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

Guest Editor
Prof. Dr. Michael Timko
Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA
Website: http://faculty.virginia.edu/timko/home.htm
E-Mail: mpt9g@virginia.edu
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: http://dallas.tamu.edu/faculty-and-staff/
E-Mail: paul.rushton@tamu.edu
Phone: +1 605 688 5749
Interests: transcriptional regulation; promoter technology; systems biology; abiotic and biotic stress response; cereals; drought

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. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. 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.

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

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)

Title: Exploring the Cysteine Protease – Cysteine Protease Inhibitor System in Soybean Nodule Development and Senescence Using RNAseq and Similar Tecnologies
Authors: Barend Juan Vorster ¹, Urte Schlüter ² Magdeleen du Plessis ², Stefan van Wyk ², Ignatious Ncube ³, Karl Kunert ² and Christine H. Foyer ⁴
Affiliation: ¹ Department of Plant Production, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
²Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
³ Biotechnology Unit School of Molecular and Life Sciences, University of Limpopo, Sovenga 0727 South Africa
⁴Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
Abstract: The lifespan of crop plants is crucial for agricultural yields. The stability of metabolism and other factors that determine organ lifespan is controlled by regulated protein degradation, a process that is accelerated during natural or stress-induced senescence, Organ senescence is final developmental stage of development before cell death. Almost all protease families are involved in the orchestration of senescence. For example, proteolysis during leaf senescence remobilizes nitrogen required for seed development. The functions of senescence-associated proteases have largely been explored either by measuring their proteolytic activities or by gene expression analysis. In contrast to leaf senescence, little is known about the genes involved in the senescence of legume nodules, which are responsible for the fixation of atmospheric nitrogen.  Moreover, information on the functions of the different proteases in legume nodule development is scarce. In this article we will consider the role of proteases in development and senescence of soybean root nodules, focussing on cysteine proteases and the cysteine protease inhibitors (cystatin) that form reversible complexes with their proteases targets, and so regulate activity. Very little is currently known about such protease inhibitors involved in nodule development. We will therefore consider current information on senescence-associated proteases and their inhibitors in nodules, particularly focusing on results obtained from the application of ‘omics” technologies, including our own recent findings characterizing in more detail the cysteine protease - cystatin system during soybean nodule development.