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Crops and Environmental Stresses: Phenomes to Genomes

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Response to Abiotic Stress and Climate Change".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 15638

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Special Issue Editors

Dr. Raju Bheemanahalli

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Guest Editor

Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
Interests: abiotic stress physiology; adaptive traits and climate resilience; remote sensing applications in phenotyping; phenome to genome

Dr. K. Raja Reddy

E-Mail Website
Guest Editor

Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
Interests: environmental plant physiology; global change; crop modeling; remote sensing applications in agriculture

Special Issue Information

Dear Colleagues,

Abiotic stresses are major yield-limiting factors in crop plants. Over 90% of the arable land is exposed to more than one stress during the growing season. Combined stresses during critical growth and developmental stages (vegetative, reproductive, and grain filling) can affect the genetic potential of crops by alerting a series of morpho-physiological, yield, and quality traits. Quantifying traits responses and connecting phenome to the genome are cornerstones for crop improvement. Therefore, accumulation of knowledge on stress physiology, trait responses, and identifying breeder-friendly markers would facilitate the development of climate-smart crops. The special issue entitled "Crops and Environmental Stresses: Phenomes to Genomes" welcomes research articles addressing knowledge gaps related to stress physiology, trait discovery, remote sensing, crop modeling, phenomics, genomics, and generating breeder-friendly phenotypic/biomarker information under individual (CO₂, drought, heat, salinity, nutrient, disease) and combined stress in monocots and dicots.

Topics covered in this section include but are not limited to the following:

Stress: CO₂, Drought, extreme temperatures, waterlogging, nutrient, UV-B, and abiotic-biotic interaction
Stage: Seedling, reproductive, and grain filling
Tissue: Root, shoot, pollen, and seed
Strategies: Phenome to the genome, remote sensing, crop modeling, plant growth regulators, biomolecules, field-based stress management mitigation, climate-smart breeding

Dr. Raju Bheemanahalli
Dr. K. Raja Reddy
Guest Editors

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Keywords

breeding
breeder-friendly traits
climate change
climate-smart crops
combined stress
crop modeling
phenotyping
remote sensing
source-sink
stress adaptive traits
stress tolerance
sustainable agriculture

Published Papers (8 papers)

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Research

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12 pages, 3043 KiB

Open AccessArticle

Examining the Corn Seedling Emergence–Temperature Relationship for Recent Hybrids: Insights from Experimental Studies

by Sahila Beegum, Charles Hunt Walne, Krishna N. Reddy, Vangimalla Reddy and Kambham Raja Reddy

Plants 2023, 12(21), 3699; https://doi.org/10.3390/plants12213699 - 27 Oct 2023

Viewed by 1208

Abstract

Corn seedling emergence is a critical factor affecting crop yields. Accurately predicting emergence is crucial for precise crop growth and development simulation in process-based crop models. While various experimental studies have investigated the relationship between corn seedling emergence and temperature, there remains a scarcity of studies focused on newer corn hybrids. In the present study, statistical models (linear and quadratic functional relationships) are developed based on the seedling emergence of ten current corn hybrids, considering soil and air temperatures as influencing factors. The data used for model development are obtained from controlled soil plant atmospheric research chamber experiments focused on corn seedling emergence at five different temperatures. Upon evaluating the developed models, the quadratic model relating the air temperature with time to emergence was found more accurate for all corn hybrids (coefficient of determination (R²): 0.97, root mean square error (RMSE): 0.42 day) followed by the quadratic model based on soil temperature (R²: 0.96, RMSE: 1.42 days), linear model based on air (R²: 0.94, RMSE: 0.53 day) and soil temperature (R²: 0.94, RMSE: 0.70 day). A growing degree day (GDD)-based model was also developed for the newer hybrids. When comparing the developed GDD-based model with the existing GDD models (based on old hybrids), it was observed that the GDD required for emergence was 16% higher than the GDD used in the current models. This showed that the existing GDD-based models need to be revisited when adopted for newer hybrids and adapted to corn crop simulation models. The developed seedling emergence model, integrated into a process-based corn crop simulation model, can benefit farmers and researchers in corn crop management. It can aid in optimizing planting schedules, supporting management decisions, and predicting corn crop growth, development, and it yields more accurately. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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14 pages, 1874 KiB

