density linkage maps has led to the development of the first functional marker in olive and provided positional candidate genes in the SI locus.
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Affiliation(s)
- Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Alice Fornasiero
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Soraya Mousavi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | | | - Federico Brizioli
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Saverio Pandolfi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Valentina Passeri
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Martina Rossi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Gabriele Magris
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | | | | | | | | | - Philippe Vernet
- University of Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | | | - Michele Morgante
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
- *Correspondence: Luciana Baldoni,
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75
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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76
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Hamburger DJS. Normative Criteria and Their Inclusion in a Regulatory Framework for New Plant Varieties Derived From Genome Editing. Front Bioeng Biotechnol 2018; 6:176. [PMID: 30619841 PMCID: PMC6305715 DOI: 10.3389/fbioe.2018.00176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/05/2018] [Indexed: 01/09/2023] Open
Abstract
Any legal regulation has to take into account fundamental interests and concerns, whether of private or public nature. This applies in particular to the politically and socially sensitive question of regulating plant biotechnology. With the advent of new breeding techniques, such as genome editing, new challenges are arising for legislators around the world. However, in coping with them not only the technical particularities of the new breeding techniques must be taken into account but also the diverse and sometimes conflicting interests of the various stakeholders. In order to be able to draft a suitable regulatory regime for these new techniques, the different interests and concerns at play are identified. Subsequently, a determination is made on how these interests relate to each other, before regulatory concepts to reconcile the conflicting demands are presented. The examined normative criteria, which can have an impact on regulatory decisions regarding genome edited plants and products derived from them, include: industry interests, farmer interests, public opinion, consumer rights and interests, human health and food safety, food security, environmental protection, consistency, and coherence of the regulatory framework and ethical or religious convictions. Since those interests differ from country to country depending on the respective political, economic, and social circumstances, the respective legislator has the task of identifying these normative criteria and must find a suitable balance between them. To this end, a concept is developed on how the different interests can be related to each other and how to deal with conflicting and irreconcilable demands. Additionally, a legislator may have recourse to a number of further analyzed regulatory measures. An approval or notification procedure can be used for a risk assessment or a socio-economic evaluation. Coexistence measures and labeling provisions are able to reconcile interests that are at odds with each other and the precautionary principle can justify certain safeguard measures. As a result, the individual country-specific regulatory outcomes regarding genome edited plants are likely to be as manifold as the interests and regulatory measures at hand.
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Affiliation(s)
- David J. S. Hamburger
- Faculty of Law, Chair of Constitutional and Administrative Law, Public International Law, European and International Economic Law, University of Passau, Passau, Germany
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77
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Radanielson AM, Gaydon DS, Rahman Khan MM, Chaki AK, Rahman MA, Angeles O, Li T, Ismail A. Varietal improvement options for higher rice productivity in salt affected areas using crop modelling. FIELD CROPS RESEARCH 2018; 229:27-36. [PMID: 31007364 PMCID: PMC6472128 DOI: 10.1016/j.fcr.2018.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 08/18/2018] [Accepted: 08/26/2018] [Indexed: 06/09/2023]
Abstract
The rice model ORYZA v3 has been recently improved to account for salt stress effect on rice crop growth and yield. This paper details subsequent studies using the improved model to explore opportunities for improving salinity tolerance in rice. The objective was to identify combinations of plant traits influencing rice responses to salinity and to quantify yield gains by improving these traits. The ORYZA v3 model was calibrated and validated with field experimental data collected between 2012 and 2014 in Satkhira, Bangladesh and Infanta, Quezon, Philippines, then used for simulations scenario considering virtual varieties possessing different combinations of crop model parameter values related to crop salinity response and the soil salinity dynamic observed at Satkhira site. Simulation results showed that (i) short duration varieties could escape end of season increase in salinity, while long duration varieties could benefit from an irrigated desalinization period occurring during the later stages of crop growth in the Satkhira situation; (ii) combining short duration growth with salt tolerance (bTR and bPN) above 12 dS m-1 and a resilience trait (aSalt) of 0.11 in a variety, allows maintenance of 65-70% of rice yield under increasing salinity levels of up to 16 dS m-1; and (iii) increasing the value of the tolerance parameter b by 1% results in 0.3-0.4% increase in yield. These results are relevant for defining directions to increase rice productivity in saline environments, based on improvements in phenology and quantifiable salt tolerance traits.
