From Genome to Phenome: A Bridge to Accelerate Adaptation of Crops to Abiotic Stress

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (25 April 2023) | Viewed by 7499

Special Issue Editors


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Guest Editor
Cereal Phenomics Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
Interests: plant molecular breeding; crop improvement; cereal genetic and genomics; transcriptomics; gene expression; phytohormones; abiotic stress tolerance; plant-environment interaction; cereal phenomics

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Guest Editor
Cereal Phenomics Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
Interests: plant molecular breeding; crop improvement; cereal genetic and genomics; transcriptomics; lipidomics; phytohormones; abiotic and biotic stress tolerance; plant–environment interaction; cereal phenomics; acceleration of cereal and legume breeding

Special Issue Information

Dear Colleagues,

Plants as sessile organisms are permanently exposed to environmental stimuli. Adverse conditions have become accentuated by global warming, shrinking water supply, and drought intensification. Soil salinity and acidity, air pollution, and accumulation of toxic metals in the environment have escalated over the years. In addition, global demands for increased plant production are growing rapidly. Altogether, effective crop adjustments for intensive production under a changing climate must be faced by scientists. In recent decades, progress in molecular methods has facilitated the in-depth investigation of plant genomes, constituting the potential to improve crop breeding processes. Next-generation sequencing and modern phenotyping techniques represent a powerful tool to explore the genetic background of plant phenotype determination under constrained conditions. Furthermore, advanced omics approaches such as genomics, transcriptomics, proteomics, and metabolomics have provided new knowledge about mechanisms of plants’ adjustment to the changing environment.

Hence, this Special Issue will cover crop response to any abiotic stress at various levels, i.e., molecular/biochemical/physiological, considered in relation to plant phenotypic plasticity. Papers centered on the association between crop genotypic and phenotypic variation will be of interest. Studies about stress-responsive genes and their effect on crop behavior, molecular breeding, and development of new genetic resources of crops as well as modern phenotyping approaches that may lead to crops’ improvement will also be welcomed.

Dr. Krzysztof Mikołajczak
Prof. Anetta Kuczyńska
Guest Editors

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Keywords

  • molecular breeding
  • modern automated phenotyping
  • functional phenotyping
  • linkage analysis
  • QTL
  • GWAS
  • NGS
  • omics approaches
  • abiotic stress tolerance
  • crop improvement
  • climate change

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Published Papers (2 papers)

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Research

19 pages, 3630 KiB  
Article
Low-Cost Hyperspectral Imaging to Detect Drought Stress in High-Throughput Phenotyping
by Andrea Genangeli, Giovanni Avola, Marco Bindi, Claudio Cantini, Francesco Cellini, Stefania Grillo, Angelo Petrozza, Ezio Riggi, Alessandra Ruggiero, Stephan Summerer, Anna Tedeschi and Beniamino Gioli
Plants 2023, 12(8), 1730; https://doi.org/10.3390/plants12081730 - 21 Apr 2023
Cited by 9 | Viewed by 2934
Abstract
Recent developments in low-cost imaging hyperspectral cameras have opened up new possibilities for high-throughput phenotyping (HTP), allowing for high-resolution spectral data to be obtained in the visible and near-infrared spectral range. This study presents, for the first time, the integration of a low-cost [...] Read more.
Recent developments in low-cost imaging hyperspectral cameras have opened up new possibilities for high-throughput phenotyping (HTP), allowing for high-resolution spectral data to be obtained in the visible and near-infrared spectral range. This study presents, for the first time, the integration of a low-cost hyperspectral camera Senop HSC-2 into an HTP platform to evaluate the drought stress resistance and physiological response of four tomato genotypes (770P, 990P, Red Setter and Torremaggiore) during two cycles of well-watered and deficit irrigation. Over 120 gigabytes of hyperspectral data were collected, and an innovative segmentation method able to reduce the hyperspectral dataset by 85.5% was developed and applied. A hyperspectral index (H-index) based on the red-edge slope was selected, and its ability to discriminate stress conditions was compared with three optical indices (OIs) obtained by the HTP platform. The analysis of variance (ANOVA) applied to the OIs and H-index revealed the better capacity of the H-index to describe the dynamic of drought stress trend compared to OIs, especially in the first stress and recovery phases. Selected OIs were instead capable of describing structural changes during plant growth. Finally, the OIs and H-index results have revealed a higher susceptibility to drought stress in 770P and 990P than Red Setter and Torremaggiore genotypes. Full article
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21 pages, 3064 KiB  
Article
Worldwide Selection Footprints for Drought and Heat in Bread Wheat (Triticum aestivum L.)
by Ana L. Gómez-Espejo, Carolina Paola Sansaloni, Juan Burgueño, Fernando H. Toledo, Adalberto Benavides-Mendoza and M. Humberto Reyes-Valdés
Plants 2022, 11(17), 2289; https://doi.org/10.3390/plants11172289 - 1 Sep 2022
Cited by 4 | Viewed by 3342
Abstract
Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, [...] Read more.
Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, heat index of mean temperature, heat index of maximum temperature, and drought index) in GEA using the FarmCPU approach with GAPIT. Historical temperature and precipitation values were obtained as monthly averages from 1970 to 2000. Based on 26,064 high-quality SNP loci, landraces were classified into ten subpopulations exhibiting high genetic differentiation. The GEA identified 59 SNPs and nearly 89 protein-encoding genes involved in the response processes to abiotic stress. Genes related to biosynthesis and signaling are mainly mediated by auxins, abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonates (JA), which are known to operate together in modulation responses to heat stress and drought in plants. In addition, we identified some proteins associated with the response and tolerance to stress by high temperatures, water deficit, and cell wall functions. The results provide candidate regions for selection aimed to improve drought and heat tolerance in bread wheat and provide insights into the genetic mechanisms involved in adaptation to extreme environments. Full article
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