Open AccessArticle

Developing Functional Relationships between Soil Moisture Content and Corn Early-Season Physiology, Growth, and Development

by Ranadheer Reddy Vennam, Purushothaman Ramamoorthy, Sadikshya Poudel, Kambham Raja Reddy, William Brien Henry and Raju Bheemanahalli

Plants 2023, 12(13), 2471; https://doi.org/10.3390/plants12132471 - 28 Jun 2023

Cited by 6 | Viewed by 1456

Abstract

Drought is a severe threat to agriculture production that affects all growth stages of plants, including corn (Zea mays L.). Any factor affecting early seedling growth and development will significantly impact yield. Despite the recurrence of low rainfall during the growing seasons, corn responses to different early-season soil moisture content levels have not been investigated. In this study, we investigated how corn morpho-physiological and biomass traits responded to varied soil moisture content during the early vegetative stage. Two corn hybrids were grown in a pot-culture facility under five different soil moisture treatments (0.15, 0.12, 0.09, 0.06, and 0.03 m³ m⁻³ volumetric water content, VWC) to assess the growth and developmental responses to varied soil moisture content during early-season growth (V2 to V7) stage. Sub-optimal soil moisture content limited plant growth and development by reducing physiological and phenotypic expression. Stomatal conductance and transpiration were decreased by an average of 65% and 59% across stress treatments relative to optimum conditions. On average, soil moisture deficit reduced the total leaf area by 71% and 72% compared to the control in ‘A6659VT2RIB’ and ‘P1316YHR’, respectively. Shoot and root dry weights were reduced by 74% and 43% under 0.03 m³ m⁻³ VWC. An increase in the root-to-shoot ratio was noticed under low VWC conditions compared to the control. Based on the stress tolerance index, the physiology and leaf growth parameters were more sensitive to soil moisture deficit. Our results highlight the impact of sub-optimal soil moisture on physiology and morphological traits during early-season growth. ‘P1316YHR’ demonstrated better physiological performance under stress conditions, while ‘A6659VT2RIB’ produced relatively better root growth. The findings suggest that biomass partitioning between shoot and root components is dynamic and depends on stress intensity. The current findings can help to prioritize traits associated with the early-season drought tolerance in corn. The functional relationships developed between soil moisture content and growth and developmental responses can be integrated into corn crop modeling to allow better irrigation management decisions. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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23 pages, 4362 KiB

Open AccessArticle

Arbuscular Mycorrhizal Fungi and Compost-Based Biostimulants Enhance Fitness, Physiological Responses, Yield, and Quality Traits of Drought-Stressed Tomato Plants

by Fatima Ezzahra Soussani, Abderrahim Boutasknit, Raja Ben-Laouane, Rachid Benkirane, Marouane Baslam and Abdelilah Meddich

Plants 2023, 12(9), 1856; https://doi.org/10.3390/plants12091856 - 30 Apr 2023

Cited by 8 | Viewed by 2615

Abstract

Climate change-driven water resource constraints cause tomatoes to suffer from drought. The use of biostimulants has emerged as an important approach to enhancing resilience to drought. However, the roles of biostimulants in the physicochemical characteristics of tomatoes in response to drought are poorly understood. In this study, we evaluated the ability of arbuscular mycorrhizal fungi (AMF) and compost (versus NPK application) to improve the agro-physiology, yield, and fruit quality of tomato plants and their tolerance to drought by comparing them with conventional chemical fertilizers (NPK). Under drought conditions, plant growth traits associated with yield and fruit bioactive compounds (carotenoids: 73%; lycopene: 53%; polyphenols: 310%; and flavonoids: 158%) were increased in the AMF-tomato treatment. Compost significantly enhanced sugars (ca. 60%) and protein contents (ca. 20%). Moreover, AMF protected the photosynthetic apparatus from drought-induced oxidative stress, improved photosynthetic efficiency, leaf water potential, and osmolytes, and reduced malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) accumulation by increasing peroxidase (POX) (140%) and polyphenol oxidase (PPO) (340%) activities compared to their controls. Our findings revealed that NPK is an important nutrient-based fertilizer for plant growth and development. However, its efficiency as a fertilizer is quite low. In addition, we highlighted different mechanisms mediated by AMF and compost, inducing drought tolerance in tomato plants. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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14 pages, 1506 KiB

