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Aggarwal PR, Muthamilarasan M, Choudhary P. Millet as a promising C4 model crop for sustainable biofuel production. J Biotechnol 2024; 395:110-121. [PMID: 39343056 DOI: 10.1016/j.jbiotec.2024.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/24/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
The rapid depletion of conventional fuel resources and rising energy demand has accelerated the search for alternative energy sources. Further, the expanding need to use bioenergy crops for sustainable fuel production has enhanced the competition for agricultural land, raising the "food vs. fuel" competition. Considering this, producing bioenergy crops on marginal land has a great perspective for achieving sustainable bioenergy production and mitigating the negative impacts of climate change. C4 crops are dual-purpose crops with better efficiency to fix atmospheric CO2 and convert solar energy into lignocellulosic biomass. Of these, millets have gained worldwide attention due to their climate resilience and nutraceutical properties. Due to close synteny with contemporary C4 bioenergy crops, millets are being considered a model crop for studying diverse agronomically important traits associated with biomass production. Millets can be cultivated on marginal land with minimum fertilizer inputs and maximum biomass production. In this regard, advanced molecular approaches, including marker-assisted breeding, multi-omics approaches, and gene-editing technologies, can be employed to genetically engineer these crops for enhanced biofuel production efficiency. The current study aims to provide an overview of millets as a sustainable bioenergy source and underlines the significance of millets as a C4 model to elucidate the genes and pathways involved in lignocellulosic biomass production using advanced molecular biology approaches.
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Affiliation(s)
- Pooja R Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Pooja Choudhary
- Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India.
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2
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Ijaz U, Zhao C, Shahbala S, Zhou M. Genome-Wide Association Study for Identification of Marker-Trait Associations Conferring Resistance to Scald from Globally Collected Barley Germplasm. PHYTOPATHOLOGY 2024; 114:1637-1645. [PMID: 38451589 DOI: 10.1094/phyto-01-24-0043-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Scald is one of the major economically important foliar diseases in barley, causing up to 40% yield loss in susceptible varieties. The identification of quantitative trait loci and elite alleles that confer resistance to scald is imperative in reducing the threats to barley production. In this study, genome-wide association studies were conducted using a panel of 697 barley genotypes to identify quantitative trait loci for scald resistance. Field experiments were conducted over three consecutive years. Among different models used for genome-wide association studies analysis, FarmCPU was shown to be the best-suited model. Nineteen significant marker-trait associations related to scald resistance were identified across six different chromosomes. Eleven of these marker-trait associations correspond to previously reported scald resistance genes Rrs1, Rrs4, and Rrs2, respectively. Eight novel marker-trait associations were identified in this study, with the candidate genes encoding a diverse class of proteins, including region leucine-rich repeats, AP2/ERF transcription factor, homeodomain-leucine zipper, and protein kinase family proteins. The combination of identified superior alleles significantly reduces disease severity scores. The results will be valuable for marker-assisted breeding for developing scald-resistant varieties.
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Affiliation(s)
- Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia
| | - Sergey Shahbala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia
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3
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Li AM, Chen ZL, Qin CX, Li ZT, Liao F, Wang MQ, Lakshmanan P, Li YR, Wang M, Pan YQ, Huang DL. Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane. BMC Genomics 2022; 23:532. [PMID: 35869434 PMCID: PMC9308345 DOI: 10.1186/s12864-022-08768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background Sugarcane is the most important sugar crop, contributing > 80% of global sugar production. High sucrose content is a key target of sugarcane breeding, yet sucrose improvement in sugarcane remains extremely slow for decades. Molecular breeding has the potential to break through the genetic bottleneck of sucrose improvement. Dissecting the molecular mechanism(s) and identifying the key genetic elements controlling sucrose accumulation will accelerate sucrose improvement by molecular breeding. In our previous work, a proteomics dataset based on 12 independent samples from high- and low-sugar genotypes treated with ethephon or water was established. However, in that study, employing conventional analysis, only 25 proteins involved in sugar metabolism were identified . Results In this work, the proteomics dataset used in our previous study was reanalyzed by three different statistical approaches, which include a logistic marginal regression, a penalized multiple logistic regression named Elastic net, as well as a Bayesian multiple logistic regression method named Stochastic search variable selection (SSVS) to identify more sugar metabolism-associated proteins. A total of 507 differentially abundant proteins (DAPs) were identified from this dataset, with 5 of them were validated by western blot. Among the DAPs, 49 proteins were found to participate in sugar metabolism-related processes including photosynthesis, carbon fixation as well as carbon, amino sugar, nucleotide sugar, starch and sucrose metabolism. Based on our studies, a putative network of key proteins regulating sucrose accumulation in sugarcane is proposed, with glucose-6-phosphate isomerase, 2-phospho-D-glycerate hydrolyase, malate dehydrogenase and phospho-glycerate kinase, as hub proteins. Conclusions The sugar metabolism-related proteins identified in this work are potential candidates for sucrose improvement by molecular breeding. Further, this work provides an alternative solution for omics data processing. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08768-2.
