Special Issue "Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops"

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A special issue of Agronomy (ISSN 2073-4395).

Deadline for manuscript submissions: closed (1 October 2013)

Special Issue Editors

Guest Editor
Prof. Dr. Michael Timko

Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA
Website | E-Mail
Interests: plant genomics, molecular breeding, abiotic and biotic stress response, legumes
Guest Editor
Dr. Paul J. Rushton

Department of Biology and Microbiology South Dakota State University, Brookings, SD 57007, USA
Website | E-Mail
Phone: +1 605 688 5749
Interests: transcriptional regulation; promoter technology; systems biology; abiotic and biotic stress response; cereals; drought

Special Issue Information

Dear Colleagues,

Agricultural productivity is particularly sensitive to environmental alteration, especially at the growth margins where temperature extremes and water availability already limit growth and yield. Predicted losses in tillable land due to global climate change and anticipated population increases in coming decades will place ever greater demands on agricultural systems to meet the increasing demands for food, forage, and bioenergy based resources. Addressing this demand will necessitate expansion of crop adaptation for cultivation in marginal environments using sustainable and low-input agronomic practices.
This special issue of Agronomy focuses on the application of innovations in omics-based research (genomics, proteomics, metabolomics, phenomics, etc ) to the genetic improvement of domesticated crop plants adapted for enhanced growth and yield under changing environmental pressures resulting from rapid and dramatic alterations in global weather patterns. Papers are sought that discuss how enhanced agro-ecological adaptation of plants to abiotic and biotic stress can be achieved using novel and emerging technologies and providing frameworks for sustainable agricultural production in the face of environmental uncertainty.

Prof. Dr. Michael P. Timko
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


Keywords

  • breeding methods
  • climate change
  • crop improvement
  • emerging technologies
  • genomic tools; genomics
  • stress tolerance
  • sustainability
  • yield

Published Papers (5 papers)

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Research

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Open AccessArticle Phenotypic Diversity of Farmers’ Traditional Rice Varieties in the Philippines
Agronomy 2014, 4(2), 217-241; doi:10.3390/agronomy4020217
Received: 22 October 2013 / Revised: 29 April 2014 / Accepted: 5 May 2014 / Published: 13 May 2014
Cited by 1 | PDF Full-text (1194 KB) | HTML Full-text | XML Full-text
Abstract
Traditional rice varieties maintained and cultivated by farmers are likely sources of germplasm for breeding new rice varieties. They possess traits potentially adaptable to a wide range of abiotic and biotic stresses. Characterization of these germplasms is essential in rice breeding and provides
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Traditional rice varieties maintained and cultivated by farmers are likely sources of germplasm for breeding new rice varieties. They possess traits potentially adaptable to a wide range of abiotic and biotic stresses. Characterization of these germplasms is essential in rice breeding and provides valued information on developing new rice cultivars. In this study, 307 traditional rice varieties newly conserved at the PhilRice genebank were characterized to assess their phenotypic diversity using 57 morphological traits. Using the standardized Shannon-Weaver diversity index, phenotypic diversity indices averaged at 0.73 and 0.45 for quantitative and qualitative traits, respectively. Correlation analyses among agro-morphological traits showed a high positive correlation in some traits such as culm number and panicle number, flag leaf width and leaf blade width, grain width and caryopsis width. Cluster analysis separated the different varieties into various groups. Principal component analysis (PCA) showed that seven independent principal components accounted for 74.95% of the total variation. Component loadings for each principal component showed morphological characters, such as culm number, panicle number and caryopsis ratio that were among the phenotypic traits contributing positive projections in three principal components that explained 48% of variation. Analyses of results showed high diversity in major traits assessed in farmers’ rice varieties. Based on plant height and maturity, 11 accessions could be potential donor parents in a rice breeding program. Future collection trips and characterization studies would further enrich diversity, in particular traits low in diversity, such as anthocyanin coloration, awn presence, awn color, culm habit, panicle type and panicle branching. Full article
Open AccessArticle A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”
Agronomy 2014, 4(1), 13-33; doi:10.3390/agronomy4010013
Received: 15 November 2013 / Revised: 9 January 2014 / Accepted: 14 January 2014 / Published: 17 January 2014
Cited by 2 | PDF Full-text (753 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We present a draft genome sequence for enset (Ensete ventricosum) available via the Sequence Read Archive (accession number SRX202265) and GenBank (accession number AMZH01. Enset feeds 15 million people in Ethiopia, but is arguably the least studied African crop. Our sequence
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We present a draft genome sequence for enset (Ensete ventricosum) available via the Sequence Read Archive (accession number SRX202265) and GenBank (accession number AMZH01. Enset feeds 15 million people in Ethiopia, but is arguably the least studied African crop. Our sequence data suggest a genome size of approximately 547 megabases, similar to the 523-megabase genome of the closely related banana (Musa acuminata). At least 1.8% of the annotated M. acuminata genes are not conserved in E. ventricosum. Furthermore, enset contains genes not present in banana, including reverse transcriptases and virus-like sequences as well as a homolog of the RPP8-like resistance gene. We hope that availability of genome-wide sequence data will stimulate and accelerate research on this important but neglected crop. Full article
Open AccessArticle Effects of Previous Crop Management, Fertilization Regime and Water Supply on Potato Tuber Proteome and Yield
Agronomy 2013, 3(1), 59-85; doi:10.3390/agronomy3010059
Received: 19 November 2012 / Revised: 7 December 2012 / Accepted: 21 December 2012 / Published: 15 January 2013
Cited by 1 | PDF Full-text (522 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
There is increasing concern about the sustainability and environmental impacts of mineral fertilizer use in agriculture. Increased recycling of nutrients via the use of animal and green manures and fertilizers made from domestic organic waste may reduce reliance on mineral fertilizers. However, the
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There is increasing concern about the sustainability and environmental impacts of mineral fertilizer use in agriculture. Increased recycling of nutrients via the use of animal and green manures and fertilizers made from domestic organic waste may reduce reliance on mineral fertilizers. However, the relative availability of nutrients (especially nitrogen) is lower in organic compared to mineral fertilizers, which can result in significantly lower yields in nutrient demanding crops such as potato. It is therefore important to gain a better understanding of the factors affecting nutrient use efficiency (yield per unit fertilizer input) from organic fertilizers. Here we show that (a) previous crop management (organic vs. conventional fertilization and crop protection regimes), (b) organic fertilizer type and rate (composted cattle manure vs. composted chicken manure pellets) and (c) watering regimes (optimized and restricted) significantly affected leaf chlorophyll content, potato tuber N-concentration, proteome and yield. Protein inference by gel matching indicated several functional groups significantly affected by previous crop management and organic fertilizer type and rate, including stress/defense response, glycolysis and protein destination and storage. These results indicate genomic pathways controlling crop responses (nutrient use efficiency and yield) according to contrasting types and rates of organic fertilizers that can be linked to the respective encoding genes. Full article
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Review