Open AccessArticle

Harnessing High Yield Potential in Wheat (Triticum aestivum L.) under Climate Change Scenario

by Hanif Khan, Harohalli Masthigowda Mamrutha, Chandra Nath Mishra, Gopalareddy Krishnappa, Ramadas Sendhil, Om Parkash, Arun Kumar Joshi, Ravish Chatrath, Bhudeva Singh Tyagi, Gyanendra Singh and Gyanendra Pratap Singh

Plants 2023, 12(6), 1271; https://doi.org/10.3390/plants12061271 - 10 Mar 2023

Cited by 1 | Viewed by 2318

Abstract

Wheat is a major staple food crop for food security in India and South Asia. The current rate (0.8–1.2%) of genetic gain in wheat is significantly shorter than the 2.4% needed to meet future demand. The changing climate and increased yield loss due to factors such as terminal heat stress necessitate the need for climate-resilient practices to sustain wheat production. At ICAR-Indian Institute of Wheat and Barley Research in Karnal, Haryana, India, a new High Yield Potential Trial (HYPT) was conceptualized and subsequently conducted at six locations in the highly productive North Western Plain Zone (NWPZ). An attempt was made to harness higher wheat yields through the best pipeline genotypes suitable for early sowing and modified agronomic practices to explore the feasibility of a new approach that is profitable to farmers. The modified agronomic practices included like early sowing, application of 150% recommended dose of fertilizers, and two sprays of growth regulators (Chlormaquate chloride and Tebuconazole) to prevent lodging. The mean yield in the HYPT was 19.4% superior compared to the best trials conducted during the normal sowing time. A highly positive and significant correlation of grain yield with grain filling duration (0.51), biomass (0.73), harvest index (0.75), normalized difference vegetation Index (0.27), chlorophyll content index (0.32), and 1000-grain weight (0.62) was observed. An increased return of USD 201.95/ha was realized in the HYPT when compared to normal sowing conditions. This study proves that new integrated practices have the potential to provide the best profitable yields in wheat in the context of climate change. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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19 pages, 3517 KiB

Open AccessArticle

Temporal Comparative Transcriptome Analysis on Wheat Response to Acute Cd Toxicity at the Seedling Stage

by Imdad Ullah Zaid, Mohammad Faheem, Muhammad Amir Zia, Zaheer Abbas, Sabahat Noor, Ghulam Muhammad Ali and Zeeshan Haider

Plants 2023, 12(3), 642; https://doi.org/10.3390/plants12030642 - 01 Feb 2023

Viewed by 1348

Abstract

Cadmium (Cd) is a non-essential and toxic metal that accumulates in plant’s tissues and diminishes plant growth and productivity. In the present study, differential root transcriptomic analysis was carried out to identify Cd stress-responsive gene networks and functional annotation under Cd stress in wheat seedlings. For this purpose, the Yannong 0428 wheat cultivar was incubated with 40 µm/L of CdCl₂·2.5H₂O for 6 h at three different seedling growth days. After the quality screening, using the Illumina Hiseq 2000 platform, more than 2482 million clean reads were retrieved. Following this, 84.8% to 89.3% of the clean reads at three time points under normal conditions and 86.5% to 89.1% of the reads from the Cd stress condition were mapped onto the wheat reference genome. In contrast, at three separate seedling growth days, the data analysis revealed a total of 6221 differentially expressed genes (DEGs), including 1543 (24.8%) up-regulated genes and 4678 (75.8%) down-regulated genes. In total, 120 DEGs were co-expressed throughout all the growth days, whereas 1096, 1088, and 2265 DEGs were found to be selectively up-/down-regulated at 7d, 14d, and 30d, respectively. However, the clustering of DEGs, through utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed that the DEGs in the metabolic category were frequently annotated for phenylpropanoid biosynthesis. In comparison, a considerable number of DEGs were linked to protein processing in the endoplasmic reticulum under the process of genetic information processing. Similarly, in categories in organismal systems and cellular processes, DEGs were found in plant hormone signal transduction pathways, and DEGs were identified in the plant–pathogen interaction pathway, respectively. However, DEGs in “endocytosis pathways” were enriched in environmental information processing. In addition, in-depth annotations of roughly specific heavy metal stress-response genes and pathways were also mined, and the expression patterns of eight DEGs were studied using quantitative real-time PCR. The results were congruent with the findings of RNA sequencing regarding transcript abundance in the studied wheat cultivar. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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27 pages, 16091 KiB