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Affiliation(s)
| | - Donald S. Gaydon
- CSIRO Agriculture and Food, Brisbane, Australia
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, Australia
| | - Md. Mahbubur Rahman Khan
- On-Farm Research Division, Bangladesh Agricultural Research Institute (BARI), Joydebpur, Gazipur 1701, Bangladesh
| | - Apurbo K. Chaki
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, Australia
- On-Farm Research Division, Bangladesh Agricultural Research Institute (BARI), Joydebpur, Gazipur 1701, Bangladesh
| | - Md. Atikur Rahman
- On-Farm Research Division, Bangladesh Agricultural Research Institute (BARI), Joydebpur, Gazipur 1701, Bangladesh
| | | | - Tao Li
- International Rice Research Institute, Philippines
| | - A. Ismail
- International Rice Research Institute, Philippines
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78
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Henry RJ, Furtado A, Rangan P. Wheat seed transcriptome reveals genes controlling key traits for human preference and crop adaptation. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:231-236. [PMID: 29779965 DOI: 10.1016/j.pbi.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 05/23/2023]
Abstract
Analysis of the transcriptome of the developing wheat grain has associated expression of genes with traits involving production (e.g. yield) and quality (e.g. bread quality). Photosynthesis in the grain may be important in retaining carbon that would be lost in respiration during grain filling and may contribute to yield in the late stages of seed formation under warm and dry environments. A small number of genes have been identified as having been selected by humans to optimize the performance of wheat for foods such as bread. Genes determining flour yield in milling have been discovered. Hardness is explained by variations in expression of pin genes. Knowledge of these genes should dramatically improve the efficiency of breeding better climate adapted wheat genotypes.
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Affiliation(s)
- Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi 110012, India
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79
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Kulkarni KP, Tayade R, Asekova S, Song JT, Shannon JG, Lee JD. Harnessing the Potential of Forage Legumes, Alfalfa, Soybean, and Cowpea for Sustainable Agriculture and Global Food Security. FRONTIERS IN PLANT SCIENCE 2018; 9:1314. [PMID: 30283466 PMCID: PMC6157451 DOI: 10.3389/fpls.2018.01314] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/20/2018] [Indexed: 05/18/2023]
Abstract
Substantial improvements in access to food and increased purchasing power are driving many people toward consuming nutrition-rich foods causing an unprecedented demand for protein food worldwide, which is expected to rise further. Forage legumes form an important source of feed for livestock and have potential to provide a sustainable solution for food and protein security. Currently, alfalfa is a commercially grown source of forage and feed in many countries. However, soybean and cowpea also have the potential to provide quality forage and fodder for animal use. The cultivation of forage legumes is under threat from changing climatic conditions, indicating the need for breeding cultivars that can sustain and acclimatize to the negative effects of climate change. Recent progress in genetic and genomic tools have facilitated the identification of quantitative trait loci and genes/alleles that can aid in developing forage cultivars through genomics-assisted breeding. Furthermore, transgenic technology can be utilized to manipulate the genetic makeup of plants to improve forage digestibility for better animal performance. In this article, we assess the genetic potential of three important legume crops, alfalfa, soybean, and cowpea in supplying quality fodder and feed for livestock. In addition, we examine the impact of climate change on forage quality and discuss efforts made in enhancing the adaptation of the plant to the abiotic stress conditions. Subsequently, we suggest the application of integrative approaches to achieve adequate forage production amid the unpredictable climatic conditions.
