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Agronomy
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Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological...
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Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops

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

Deadline for manuscript submissions: closed (1 October 2013) | Viewed by 65934

Special Issue Editors

Prof. Dr. Michael Timko

E-Mail Website
Guest Editor
Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
Interests: plant genomics; molecular breeding; nutraceuticals; human therapeutics; abiotic and biotic stress response
Special Issues, Collections and Topics in MDPI journals
Dr. Paul J. Rushton

E-Mail Website
Guest Editor
Department of Biology and Microbiology South Dakota State University, Brookings, SD 57007, USA
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

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind 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 monthly 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 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

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

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Published Papers (5 papers)

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Research

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1194 KiB  
Article
Phenotypic Diversity of Farmers’ Traditional Rice Varieties in the Philippines
by Roel C. Rabara, Marilyn C. Ferrer, Celia L. Diaz, Ma. Cristina V. Newingham and Gabriel O. Romero
Agronomy 2014, 4(2), 217-241; https://doi.org/10.3390/agronomy4020217 - 13 May 2014
Cited by 44 | Viewed by 24550
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 [...] Read more.
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
(This article belongs to the Special Issue Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops)
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753 KiB  
Article
A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”
by James Harrison, Karen A. Moore, Konrad Paszkiewicz, Thomas Jones, Murray R. Grant, Daniel Ambacheew, Sadik Muzemil and David J. Studholme
Agronomy 2014, 4(1), 13-33; https://doi.org/10.3390/agronomy4010013 - 17 Jan 2014
Cited by 18 | Viewed by 13210
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 [...] Read more.
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
(This article belongs to the Special Issue Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops)
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522 KiB  
Article
Effects of Previous Crop Management, Fertilization Regime and Water Supply on Potato Tuber Proteome and Yield
by Catherine Tétard-Jones, Martin G. Edwards, Leonidas Rempelos, Angharad M.R. Gatehouse, Mick Eyre, Stephen J. Wilcockson and Carlo Leifert
Agronomy 2013, 3(1), 59-85; https://doi.org/10.3390/agronomy3010059 - 15 Jan 2013
Cited by 10 | Viewed by 7988
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 [...] Read more.
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
(This article belongs to the Special Issue Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops)
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Review

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181 KiB  
Review
New Approaches for Crop Genetic Adaptation to the Abiotic Stresses Predicted with Climate Change
by Robert Redden
Agronomy 2013, 3(2), 419-432; https://doi.org/10.3390/agronomy3020419 - 10 May 2013
Cited by 33 | Viewed by 8150
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 [...] Read more.
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
(This article belongs to the Special Issue Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops)

Other

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931 KiB  
Discussion
The Cysteine Protease–Cysteine Protease Inhibitor System Explored in Soybean Nodule Development
by Barend Juan Vorster, Urte Schlüter, Magdeleen Du Plessis, Stefan Van Wyk, Matome Eugene Makgopa, Ignatious Ncube, Marian Dorcas Quain, Karl Kunert and Christine Helen Foyer
Agronomy 2013, 3(3), 550-570; https://doi.org/10.3390/agronomy3030550 - 20 Aug 2013
Cited by 10 | Viewed by 11051
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 [...] Read more.
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
(This article belongs to the Special Issue Utilization of Genetic Resources and Emerging-Omics Technologies to Expand Agro-ecological Adaptation of Crops)
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