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4
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Advanced Breeding for Biotic Stress Resistance in Poplar. PLANTS 2022; 11:plants11152032. [PMID: 35956510 PMCID: PMC9370193 DOI: 10.3390/plants11152032] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 12/20/2022]
Abstract
Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.
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5
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Eckert C, Wildhagen H, Paulo MJ, Scalabrin S, Ballauff J, Schnabel SK, Vendramin V, Keurentjes JJB, Bogeat-Triboulot MB, Taylor G, Polle A. Genotypic and tissue-specific variation of Populus nigra transcriptome profiles in response to drought. Sci Data 2022; 9:297. [PMID: 35701429 PMCID: PMC9197931 DOI: 10.1038/s41597-022-01417-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Climate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis. Measurement(s) | transcriptome | Technology Type(s) | illumina sequencing | Factor Type(s) | treatment | Sample Characteristic - Organism | Populus nigra | Sample Characteristic - Environment | greenhouse experiment |
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Affiliation(s)
- Christian Eckert
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| | - Henning Wildhagen
- HAWK University of Applied Sciences and Arts, Faculty of Resource Management, Büsgenweg 1a, 37077, Göttingen, Germany.
| | - Maria João Paulo
- Biometris, Wageningen UR Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | | | - Johannes Ballauff
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| | - Sabine K Schnabel
- Biometris, Wageningen UR Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Vera Vendramin
- IGA Technology Services, via Jacopo Linussio 51, Udine, Italy
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | | | - Gail Taylor
- Department of Plant Sciences, University of California, One Shields Ave, Davis, CA, USA
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
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Motto M, Sahay S. Energy plants (crops): potential natural and future designer plants. HANDBOOK OF BIOFUELS 2022:73-114. [DOI: 10.1016/b978-0-12-822810-4.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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7
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Assessment of Molecular Diversity in Biofuel Crops. Methods Mol Biol 2021. [PMID: 34009589 DOI: 10.1007/978-1-0716-1323-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Sustainable biofuel sources require the new sources of biofuel crops that can be developed into scalable plantation to meet the growing energy demands. Diverse supply sources of bioenergy plantations (edible, nonedible, and perennial grasses) will enable de-risking impact on geography and climate change that humans are likely to face in future. Use of phenotypic descriptors alone does not provide a deep insight into plantation population dynamics and molecular diversity of a biofuel crop. We provide protocols and methods to rapidly assess population parameters for emerging biofuel crops using genomics. This article has an application focus on next-generation sequencing to assess biofuel crop diversity. Use of these methods can accelerate germplasm assessment to accelerate population development and creation of sustainable biofuel plantations.
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Zhao X, Kang L, Wang Q, Lin C, Liu W, Chen W, Sang T, Yan J. Water Use Efficiency and Stress Tolerance of the Potential Energy Crop Miscanthus lutarioriparius Grown on the Loess Plateau of China. PLANTS 2021; 10:plants10030544. [PMID: 33805780 PMCID: PMC8001145 DOI: 10.3390/plants10030544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 12/11/2022]
Abstract
As a potential energy crop with high biomass yield, Miscanthus lutarioriparius (M. lutarioriparius), endemic to the Long River Range in central China, needs to be investigated for its acclimation to stressful climatic and soil conditions often found on the marginal land. In this study, traits related to acclimation and yield, including survival rates, plant height (PH), stem diameter (SD), tiller number (TN), water use efficiency (WUE), and photosynthetic rates (A), were examined for 41 M. lutarioriparius populations that transplanted to the arid and cold Loess Plateau of China. The results showed that the average survival rate of M. lutarioriparius populations was only 4.16% over the first winter but the overwinter rate increased to 35.03% after the second winter, suggesting that plants having survived the first winter could have acclaimed to the low temperature. The strikingly high survival rates over the second winter were found to be 95.83% and 80.85%, respectively, for HG18 and HG39 populations. These populations might be especially valuable for the selection of energy crops for such an area. Those individuals surviving for the two consecutive winters showed significantly higher WUE than those measured after the first winter. The high WUE and low stomatal conductance (gs) observed in survived individuals could have been responsible for their acclimation to this new and harsh environment. A total of 61 individuals with productive growth traits and strong resistance to cold and drought were identified for further energy crop development. This study showed that the variation of M. lutarioriparius held great potential for developing energy crops following continuous field selection.
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Affiliation(s)
- Xuhong Zhao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (X.Z.); (L.K.); (Q.W.); (C.L.); (W.L.); (T.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifang Kang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (X.Z.); (L.K.); (Q.W.); (C.L.); (W.L.); (T.S.)
| | - Qian Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (X.Z.); (L.K.); (Q.W.); (C.L.); (W.L.); (T.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Cong Lin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (X.Z.); (L.K.); (Q.W.); (C.L.); (W.L.); (T.S.)
| | - Wei Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (X.Z.); (L.K.); (Q.W.); (C.L.); (W.L.); (T.S.)