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Affiliation(s)
| | - Rupesh Tayade
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Sovetgul Asekova
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, South Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - J. Grover Shannon
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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80
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Cerda‐Hurtado IM, Mayek‐Pérez N, Hernández‐Delgado S, Muruaga‐Martínez JS, Reyes‐Lara MA, Reyes‐Valdés MH, González‐Prieto JM. Climatic adaptation and ecological descriptors of wild beans from Mexico. Ecol Evol 2018; 8:6492-6504. [PMID: 30038751 PMCID: PMC6053573 DOI: 10.1002/ece3.4106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/06/2018] [Accepted: 03/24/2018] [Indexed: 12/04/2022] Open
Abstract
Despite its economic, social, biological, and cultural importance, wild forms of the genus Phaseolus are not well represented in germplasm banks, and they are at great risk due to changes in land use as well as climate change. To improve our understanding of the potential geographical distribution of wild beans (Phaseolus spp.) from Mexico and support in situ and ex situ conservation programs, we determined the climatic adaptation ranges of 29 species and two subspecies of Phaseolus collected throughout Mexico. Based on five biotic and 117 abiotic variables obtained from different databases-WorldClim, Global-Aridity, and Global-PET-we performed principal component and cluster analyses. Germplasm was distributed among 12 climatic types from a possible 28. The general climatic ranges were as follows: 8-3,083 m above sea level; 12.07-26.96°C annual mean temperature; 10.33-202.68 mm annual precipitation; 9.33-16.56 W/m2 of net radiation; 11.68-14.23 hr photoperiod; 0.06-1.57 aridity index; and 10-1,728 mm/month of annual potential evapotranspiration. Most descriptive variables (25) clustered species into two groups: One included germplasm from semihot climates, and the other included germplasm from temperate climates. Species clustering showed 45% to 54% coincidence with species previously grouped using molecular data. The species P. filiformis, P. purpusii, and P. maculatus were found at low-humidity locations; these species could be used to improve our understanding of the extreme aridity adaptation mechanisms used by wild beans to avoid or tolerate climate change as well as to introgress favorable alleles into new cultivars adapted to hot, dry environments.
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Affiliation(s)
| | - Netzahualcoyotl Mayek‐Pérez
- Instituto Politécnico NacionalCentro de Biotecnología GenómicaReynosaMexico
- Universidad Mexico Americana del NorteReynosaMexico
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81
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Ali J, Jewel ZA, Mahender A, Anandan A, Hernandez J, Li Z. Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice. Int J Mol Sci 2018; 19:E1762. [PMID: 29899204 PMCID: PMC6032200 DOI: 10.3390/ijms19061762] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/26/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022] Open
Abstract
In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.
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Affiliation(s)
- Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Zilhas Ahmed Jewel
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jose Hernandez
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
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82
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Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis. Int J Mol Sci 2018; 19:ijms19061727. [PMID: 29891774 PMCID: PMC6032310 DOI: 10.3390/ijms19061727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/29/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022] Open
Abstract
For sustainable crop cultivation in the face of global warming, it is important to unravel the genetic mechanisms underlying plant adaptation to a warming climate and apply this information to breeding. Thermomorphogenesis and ambient temperature signaling pathways have been well studied in model plants, but little information is available for vegetable crops. Here, we investigated genes responsive to warming conditions from two Brassica rapa inbred lines with different geographic origins: subtropical (Kenshin) and temperate (Chiifu). Genes in Gene Ontology categories “response to heat”, “heat acclimation”, “response to light intensity”, “response to oxidative stress”, and “response to temperature stimulus” were upregulated under warming treatment in both lines, but genes involved in “response to auxin stimulus” were upregulated only in Kenshin under both warming and minor-warming conditions. We identified 16 putative high temperature (HT) adaptation-related genes, including 10 heat-shock response genes, 2 transcription factor genes, 1 splicing factor gene, and 3 others. BrPIF4, BrROF2, and BrMPSR1 are candidate genes that might function in HT adaptation. Auxin response, alternative splicing of BrHSFA2, and heat shock memory appear to be indispensable for HT adaptation in B. rapa. These results lay the foundation for molecular breeding and marker development to improve warming tolerance in B. rapa.