Open AccessArticle

The TaGSK1, TaSRG, TaPTF1, and TaP5CS Gene Transcripts Confirm Salinity Tolerance by Increasing Proline Production in Wheat (Triticum aestivum L.)

by Murat Aycan, Marouane Baslam, Toshiaki Mitsui and Mustafa Yildiz

Plants 2022, 11(23), 3401; https://doi.org/10.3390/plants11233401 - 06 Dec 2022

Cited by 7 | Viewed by 1718

Abstract

Salinity is an abiotic stress factor that reduces yield and threatens food security in the world’s arid and semi-arid regions. The development of salt-tolerant genotypes is critical for mitigating yield losses, and this journey begins with the identification of sensitive and tolerant plants. Numerous physiologic and molecular markers for detecting salt-tolerant wheat genotypes have been developed. One of them is proline, which has been used for a long time but has received little information about proline-related genes in wheat genotypes. In this study, proline content and the expression levels of proline-related genes (TaPTF1, TaDHN, TaSRG, TaSC, TaPIMP1, TaMIP, TaHKT1;4, TaGSK, TaP5CS, and TaMYB) were examined in sensitive, moderate, and tolerant genotypes under salt stress (0, 50, 150, and 250 mM NaCl) for 0, 12, and 24 h. Our results show that salt stress increased the proline content in all genotypes, but it was found higher in salt-tolerant genotypes than in moderate and sensitive genotypes. The salinity stress increased gene expression levels in salt-tolerant and moderate genotypes. While salt-stress exposure for 12 and 24 h had a substantial effect on gene expression in wheat, TaPTF1, TaPIMP1, TaMIP, TaHKT1;4, and TaMYB genes were considerably upregulated in 24 h. The salt-tolerant genotypes showed a higher positive interaction than a negative interaction. The TaPTF1, TaP5CS, TaGSK1, and TaSRG genes were found to be more selective than the other analyzed genes under salt-stress conditions. Despite each gene’s specific function, increasing proline biosynthesis functioned as a common mechanism for separating salt tolerance from sensitivity. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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23 pages, 3723 KiB

Open AccessArticle

Genetic Dissection of Alkalinity Tolerance at the Seedling Stage in Rice (Oryza sativa) Using a High-Resolution Linkage Map

by Lovepreet Singh, Sapphire Coronejo, Rajat Pruthi, Sandeep Chapagain, Uttam Bhattarai and Prasanta K. Subudhi

Plants 2022, 11(23), 3347; https://doi.org/10.3390/plants11233347 - 02 Dec 2022

Cited by 5 | Viewed by 1647

Abstract

Although both salinity and alkalinity result from accumulation of soluble salts in soil, high pH and ionic imbalance make alkaline stress more harmful to plants. This study aimed to provide molecular insights into the alkalinity tolerance using a recombinant inbred line (RIL) population developed from a cross between Cocodrie and Dular with contrasting response to alkalinity stress. Forty-six additive QTLs for nine morpho-physiological traits were mapped on to a linkage map of 4679 SNPs under alkalinity stress at the seedling stage and seven major-effect QTLs were for alkalinity tolerance scoring, Na⁺ and K⁺ concentrations and Na⁺:K⁺ ratio. The candidate genes were identified based on the comparison of the impacts of variants of genes present in five QTL intervals using the whole genome sequences of both parents. Differential expression of no apical meristem protein, cysteine protease precursor, retrotransposon protein, OsWAK28, MYB transcription factor, protein kinase, ubiquitin-carboxyl protein, and NAD binding protein genes in parents indicated their role in response to alkali stress. Our study suggests that the genetic basis of tolerance to alkalinity stress is most likely different from that of salinity stress. Introgression and validation of the QTLs and genes can be useful for improving alkalinity tolerance in rice at the seedling stage and advancing understanding of the molecular genetic basis of alkalinity stress adaptation. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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33 pages, 2370 KiB

Open AccessReview

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

by Kasinathan Rakkammal, Arumugam Priya, Subramani Pandian, Theivanayagam Maharajan, Periyasamy Rathinapriya, Lakkakula Satish, Stanislaus Antony Ceasar, Soo-In Sohn and Manikandan Ramesh

Plants 2022, 11(21), 2852; https://doi.org/10.3390/plants11212852 - 26 Oct 2022

Cited by 7 | Viewed by 2531

Abstract

Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study. Full article

(This article belongs to the Special Issue Crops and Environmental Stresses: Phenomes to Genomes)

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