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (X.Z.); (L.K.); (Q.W.); (C.L.); (W.L.); (T.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence:
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9
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Abstract
Energy security and climate change have cascading effects on the world's burgeoning population in terms of food security, environment, and sustainability. Due to depletion of fossil fuels and undesirable changes of climatic conditions, increase in air and water pollution, mankind started exploring alternate and sustainable means of meeting growing energy needs. One of the options is to use renewable sources of fuel-biofuel. In this chapter the authors have reviewed and presented sustainability impact on production of biofuels. Authors further reviewed state-of-the-art gene editing technologies toward improvement of biofuel crops. The authors recommend a phased transition from first-generation biofuel, and an acceleration toward use of technology to drive adoption of second-generation biofuels. Key aspects of technology and application of resource management models will enable these crops to bridge the global energy demand before we can completely transition to a more sustainable biofuel economy.
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Li G, Lin R, Egekwu C, Blakeslee J, Lin J, Pettengill E, Murphy AS, Peer WA, Islam N, Babst BA, Gao F, Komarov S, Tai YC, Coleman GD. Seasonal nitrogen remobilization and the role of auxin transport in poplar trees. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4512-4530. [PMID: 32161967 PMCID: PMC7382381 DOI: 10.1093/jxb/eraa130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 03/06/2020] [Indexed: 05/31/2023]
Abstract
Seasonal nitrogen (N) cycling in Populus, involves bark storage proteins (BSPs) that accumulate in bark phloem parenchyma in the autumn and decline when shoot growth resumes in the spring. Little is known about the contribution of BSPs to growth or the signals regulating N remobilization from BSPs. Knockdown of BSP accumulation via RNAi and N sink manipulations were used to understand how BSP storage influences shoot growth. Reduced accumulation of BSPs delayed bud break and reduced shoot growth following dormancy. Further, 13N tracer studies also showed that BSP accumulation is an important factor in N partitioning from senescing leaves to bark. Thus, BSP accumulation has a role in N remobilization during N partitioning both from senescing leaves to bark and from bark to expanding shoots once growth commences following dormancy. The bark transcriptome during BSP catabolism and N remobilization was enriched in genes associated with auxin transport and signaling, and manipulation of the source of auxin or auxin transport revealed a role for auxin in regulating BSP catabolism and N remobilization. Therefore, N remobilization appears to be regulated by auxin produced in expanding buds and shoots that is transported to bark where it regulates protease gene expression and BSP catabolism.
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Affiliation(s)
- Gen Li
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Rongshoung Lin
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Chioma Egekwu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Joshua Blakeslee
- OARDC Metabolite Analysis Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, USA
| | - Jinshan Lin
- OARDC Metabolite Analysis Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, USA
| | - Emily Pettengill
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Angus S Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Wendy A Peer
- Department of Environmental Science and Technology, University of Maryland, College Park, USA
| | - Nazrul Islam
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Benjamin A Babst
- College of Forestry, Agriculture and Natural Resources, University of Arkansas at Monticello, Monticello, USA
| | - Fei Gao
- College of Forestry, Agriculture and Natural Resources, University of Arkansas at Monticello, Monticello, USA
| | - Sergey Komarov
- Department of Radiology, Washington University in St. Louis, St. Louis, USA
| | - Yuan-Chuan Tai
- Department of Radiology, Washington University in St. Louis, St. Louis, USA
| | - Gary D Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
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11
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Pancaldi F, Trindade LM. Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:227. [PMID: 32194604 PMCID: PMC7062921 DOI: 10.3389/fpls.2020.00227] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/13/2020] [Indexed: 05/09/2023]
Abstract
The biomass demand to fuel a growing global bio-based economy is expected to tremendously increase over the next decades, and projections indicate that dedicated biomass crops will satisfy a large portion of it. The establishment of dedicated biomass crops raises huge concerns, as they can subtract land that is required for food production, undermining food security. In this context, perennial biomass crops suitable for cultivation on marginal lands (MALs) raise attraction, as they could supply biomass without competing for land with food supply. While these crops withstand marginal conditions well, their biomass yield and quality do not ensure acceptable economic returns to farmers and cost-effective biomass conversion into bio-based products, claiming genetic improvement. However, this is constrained by the lack of genetic resources for most of these crops. Here we first review the advantages of cultivating novel perennial biomass crops on MALs, highlighting management practices to enhance the environmental and economic sustainability of these agro-systems. Subsequently, we discuss the preeminent breeding targets to improve the yield and quality of the biomass obtainable from these crops, as well as the stability of biomass production under MALs conditions. These targets include crop architecture and phenology, efficiency in the use of resources, lignocellulose composition in relation to bio-based applications, and tolerance to abiotic stresses. For each target trait, we outline optimal ideotypes, discuss the available breeding resources in the context of (orphan) biomass crops, and provide meaningful examples of genetic improvement. Finally, we discuss the available tools to breed novel perennial biomass crops. These comprise conventional breeding methods (recurrent selection and hybridization), molecular techniques to dissect the genetics of complex traits, speed up selection, and perform transgenic modification (genetic mapping, QTL and GWAS analysis, marker-assisted selection, genomic selection, transformation protocols), and novel high-throughput phenotyping platforms. Furthermore, novel tools to transfer genetic knowledge from model to orphan crops (i.e., universal markers) are also conceptualized, with the belief that their development will enhance the efficiency of plant breeding in orphan biomass crops, enabling a sustainable use of MALs for biomass provision.