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83
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Williams A, Jordan NR, Smith RG, Hunter MC, Kammerer M, Kane DA, Koide RT, Davis AS. A regionally-adapted implementation of conservation agriculture delivers rapid improvements to soil properties associated with crop yield stability. Sci Rep 2018; 8:8467. [PMID: 29855528 PMCID: PMC5981580 DOI: 10.1038/s41598-018-26896-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/21/2018] [Indexed: 11/13/2022] Open
Abstract
Climate models predict increasing weather variability, with negative consequences for crop production. Conservation agriculture (CA) may enhance climate resilience by generating certain soil improvements. However, the rate at which these improvements accrue is unclear, and some evidence suggests CA can lower yields relative to conventional systems unless all three CA elements are implemented: reduced tillage, sustained soil cover, and crop rotational diversity. These cost-benefit issues are important considerations for potential adopters of CA. Given that CA can be implemented across a wide variety of regions and cropping systems, more detailed and mechanistic understanding is required on whether and how regionally-adapted CA can improve soil properties while minimizing potential negative crop yield impacts. Across four US states, we assessed short-term impacts of regionally-adapted CA systems on soil properties and explored linkages with maize and soybean yield stability. Structural equation modeling revealed increases in soil organic matter generated by cover cropping increased soil cation exchange capacity, which improved soybean yield stability. Cover cropping also enhanced maize minimum yield potential. Our results demonstrate individual CA elements can deliver rapid improvements in soil properties associated with crop yield stability, suggesting that regionally-adapted CA may play an important role in developing high-yielding, climate-resilient agricultural systems.
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Affiliation(s)
- Alwyn Williams
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA.
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia.
| | - Nicholas R Jordan
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - Richard G Smith
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Mitchell C Hunter
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Kammerer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Daniel A Kane
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Adam S Davis
- USDA-ARS, Global Change and Photosynthesis Research Unit, Urbana, IL, USA
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84
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Mushtaq M, Bhat JA, Mir ZA, Sakina A, Ali S, Singh AK, Tyagi A, Salgotra RK, Dar AA, Bhat R. CRISPR/Cas approach: A new way of looking at plant-abiotic interactions. JOURNAL OF PLANT PHYSIOLOGY 2018; 224-225:156-162. [PMID: 29655033 DOI: 10.1016/j.jplph.2018.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/26/2018] [Accepted: 04/02/2018] [Indexed: 05/20/2023]
Abstract
It is not the most grounded of the species that survive, nor the most shrewd, however one most receptive to change. Crop plants being sessile are subjected to various abiotic stresses resulting significant yield losses about an average of more than 50 percent, thus greatly threatening the global crop production. In this regard, plant breeding innovations and genetic engineering approaches have been used in the past for generating stress tolerant crop genotypes, but due to complex inheritance of abiotic stress tolerance these approaches are not enough to bring significant trait improvement and to guarantee world's future sustenance security. Although, RNA interference (RNAi) technology has been utilized amid the most recent decades to produce plants tolerant to environmental stress. But this technique ordinarily prompts to down-regulate as opposed to complete inhibition of target genes. Therefore, scientist/researchers were looking for techniques that should be efficient, precise and reliable as well as have potential to solve the issues experienced by previous approaches, and hence the CRISPR/Cas system came into spotlight. Although, only few studies using CRISPR/Cas approach for targeting abiotic stress tolerance related genes have been reported, but suggested its effective role for future applications in molecular breeding to improve abiotic stress tolerance. Hence, genome engineering via CRISPR-Cas system for targeted mutagenesis promise its immense potential in generating elite cultivars of crop plants with enhanced and durable climate resilience. Lastly, CRISPR-Cas will be future of crop breeding as well as to target minor gene variation of complex quantitative traits, and thus will be the key approach to release global hunger and maintain food security.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India.