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Open AccessReview New Approaches for Crop Genetic Adaptation to the Abiotic Stresses Predicted with Climate Change
Agronomy 2013, 3(2), 419-432; doi:10.3390/agronomy3020419
Received: 24 January 2013 / Revised: 1 April 2013 / Accepted: 25 April 2013 / Published: 10 May 2013
Cited by 2 | PDF Full-text (181 KB) | HTML Full-text | XML Full-text
Abstract
Extreme climatic variation is predicted with climate change this century. In many cropping regions, the crop environment will tend to be warmer with more irregular rainfall and spikes in stress levels will be more severe. The challenge is not only to raise agricultural
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Extreme climatic variation is predicted with climate change this century. In many cropping regions, the crop environment will tend to be warmer with more irregular rainfall and spikes in stress levels will be more severe. The challenge is not only to raise agricultural production for an expanding population, but to achieve this under more adverse environmental conditions. It is now possible to systematically explore the genetic variation in historic local landraces by using GPS locators and world climate maps to describe the natural selection for local adaptation, and to identify candidate germplasm for tolerances to extreme stresses. The physiological and biochemical components of these expressions can be genomically investigated with candidate gene approaches and next generation sequencing. Wild relatives of crops have largely untapped genetic variation for abiotic and biotic stress tolerances, and could greatly expand the available domesticated gene pools to assist crops to survive in the predicted extremes of climate change, a survivalomics strategy. Genomic strategies can assist in the introgression of these valuable traits into the domesticated crop gene pools, where they can be better evaluated for crop improvement. The challenge is to increase agricultural productivity despite climate change. This calls for the integration of many disciplines from eco-geographical analyses of genetic resources to new advances in genomics, agronomy and farm management, underpinned by an understanding of how crop adaptation to climate is affected by genotype × environment interaction. Full article