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Affiliation(s)
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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12
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Shimizu FL, Zamora HDZ, Schmatz AA, Melati RB, Bueno D, Brienzo M. Biofuels Generation Based on Technical Process and Biomass Quality. CLEAN ENERGY PRODUCTION TECHNOLOGIES 2020. [DOI: 10.1007/978-981-13-8637-4_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Taylor G, Donnison IS, Murphy-Bokern D, Morgante M, Bogeat-Triboulot MB, Bhalerao R, Hertzberg M, Polle A, Harfouche A, Alasia F, Petoussi V, Trebbi D, Schwarz K, Keurentjes JJB, Centritto M, Genty B, Flexas J, Grill E, Salvi S, Davies WJ. Sustainable bioenergy for climate mitigation: developing drought-tolerant trees and grasses. ANNALS OF BOTANY 2019; 124:513-520. [PMID: 31665761 PMCID: PMC6821384 DOI: 10.1093/aob/mcz146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Bioenergy crops are central to climate mitigation strategies that utilize biogenic carbon, such as BECCS (bioenergy with carbon capture and storage), alongside the use of biomass for heat, power, liquid fuels and, in the future, biorefining to chemicals. Several promising lignocellulosic crops are emerging that have no food role - fast-growing trees and grasses - but are well suited as bioenergy feedstocks, including Populus, Salix, Arundo, Miscanthus, Panicum and Sorghum. SCOPE These promising crops remain largely undomesticated and, until recently, have had limited germplasm resources. In order to avoid competition with food crops for land and nature conservation, it is likely that future bioenergy crops will be grown on marginal land that is not needed for food production and is of poor quality and subject to drought stress. Thus, here we define an ideotype for drought tolerance that will enable biomass production to be maintained in the face of moderate drought stress. This includes traits that can readily be measured in wide populations of several hundred unique genotypes for genome-wide association studies, alongside traits that are informative but can only easily be assessed in limited numbers or training populations that may be more suitable for genomic selection. Phenotyping, not genotyping, is now the major bottleneck for progress, since in all lignocellulosic crops studied extensive use has been made of next-generation sequencing such that several thousand markers are now available and populations are emerging that will enable rapid progress for drought-tolerance breeding. The emergence of novel technologies for targeted genotyping by sequencing are particularly welcome. Genome editing has already been demonstrated for Populus and offers significant potential for rapid deployment of drought-tolerant crops through manipulation of ABA receptors, as demonstrated in Arabidopsis, with other gene targets yet to be tested. CONCLUSIONS Bioenergy is predicted to be the fastest-developing renewable energy over the coming decade and significant investment over the past decade has been made in developing genomic resources and in collecting wild germplasm from within the natural ranges of several tree and grass crops. Harnessing these resources for climate-resilient crops for the future remains a challenge but one that is likely to be successful.
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Affiliation(s)
- G Taylor
- School of Biological Sciences, University of Southampton, Southampton, UK
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - I S Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
| | | | - M Morgante
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze, Udine, Italy
| | | | - R Bhalerao
- Department of Forest Genetics and Plant Physiology, Umea Plant Sciences Centre, Swedish University of Agricultural Sciences, Umea, Sweden
| | - M Hertzberg
- SweTree Technologies AB, SE-904 03 Umeå, Sweden
| | - A Polle
- Büsgen‐Institute, Department of Forest Botany and Tree Physiology, Georg‐August University, Göttingen, Germany
| | - A Harfouche
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, Italy
| | - F Alasia
- Franco Alasia Vivai, Strada Solerette, Savigliano, Italy
| | - V Petoussi
- Department of Sociology, University of Crete, Rethymno, Greece
| | - D Trebbi
- Geneticlab, Via Roveredo, Pordenone, Italy
| | - K Schwarz
- Julius Kühn‐Institut (JKI) Bundesforschungsinstitut für Kulturpflanzen, Institute for Crop and Soil Science, Bundesallee 50, D‐38116 Braunschweig, Germany
| | - J J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - M Centritto
- Trees and Timber Institute, National Research Council of Italy, Sesto Fiorentino, Italy
| | - B Genty
- Aix-Marseille University, CEA, CNRS, BIAM, UMR 7265, Saint Paul lez Durance, France
| | - J Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, Palma de Mallorca, Illes Balears, Spain
| | - E Grill
- Lehrstuhl für Botanik, Technische Universität München, Freising, Germany
| | - S Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin, Bologna, Italy
| | - W J Davies
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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Carlson CH, Gouker FE, Crowell CR, Evans L, DiFazio SP, Smart CD, Smart LB. Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.). ANNALS OF BOTANY 2019; 124:701-716. [PMID: 31008500 PMCID: PMC6821232 DOI: 10.1093/aob/mcz047] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/08/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. METHODS A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. KEY RESULTS Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. CONCLUSIONS This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.