| | - Javaid Akhter Bhat
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Zahoor A Mir
- National Research Centre for Plant Biotechnology, New Delhi, India
| | - Afreen Sakina
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Sajad Ali
- Centre of Research for Develoment, University of Kashmir, Srinagar, India
| | - Anil Kumar Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Anshika Tyagi
- National Research Centre for Plant Biotechnology, New Delhi, India
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Ajaz Ahmad Dar
- Division of Mirobiology, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
| | - Rohini Bhat
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, India
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85
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Roorkiwal M, Jain A, Kale SM, Doddamani D, Chitikineni A, Thudi M, Varshney RK. Development and evaluation of high-density Axiom ® CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:890-901. [PMID: 28913885 PMCID: PMC5866945 DOI: 10.1111/pbi.12836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/06/2017] [Accepted: 09/10/2017] [Indexed: 05/04/2023]
Abstract
To accelerate genomics research and molecular breeding applications in chickpea, a high-throughput SNP genotyping platform 'Axiom® CicerSNP Array' has been designed, developed and validated. Screening of whole-genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70 463 high-quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p-convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom® CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High-density genetic maps comprising 13 679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main-effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications.
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Affiliation(s)
- Manish Roorkiwal
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ankit Jain
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Mahendar Thudi
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- School of Agriculture and Environment & Institute of AgricultureThe University of Western AustraliaCrawleyPerthAustralia
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86
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Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS. Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:380. [PMID: 29636761 PMCID: PMC5881291 DOI: 10.3389/fpls.2018.00380] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 03/08/2018] [Indexed: 05/03/2023]
Abstract
Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2 ) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. HIGHLIGHTS Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.
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Affiliation(s)
- Amira M. I. Mourad
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Stephen Wegulo
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Robert Bowden
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Yue Jin
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Ezzat Mahdy
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Bahy Bakheit
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Atif A. El-Wafaa
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Jesse Poland
- Plant Sciences Center, Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
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87
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Kroeger CM, Garza C, Lynch CJ, Myers E, Rowe S, Schneeman BO, Sharma AM, Allison DB. Scientific rigor and credibility in the nutrition research landscape. Am J Clin Nutr 2018; 107:484-494. [PMID: 29566196 PMCID: PMC6248649 DOI: 10.1093/ajcn/nqx067] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/27/2022] Open
Abstract
Scientific progress depends on the quality and credibility of research methods. As discourse on rigor, transparency, and reproducibility joins the cacophony of nutrition information and misinformation in mass media, buttressing the real and perceived reliability of nutrition science is more important than ever. This broad topic was the focus of a 2016 plenary session, "Scientific Rigor and Competing Interests in the Nutrition Research Landscape." This article summarizes and expands on this session in an effort to increase understanding and dialogue with regard to factors that limit the real and perceived reliability of nutrition science and steps that can be taken to mitigate those factors. The end goal is to both earn and merit greater trust in nutrition science by both the scientific community and the general public. The authors offer suggestions in each of the domains of education and training, communications, research conduct, and procedures and policies to help achieve this goal. The authors emphasize the need for adequate funding to support these efforts toward greater rigor and transparency, which will be resource demanding and may require either increased research funding or the recognition that a greater proportion of research funding may need to be allocated to these tasks.
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Affiliation(s)
- Cynthia M Kroeger
- Department of Epidemiology and Biostatistics, Indiana University School of
Public Health-Bloomington, Bloomington, IN
| | | | - Christopher J Lynch
- National Institutes of Diabetes and Digestive and Kidney Diseases, NIH,
Bethesda, MD
| | | | | | | | | | - David B Allison
- Department of Epidemiology and Biostatistics, Indiana University School of
Public Health-Bloomington, Bloomington, IN
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88
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Tadele Z. African Orphan Crops under Abiotic Stresses: Challenges and Opportunities. SCIENTIFICA 2018; 2018:1451894. [PMID: 29623231 PMCID: PMC5829434 DOI: 10.1155/2018/1451894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/17/2017] [Indexed: 05/23/2023]
Abstract
A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as "orphan crops") including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented.