Other

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Open AccessDiscussion The Cysteine Protease–Cysteine Protease Inhibitor System Explored in Soybean Nodule Development
Agronomy 2013, 3(3), 550-570; doi:10.3390/agronomy3030550
Received: 29 May 2013 / Revised: 12 July 2013 / Accepted: 22 July 2013 / Published: 20 August 2013
Cited by 5 | PDF Full-text (931 KB) | HTML Full-text | XML Full-text
Abstract
Almost all protease families have been associated with plant development, particularly senescence, which is the final developmental stage of every organ before cell death. Proteolysis remobilizes and recycles nitrogen from senescent organs that is required, for example, seed development. Senescence-associated expression of proteases
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Almost all protease families have been associated with plant development, particularly senescence, which is the final developmental stage of every organ before cell death. Proteolysis remobilizes and recycles nitrogen from senescent organs that is required, for example, seed development. Senescence-associated expression of proteases has recently been characterized using large-scale gene expression analysis seeking to identify and characterize senescence-related genes. Increasing activities of proteolytic enzymes, particularly cysteine proteases, are observed during the senescence of legume nodules, in which a symbiotic relationship between the host plant and bacteria (Rhizobia) facilitate the fixation of atmospheric nitrogen. It is generally considered that cysteine proteases are compartmentalized to prevent uncontrolled proteolysis in nitrogen-fixing nodules. In addition, the activities of cysteine proteases are regulated by endogenous cysteine protease inhibitors called cystatins. These small proteins form reversible complexes with cysteine proteases, leading to inactivation. However, very little is currently known about how the cysteine protease-cysteine protease inhibitor (cystatin) system is regulated during nodule development. Moreover, our current understanding of the expression and functions of proteases and protease inhibitors in nodules is fragmented. To address this issue, we have summarized the current knowledge and techniques used for studying proteases and their inhibitors including the application of “omics” tools, with a particular focus on changes in the cysteine protease-cystatin system during nodule development. Full article

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Title: Systems Biology Dissection of Germination Efficiency in Maize Seeds: Genetic, Physiological, and Metabolomic Correlations under Optimal and Cool Temperature Environments
Authors: Miaoqing Shen 1,*, Nicholas Kaczmar 1, Corey D. Broeckling 2, Gregory Ziegler 3, Ivan R. Baxter 3, Jessica E. Prenni 2 and Owen A. Hoekenga 1
Affiliations: 1 USDA-ARS, RW Holley Center for Agriculture and Health, Ithaca NY 14853, USA
2
Colorado State University, Proteomics and Metabolomics Facility, Fort Collins CO 80523, USA
3
USDA-ARS, Plant Genetics Research Unit, St Louis MO 63132, USA
* Current address: Advion, Inc., Ithaca NY 14850 US
Abstract : Global climate change is affecting crop performance. Fluctuation in spring temperatures can have a negative outcome for germination efficiency and ultimately crop yield in susceptible varieties; defining the genetic and physiological bases for germination efficiency under cooler than expected temperatures is a useful goal. We are using genome wide association studies to analyze germination efficiency in a well-characterized panel of diverse maize inbred varieties. In parallel, we have used non-targeted mass spectrometry paired with network analysis to characterize the maize grain metabolome. We combine physiological and metabolomic phenotyping within a statistical genomics framework to identify potential key factors for germination efficiency under optimal and sub-optimal temperatures.

Type of Article: Review
Title: Crop Adaptation to Changing Climate Conditions: Recent Approaches to Better Exploit Functional Diversity in African Crops and their Wild Relatives
Authors: N. Kane 1, Y. Vigouroux 2,3,* and C. Berthouly-Salazard 2,3
Affiliations: 1 Institut Sénégalais de Recherche Agronomique, ISRA, Dakar, Sénégal
2 Institut de recherche pour le développement, IRD, Montpellier, France
3 University Montpellier II, Montpellier, France
Abstract:

- African agriculture challenge by strong environmental changes and a growing populations
- A untapped  functional diversity exist in African crops (millet, sorghum and fonio)

  • Crop functional diversity might be useful to cope to changing climate (example pearl millet in Niger) and feed a growing populations (fonio as diversification)
  • Wild relative diversity interesting because wild relatives grows in drier environment (ex: pearl millet and sorghum)

- Next generation sequencing approaches offers new tool to unlock functional genetic diversity

  • Inventory/example of NGS approach and their uses
  • Examples

- Genome wide association mapping and genome wide selection scan offer opportunity to identify agronomic QTLs

  • Explanation of association mapping, its interest and new recent development
  • Explanation of selection scan approaches, their interest and recent development
  • Combining association mapping and selection scan (examples)
Keywords: adaptation; african crop; detection of selection; association study; functional genetic variation

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