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Affiliation(s)
- Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Chase R Crowell
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Luke Evans
- Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
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15
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Scaglione D, Pinosio S, Marroni F, Di Centa E, Fornasiero A, Magris G, Scalabrin S, Cattonaro F, Taylor G, Morgante M. Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. ANNALS OF BOTANY 2019; 124:543-552. [PMID: 30932149 PMCID: PMC6821380 DOI: 10.1093/aob/mcz054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/25/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared with array-based platforms which have been shown to offer very robust assays. The latter, however, has the drawback of being limited to analyse only the genetic diversity accounted during selection of a set of polymorphisms and design of the assay. In contrast, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has been shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories. METHODS Here we present a first adoption of single-primer enrichment technology (SPET) which provides a highly efficient and scalable system to obtain targeted sequence-based large genotyping data sets, bridging the gaps between array-based systems and traditional sequencing-based protocols. To fully explore SPET performance, we conducted a benchmark study in ten Zea mays lines and a large-scale study of a natural black poplar population of 540 individuals with the aim of discovering polymorphisms associated with biomass-related traits. KEY RESULTS Our results showed the ability of this technology to provide dense genotype information on a customized panel of selected polymorphisms, while yielding hundreds of thousands of untargeted variable sites. This provided an ideal resource for association analysis of natural populations harbouring unexplored allelic diversities and structure such as in black poplar. CONCLUSION The improvement of sequencing throughput and the development of efficient library preparation methods has made it feasible to carry out targeted genotyping-by-sequencing experiments cost-competitively with either random complexity reduction systems or traditional array-based platforms, while maintaining the key advantages of both technologies.
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Affiliation(s)
- Davide Scaglione
- IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy
- correspondence. E-mail
| | - Sara Pinosio
- IGA – Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy
| | - Fabio Marroni
- IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy
| | | | - Alice Fornasiero
- IGA – Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy
| | - Gabriele Magris
- Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
| | - Simone Scalabrin
- IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy
| | | | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, UK
| | - Michele Morgante
- IGA – Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy
- Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy
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16
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Papacek M, Christmann A, Grill E. Increased water use efficiency and water productivity of arabidopsis by abscisic acid receptors from Populus canescens. ANNALS OF BOTANY 2019; 124:581-590. [PMID: 30629104 PMCID: PMC6821255 DOI: 10.1093/aob/mcy225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/06/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Water deficit is the single most important factor limiting plant productivity in the field. Poplar is a crop used for second-generation bioenergy production that can be cultivated on marginal land without competing for land use in food production. Poplar has a high demand for water, which makes improving its water use efficiency (WUE) an attractive goal. Recently, we showed that enhanced expression of specific receptors of arabidopsis for the phytohormone abscisic acid (ABA) can improve WUE in arabidopsis and water productivity, i.e. more biomass is formed per unit of water over time. In this study, we examined whether ABA receptors from poplar can enhance WUE and water productivity in arabidopsis. METHODS ABA receptors from poplar were stably introduced into arabidopsis for analysis of their effect on water use efficiency. Physiological analysis included growth assessment and gas exchange measurements. KEY RESULTS The data presented here are in agreement with the functionality of poplar ABA receptors in arabidopsis, which led to ABA-hypersensitive seed germination and root growth. In addition, arabidopsis lines expressing poplar RCAR10, but not RCAR9, showed increased WUE by up to 26 % compared with the wild type with few trade-offs in growth that also resulted in higher water productivity during drought. The improved WUE was mediated by reduced stomatal conductance, a steeper CO2 gradient at the leaf boundary and sustained photosynthesis resulting in an increased intrinsic WUE (iWUE). CONCLUSIONS The analysis is a case study supporting the use of poplar ABA receptors for improving WUE and showing the feasibility of using a heterologous expression strategy for generating plants with improved water productivity.
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Affiliation(s)
- Michael Papacek
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße, Freising, Germany
| | - Alexander Christmann
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße, Freising, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße, Freising, Germany
- For correspondence. E-mail
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Allona I, Kirst M, Boerjan W, Strauss S, Sederoff R. Editorial: Forest Genomics and Biotechnology. FRONTIERS IN PLANT SCIENCE 2019; 10:1187. [PMID: 31681350 PMCID: PMC6806019 DOI: 10.3389/fpls.2019.01187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Isabel Allona
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steven Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
| | - Ronald Sederoff
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
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18
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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19
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Hallingbäck HR, Berlin S, Nordh NE, Weih M, Rönnberg-Wästljung AC. Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [ Salix viminalis (L.)]. FRONTIERS IN PLANT SCIENCE 2019; 10:753. [PMID: 31249579 PMCID: PMC6582754 DOI: 10.3389/fpls.2019.00753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/23/2019] [Indexed: 05/10/2023]
Abstract
The short rotation biomass crop willow (Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.