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Affiliation(s)
- Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Center for Development and Environment (CDE), University of Bern, Bern, Switzerland
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
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89
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Eigenbrode SD, Binns WP, Huggins DR. Confronting Climate Change Challenges to Dryland Cereal Production: A Call for Collaborative, Transdisciplinary Research, and Producer Engagement. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2017.00164] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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90
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Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS. Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 29636761 DOI: 10.3389/fpls.2018.00380/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
UNLABELLED Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2 ) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. HIGHLIGHTS Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.
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Affiliation(s)
- Amira M I Mourad
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Stephen Wegulo
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Robert Bowden
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Yue Jin
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Ezzat Mahdy
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Bahy Bakheit
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Atif A El-Wafaa
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Jesse Poland
- Plant Sciences Center, Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter S Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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91
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Hori K, Yamamoto T, Yano M. Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars. BREEDING SCIENCE 2017; 67:427-434. [PMID: 29398936 PMCID: PMC5790047 DOI: 10.1270/jsbbs.17053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/11/2017] [Indexed: 05/15/2023]
Abstract
Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice (Oryza sativa L.) have been detected by using segregating populations derived from crosses between indica and japonica subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate japonica rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate japonica rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate japonica rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.
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92
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Chen G, Liu C, Gao Z, Zhang Y, Jiang H, Zhu L, Ren D, Yu L, Xu G, Qian Q. OsHAK1, a High-Affinity Potassium Transporter, Positively Regulates Responses to Drought Stress in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1885. [PMID: 29163608 PMCID: PMC5671996 DOI: 10.3389/fpls.2017.01885] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/17/2017] [Indexed: 05/04/2023]
Abstract
Drought is one of the environmental factors that severely restrict plant distribution and crop production. Recently, we reported that the high-affinity potassium transporter OsHAK1 plays important roles in K acquisition and translocation in rice over low and high K concentration ranges, however, knowledge on the regulatory roles of OsHAK1 in osmotic/drought stress is limited. Here, transcript levels of OsHAK1 were found transiently elevated by water deficit in roots and shoots, consistent with the enhanced GUS activity in transgenic plants under stress. Under drought conditions, OsHAK1 knockout mutants (KO) presented lower tolerance to the stress and displayed stunted growth at both the vegetative and reproductive stages. Phenotypic analysis of OsHAK1 overexpression seedlings (Ox) demonstrated that they present better tolerance to drought stress than wild-type (WT). Compared to WT seedlings, OsHAK1 overexpressors had lower level of lipid peroxidation, higher activities of antioxidant enzymes (POX and CAT) and higher proline accumulation. Furthermore, qPCR analysis revealed that OsHAK1 act as a positive regulator of the expression of stress-responsive genes as well as of two well-known rice channel genes (OsTPKb and OsAKT1) involved in K homeostasis and stress responses in transgenic plants under dehydration. Most important, OsHAK1-Ox plants displayed enhanced drought tolerance at the reproductive stage, resulting in 35% more grain yield than WT under drought conditions, and without exhibiting significant differences under normal growth conditions. Consequently, OsHAK1 can be considered to be used in molecular breeding for improvement of drought tolerance in rice.