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Affiliation(s)
- Henrik R. Hallingbäck
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nils-Erik Nordh
- Department of Crop Production Ecology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Martin Weih
- Department of Crop Production Ecology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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20
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Brew-Appiah RAT, Peracchi LM, Sanguinet KA. Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon. PLANTS 2019; 8:plants8060153. [PMID: 31174296 PMCID: PMC6630600 DOI: 10.3390/plants8060153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 11/25/2022]
Abstract
Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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21
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Pazhany AS, Henry RJ. Genetic Modification of Biomass to Alter Lignin Content and Structure. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b01163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Adhini S. Pazhany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, 4072 Queensland, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, 641 007 Tamil Nadu, India
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, 4072 Queensland, Australia
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22
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Brew-Appiah RAT, Sanguinet KA. Considerations of AOX Functionality Revealed by Critical Motifs and Unique Domains. Int J Mol Sci 2018; 19:ijms19102972. [PMID: 30274246 PMCID: PMC6213860 DOI: 10.3390/ijms19102972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/14/2018] [Accepted: 09/28/2018] [Indexed: 12/28/2022] Open
Abstract
An understanding of the genes and mechanisms regulating environmental stress in crops is critical for boosting agricultural yield and safeguarding food security. Under adverse conditions, response pathways are activated for tolerance or resistance. In multiple species, the alternative oxidase (AOX) genes encode proteins which help in this process. Recently, this gene family has been extensively investigated in the vital crop plants, wheat, barley and rice. Cumulatively, these three species and/or their wild ancestors contain the genes for AOX1a, AOX1c, AOX1e, and AOX1d, and common patterns in the protein isoforms have been documented. Here, we add more information on these trends by emphasizing motifs that could affect expression, and by utilizing the most recent discoveries from the AOX isoform in Trypanosoma brucei to highlight clade-dependent biases. The new perspectives may have implications on how the AOX gene family has evolved and functions in monocots. The common or divergent amino acid substitutions between these grasses and the parasite are noted, and the potential effects of these changes are discussed. There is the hope that the insights gained will inform the way future AOX research is performed in monocots, in order to optimize crop production for food, feed, and fuel.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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23
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Cánovas FM, Cañas RA, de la Torre FN, Pascual MB, Castro-Rodríguez V, Avila C. Nitrogen Metabolism and Biomass Production in Forest Trees. FRONTIERS IN PLANT SCIENCE 2018; 9:1449. [PMID: 30323829 PMCID: PMC6172323 DOI: 10.3389/fpls.2018.01449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
Low nitrogen (N) availability is a major limiting factor for tree growth and development. N uptake, assimilation, storage and remobilization are key processes in the economy of this essential nutrient, and its efficient metabolic use largely determines vascular development, tree productivity and biomass production. Recently, advances have been made that improve our knowledge about the molecular regulation of acquisition, assimilation and internal recycling of N in forest trees. In poplar, a model tree widely used for molecular and functional studies, the biosynthesis of glutamine plays a central role in N metabolism, influencing multiple pathways both in primary and secondary metabolism. Moreover, the molecular regulation of glutamine biosynthesis is particularly relevant for accumulation of N reserves during dormancy and in N remobilization that takes place at the onset of the next growing season. The characterization of transgenic poplars overexpressing structural and regulatory genes involved in glutamine biosynthesis has provided insights into how glutamine metabolism may influence the N economy and biomass production in forest trees. Here, a general overview of this research topic is outlined, recent progress are analyzed and challenges for future research are discussed.
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Affiliation(s)
- Francisco M. Cánovas
- Grupo de Biología Molecular y Biotecnología de Plantas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
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24
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Yabe S, Hara T, Ueno M, Enoki H, Kimura T, Nishimura S, Yasui Y, Ohsawa R, Iwata H. Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat. FRONTIERS IN PLANT SCIENCE 2018; 9:276. [PMID: 29619035 PMCID: PMC5871932 DOI: 10.3389/fpls.2018.00276] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 02/16/2018] [Indexed: 05/20/2023]
Abstract
To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598-50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.
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Affiliation(s)
- Shiori Yabe
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Takashi Hara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mariko Ueno
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Enoki
- Biotechnology and Afforestation Laboratory, Agriculture & Biotechnology Business Division, Toyota Motor Corporation, Miyoshi, Japan
| | - Tatsuro Kimura
- Biotechnology and Afforestation Laboratory, Agriculture & Biotechnology Business Division, Toyota Motor Corporation, Miyoshi, Japan
| | - Satoru Nishimura
- Information System Development Department, X-Frontier Division, Frontier Research Center, Toyota Motor Corporation, Nagoya, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ryo Ohsawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
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25
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Wildhagen H, Paul S, Allwright M, Smith HK, Malinowska M, Schnabel SK, Paulo MJ, Cattonaro F, Vendramin V, Scalabrin S, Janz D, Douthe C, Brendel O, Buré C, Cohen D, Hummel I, Le Thiec D, van Eeuwijk F, Keurentjes JJB, Flexas J, Morgante M, Robson P, Bogeat-Triboulot MB, Taylor G, Polle A. Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra. TREE PHYSIOLOGY 2018; 38:320-339. [PMID: 28541580 PMCID: PMC5982782 DOI: 10.1093/treephys/tpx054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/03/2017] [Indexed: 05/03/2023]
Abstract
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential. The three poplar genotypes differed in wood anatomy, lignin content and saccharification potential. Drought resulted in reduced cambial activity, decreased vessel and fiber lumina, and increased the saccharification potential. The saccharification potential was unrelated to lignin content as well as to most wood anatomical traits. RNA sequencing of the developing xylem revealed that 1.5% of the analyzed genes were differentially expressed in response to drought, while 67% differed among the genotypes. Weighted gene correlation network analysis identified modules of co-expressed genes correlated with saccharification potential. These modules were enriched in gene ontology terms related to cell wall polysaccharide biosynthesis and modification and vesicle transport, but not to lignin biosynthesis. Among the most strongly saccharification-correlated genes, those with regulatory functions, especially kinases, were prominent. We further identified transcription factors whose transcript abundances differed among genotypes, and which were co-regulated with genes for biosynthesis and modifications of hemicelluloses and pectin. Overall, our study suggests that the regulation of pectin and hemicellulose metabolism is a promising target for improving wood quality of second generation bioenergy crops. The causal relationship of the identified genes and pathways with saccharification potential needs to be validated in further experiments.
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Affiliation(s)
- Henning Wildhagen
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
- HAWK University of Applied Sciences and Arts, Faculty of Resource Management, Büsgenweg 1a, 37077 Göttingen, Germany
| | - Shanty Paul
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Mike Allwright
- Center for Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Hazel K Smith
- Center for Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Marta Malinowska
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY233EE, UK
| | - Sabine K Schnabel
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Vera Vendramin
- IGA Technology Services, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Simone Scalabrin
- IGA Technology Services, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Dennis Janz
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Cyril Douthe
- Universidad de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Oliver Brendel
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Cyril Buré
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - David Cohen
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Irène Hummel
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Didier Le Thiec
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Fred van Eeuwijk
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jaume Flexas
- Universidad de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Michele Morgante
- Università Di Udine, Istituto di Genomica Applicata, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Paul Robson
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY233EE, UK
| | | | - Gail Taylor
- Center for Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Andrea Polle
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
- Corresponding author ()
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You Q, Yang X, Peng Z, Xu L, Wang J. Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array. FRONTIERS IN PLANT SCIENCE 2018; 9:104. [PMID: 29467780 PMCID: PMC5808122 DOI: 10.3389/fpls.2018.00104] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/19/2018] [Indexed: 05/18/2023]
Abstract
Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.
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Affiliation(s)
- Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Liping Xu
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, United States
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Jianping Wang
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Papacek M, Christmann A, Grill E. Interaction network of ABA receptors in grey poplar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:199-210. [PMID: 28746755 DOI: 10.1111/tpj.13646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
The plant hormone abscisic acid (ABA) is a key player in responses to abiotic stress. ABA regulates a plant's water status and mediates drought tolerance by controlling stomatal gas exchange, water conductance and differential gene expression. ABA is recognized and bound by the Regulatory Component of ABA Receptors (RCARs)/PYR1/PYL (Pyrabactin Resistance 1/PYR1-like). Ligand binding stabilizes the interaction of RCARs with type 2C protein phosphatases (PP2C), which are ABA co-receptors. While the core pathway of ABA signalling has been elucidated, the large number of different ABA receptors and co-receptors within a plant species generates a complexity of heteromeric receptor complexes that has not functionally been resolved in any plant species to date. In this study, we characterized ABA receptors and co-receptors of grey poplar (Populus x canescens [Ait.] Sm.) and their capacity to regulate ABA responses. We observed a high number of regulatory combinations of holo-receptor complexes, but also some preferential and selective RCAR-PP2C interactions. Poplar and Arabidopsis ABA receptor components revealed a strong structural and functional conservation. Heterologous receptor complexes of poplar and Arabidopsis components showed functionality in vitro and regulated ABA-responsive gene expression in cells of both species. ABA-responsive promoters of Arabidopsis were also active in poplar, which was explored to generate poplar reporter lines expressing green fluorescent protein in response to ABA. The study presents a detailed analysis of receptor complexes of a tree species and shows high conservation of ABA receptor components between an annual and a perennial plant.