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Affiliation(s)
- Guang Chen
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Chaolei Liu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hongzhen Jiang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ling Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
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93
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Silva Monteiro de Almeida D, Oliveira Jordão do Amaral D, Del-Bem LE, Bronze dos Santos E, Santana Silva RJ, Peres Gramacho K, Vincentz M, Micheli F. Genome-wide identification and characterization of cacao WRKY transcription factors and analysis of their expression in response to witches' broom disease. PLoS One 2017; 12:e0187346. [PMID: 29084273 PMCID: PMC5662177 DOI: 10.1371/journal.pone.0187346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/18/2017] [Indexed: 12/01/2022] Open
Abstract
Transcriptional regulation, led by transcription factors (TFs) such as those of the WRKY family, is a mechanism used by the organism to enhance or repress gene expression in response to stimuli. Here, we report on the genome-wide analysis of the Theobroma cacao WRKY TF family and also investigate the expression of WRKY genes in cacao infected by the fungus Moniliophthora perniciosa. In the cacao genome, 61 non-redundant WRKY sequences were found and classified in three groups (I to III) according to the WRKY and zinc-finger motif types. The 61 putative WRKY sequences were distributed on the 10 cacao chromosomes and 24 of them came from duplication events. The sequences were phylogenetically organized according to the general WRKY groups. The phylogenetic analysis revealed that subgroups IIa and IIb are sister groups and share a common ancestor, as well as subgroups IId and IIe. The most divergent groups according to the plant origin were IIc and III. According to the phylogenetic analysis, 7 TcWRKY genes were selected and analyzed by RT-qPCR in susceptible and resistant cacao plants infected (or not) with M. perniciosa. Some TcWRKY genes presented interesting responses to M. perniciosa such as Tc01_p014750/Tc06_p013130/AtWRKY28, Tc09_p001530/Tc06_p004420/AtWRKY40, Tc04_p016130/AtWRKY54 and Tc10_p016570/ AtWRKY70. Our results can help to select appropriate candidate genes for further characterization in cacao or in other Theobroma species.
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Affiliation(s)
- Dayanne Silva Monteiro de Almeida
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | - Daniel Oliveira Jordão do Amaral
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | - Luiz-Eduardo Del-Bem
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brasil
| | - Emily Bronze dos Santos
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | - Raner José Santana Silva
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | | | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brasil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
- CIRAD, UMR AGAP, Montpellier, France
- * E-mail:
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94
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Nirmal RC, Furtado A, Rangan P, Henry RJ. Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat. Sci Rep 2017; 7:12539. [PMID: 28970511 PMCID: PMC5624953 DOI: 10.1038/s41598-017-12845-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/14/2017] [Indexed: 12/14/2022] Open
Abstract
A large portion of the global wheat crop is milled to produce flour for use in the production of foods such as bread. Pressure to increase food supplies sustainably can be address directly by reducing post-harvest losses during processes such as flour milling. The recovery of flour in the milling of wheat is genetically determined but difficult to assess in wheat breeding due to the requirement for a large sample. Here we report the discovery that human selection for altered expression of putative cell adhesion proteins is associated with wheats that give high yields of flour on milling. Genes encoding fasciclin-like arabinogalactan proteins are expressed at low levels in high milling wheat genotypes at mid grain development. Thirty worldwide wheat genotypes were grouped into good and poor millers based flour yield obtained from laboratory scale milling of mature seeds. Differentially expressed genes were identified by comparing transcript profiles at 14 and 30 days post anthesis obtained from RNA-seq data of all the genotypes. Direct selection for genotypes with appropriate expression of these genes will greatly accelerate wheat breeding and ensure high recoveries of flour from wheat by resulting in grains that break up more easily on milling.
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Affiliation(s)
- Ravi C Nirmal
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Qld, Australia
| | - Parimalan Rangan
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Qld, Australia.