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Affiliation(s)
- Michael Papacek
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| | - Alexander Christmann
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
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Xu Y, Li P, Zou C, Lu Y, Xie C, Zhang X, Prasanna BM, Olsen MS. Enhancing genetic gain in the era of molecular breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2641-2666. [PMID: 28830098 DOI: 10.1093/jxb/erx135] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/03/2017] [Indexed: 05/20/2023]
Abstract
As one of the important concepts in conventional quantitative genetics and breeding, genetic gain can be defined as the amount of increase in performance that is achieved annually through artificial selection. To develop pro ducts that meet the increasing demand of mankind, especially for food and feed, in addition to various industrial uses, breeders are challenged to enhance the potential of genetic gain continuously, at ever higher rates, while they close the gaps that remain between the yield potential in breeders' demonstration trials and the actual yield in farmers' fields. Factors affecting genetic gain include genetic variation available in breeding materials, heritability for traits of interest, selection intensity, and the time required to complete a breeding cycle. Genetic gain can be improved through enhancing the potential and closing the gaps, which has been evolving and complemented with modern breeding techniques and platforms, mainly driven by molecular and genomic tools, combined with improved agronomic practice. Several key strategies are reviewed in this article. Favorable genetic variation can be unlocked and created through molecular and genomic approaches including mutation, gene mapping and discovery, and transgene and genome editing. Estimation of heritability can be improved by refining field experiments through well-controlled and precisely assayed environmental factors or envirotyping, particularly for understanding and controlling spatial heterogeneity at the field level. Selection intensity can be significantly heightened through improvements in the scale and precision of genotyping and phenotyping. The breeding cycle time can be shortened by accelerating breeding procedures through integrated breeding approaches such as marker-assisted selection and doubled haploid development. All the strategies can be integrated with other widely used conventional approaches in breeding programs to enhance genetic gain. More transdisciplinary approaches, team breeding, will be required to address the challenge of maintaining a plentiful and safe food supply for future generations. New opportunities for enhancing genetic gain, a high efficiency breeding pipeline, and broad-sense genetic gain are also discussed prospectively.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Ping Li
- Nantong Xinhe Bio-Technology, Nantong 226019, PR China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Boddupalli M Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
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30
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Popp J, Harangi-Rákos M, Gabnai Z, Balogh P, Antal G, Bai A. Biofuels and Their Co-Products as Livestock Feed: Global Economic and Environmental Implications. Molecules 2016; 21:285. [PMID: 26938514 PMCID: PMC6273624 DOI: 10.3390/molecules21030285] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/03/2016] [Accepted: 02/24/2016] [Indexed: 11/16/2022] Open
Abstract
This review studies biofuel expansion in terms of competition between conventional and advanced biofuels based on bioenergy potential. Production of advanced biofuels is generally more expensive than current biofuels because products are not yet cost competitive. What is overlooked in the discussion about biofuel is the contribution the industry makes to the global animal feed supply and land use for cultivation of feedstocks. The global ethanol industry produces 44 million metric tonnes of high-quality feed, however, the co-products of biodiesel production have a moderate impact on the feed market contributing to just 8-9 million tonnes of protein meal output a year. By economically displacing traditional feed ingredients co-products from biofuel production are an important and valuable component of the biofuels sector and the global feed market. The return of co-products to the feed market has agricultural land use (and GHG emissions) implications as well. The use of co-products generated from grains and oilseeds can reduce net land use by 11% to 40%. The proportion of global cropland used for biofuels is currently some 2% (30-35 million hectares). By adding co-products substituted for grains and oilseeds the land required for cultivation of feedstocks declines to 1.5% of the global crop area.
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Affiliation(s)
- József Popp
- Institute of Sectoral Economics and Methodology, Faculty of Economics and Business, University of Debrecen, Debrecen 4032, Hungary.
| | - Mónika Harangi-Rákos
- Institute of Sectoral Economics and Methodology, Faculty of Economics and Business, University of Debrecen, Debrecen 4032, Hungary.
| | - Zoltán Gabnai
- Institute of Business Economics, Faculty of Economics and Business, University of Debrecen, Debrecen 4032, Hungary.
| | - Péter Balogh
- Institute of Sectoral Economics and Methodology, Faculty of Economics and Business, University of Debrecen, Debrecen 4032, Hungary.
| | - Gabriella Antal
- Institute of Sectoral Economics and Methodology, Faculty of Economics and Business, University of Debrecen, Debrecen 4032, Hungary.
| | - Attila Bai
- Institute of Business Economics, Faculty of Economics and Business, University of Debrecen, Debrecen 4032, Hungary.
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Allwright MR, Payne A, Emiliani G, Milner S, Viger M, Rouse F, Keurentjes JJB, Bérard A, Wildhagen H, Faivre-Rampant P, Polle A, Morgante M, Taylor G. Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). BIOTECHNOLOGY FOR BIOFUELS 2016; 9:195. [PMID: 27617034 PMCID: PMC5017058 DOI: 10.1186/s13068-016-0603-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species. RESULTS We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population. CONCLUSIONS The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.
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Affiliation(s)
- Mike Robert Allwright
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Adrienne Payne
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Giovanni Emiliani
- CNR-IVALSA, Sesto Fiorentino, via Madonna del Piano, 10, 50019 Sesto Fiorentino, FI Italy
| | - Suzanne Milner
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Maud Viger
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Franchesca Rouse
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Joost J. B. Keurentjes
- Laboratory of Genetics, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | | | - Andrea Polle
- Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Michele Morgante
- Dipartimento di Scienze agroalimentari, ambientali e animali, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy
- Istituto di Genomica Applicata (IGA), via J. Linussio 51, 33100 Udine, Italy
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
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