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95
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Wu M, Liu H, Han G, Cai R, Pan F, Xiang Y. A moso bamboo WRKY gene PeWRKY83 confers salinity tolerance in transgenic Arabidopsis plants. Sci Rep 2017; 7:11721. [PMID: 28916739 PMCID: PMC5601430 DOI: 10.1038/s41598-017-10795-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/15/2017] [Indexed: 11/24/2022] Open
Abstract
The WRKY family are transcription factors, involved in plant development, and response to biotic and abiotic stresses. Moso bamboo is an important bamboo that has high ecological, economic and cultural value and is widely distributed in the south of China. In this study, we performed a genome-wide identification of WRKY members in moso bamboo and identified 89 members. By comparative analysis in six grass genomes, we found the WRKY gene family may have experienced or be experiencing purifying selection. Based on relative expression levels among WRKY IIc members under three abiotic stresses, PeWRKY83 functioned as a transcription factor and was selected for detailed analysis. The transgenic Arabidopsis of PeWRKY83 showed superior physiological properties compared with the WT under salt stress. Overexpression plants were less sensitive to ABA at both germination and postgermination stages and accumulated more endogenous ABA under salt stress conditions. Further studies demonstrated that overexpression of PeWRKY83 could regulate the expression of some ABA biosynthesis genes (AtAAO3, AtNCED2, AtNCED3), signaling genes (AtABI1, AtPP2CA) and responsive genes (AtRD29A, AtRD29B, AtABF1) under salt stress. Together, these results suggested that PeWRKY83 functions as a novel WRKY-related TF which plays a positive role in salt tolerance by regulating stress-induced ABA synthesis.
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Affiliation(s)
- Min Wu
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Guomin Han
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Feng Pan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau.@sina.com.,Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau.@sina.com
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96
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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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97
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Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. MOLECULAR PLANT 2017; 10:1047-1064. [PMID: 28669791 DOI: 10.1016/j.molp.2017.06.008] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 05/18/2023]
Abstract
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Khan
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - Yunbi Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China.
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98
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Wang C, Hu S, Gardner C, Lübberstedt T. Emerging Avenues for Utilization of Exotic Germplasm. TRENDS IN PLANT SCIENCE 2017; 22:624-637. [PMID: 28476651 DOI: 10.1016/j.tplants.2017.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/13/2017] [Accepted: 04/04/2017] [Indexed: 05/21/2023]
Abstract
Breeders have been successful in increasing crop performance by exploiting genetic diversity over time. However, the reported annual yield increases are not sufficient in view of rapid human population growth and global environmental changes. Exotic germplasm possesses high levels of genetic diversity for valuable traits. However, only a small fraction of naturally occurring genetic diversity is utilized. Moreover, the yield gap between elite and exotic germplasm widens, which increases the effort needed to use exotic germplasm and to identify beneficial alleles and for their introgression. The advent of high-throughput genotyping and phenotyping technologies together with emerging biotechnologies provide new opportunities to explore exotic genetic variation. This review will summarize potential challenges for utilization of exotic germplasm and provide solutions.
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Affiliation(s)
- Cuiling Wang
- Department of Agronomy, Henan University of Science and Technology, 263 Kaiyuan Avenue, Luoyang, Henan 471023, China; Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhenzhou, Henan 450002, China
| | - Songlin Hu
- Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA
| | - Candice Gardner
- Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA; US Department of Agrigulture (USDA) Agricultural Research Service (ARS) Plant Introduction Research Unit, 100 Osborn Drive, Iowa State University, Ames, IA 50011, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA.
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99
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Prohens J, Gramazio P, Plazas M, Dempewolf H, Kilian B, Díez MJ, Fita A, Herraiz FJ, Rodríguez-Burruezo A, Soler S, Knapp S, Vilanova S. Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. EUPHYTICA 2017; 213:158. [PMID: 0 DOI: 10.1007/s10681-017-1938-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 06/23/2017] [Indexed: 05/29/2023]
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100
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Saeed A, Darvishzadeh R. Association analysis of biotic and abiotic stresses resistance in chickpea ( Cicer spp.) using AFLP markers. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1333455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Ali Saeed
- Department of Seed and Plant Improvement, West Azerbaijan Agricultural and Natural Resources Research & Education Centre, Agricultural Research, Education and Extension Organization (AREEO), Urmia, Iran
| | - Reza Darvishzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
- Department of Agricultural Biotechnology, Institue of Biotechnology, Urmia University, Urmia, Iran
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