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Crop Improvement under a Changing Climate

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

Deadline for manuscript submissions: 31 July 2024 | Viewed by 7554

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Dr. Rajib Roychowdhury

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Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO) – Volcani Center, Rishon Lezion, Israel
Interests: genetics and genomics; marker-assisted breeding; disease resistance in plants; abiotic stress tolerance
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Special Issue Information

Dear Colleagues,

The natural and cultivated habitats of the world's major agricultural crops are continually being challenged by climate change, which is hastening the onset of negative impacts on biological processes through abiotic stressors and disease pressure. Drought (lack of water), salt, flood, cold, heat, toxic metals, metalloids, oxidizing agents, irradiation, and other abiotic stressors are significant influencing factors, while fungal agents, bacteria, and viruses are prevalent biotic stressors that induce disease and infection in plants. Such unfavorable conditions have an impact on crop development, physio-biochemical processes, production, and nutritional quality. Aside from these implications, there is an urgent need to improve various agricultural crop features for the benefit of sustainable agriculture. It is critical we determine the correct management of climate-smart crops with increased tolerance (mitigation) to ensure global food security. This Special Issue welcomes research aiming to improve crops by combining agronomic practices (by using genetics, breeding, and phenotyping tools) and biotechnological applications, such as molecular markers, QTL and haplotype mapping, genetic engineering, tissue culture, various omics applications, and gene editing tools. Furthermore, articles detailing basic and practical knowledge on crop growth, stress responses, and tolerance mechanisms are of interest. Because we cannot change the environment on a large scale, scientific study on agricultural plants utilizing modern breeding technology may help to reduce the barrier to improving crops for the world's inhabitants.

We welcome various manuscript types (original research, reviews, research communication/preliminary research) based on the following themes, among other relevant topics:

Agronomic characterization
Genetics and breeding
Trait improvement
Genotype–environment interaction (GxE)
Abiotic stress response
Disease resistance
Crop phenotyping and phenomics
Genomic-assisted breeding
Multi-omics tools
Gene editing and silencing
Crop biotechnology

Dr. Rajib Roychowdhury
Guest Editor

Manuscript Submission Information

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. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short 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 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. Plants is an international peer-reviewed open access semimonthly 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 2700 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.

Published Papers (7 papers)

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Research

22 pages, 10107 KiB

Open AccessArticle

Stability Analysis and Identification of Superior Hybrids in Pearl Millet [Pennisetum glaucum (L.) R. Br.] Using the Multi Trait Stability Index

by Vikas Khandelwal, Rumit Patel, Khushwant B. Choudhary, S. B. Pawar, M. S. Patel, K. Iyanar, K. D. Mungra, Sushil Kumar and C. Tara Satyavathi

Plants 2024, 13(8), 1101; https://doi.org/10.3390/plants13081101 - 15 Apr 2024

Viewed by 510

Abstract

Pearl millet stands as an important staple food and feed for arid and semi-arid regions of India and South Africa. It is also a quick supplier of important micronutrients like Fe and Zn via grain to combat micronutrient deficiencies among people in developing countries. India has notably spearheaded advancements in pearl millet production and productivity through the All India Coordinated Pearl Millet Improvement Project. There were 21 hybrids evaluated over arid and semi-arid ecologies of the western and southern regions of India. AMMI and GGE biplot models were adopted to recommend a specific hybrid for the particular locality. A joint analysis of variation indicated a significant genotype–environment interaction for most of the agronomical and grain micronutrient parameters. Pearson’s correlation values dissected the significant and positive correlation among agronomic traits and the negative correlation with grain micronutrient traits. GGE biplot analysis recommended the SHT 106 as a dual-purpose hybrid and SHT 115 as a biofortified hybrid for the grain’s Fe and Zn content. SHT 110 and SHT 108 were selected as stable and high grain yield-producing hybrids across all environments and specifically for E1, E2, and E4 as per the Which-Won-Where and What biplot. SHT 109 and SHT 103 hybrids were stable and high dry fodder yield-producing hybrids across all environments. In this study, the Multi-Trait Stability Index (MTSI) was employed to select the most stable and high-performing hybrids for all traits. It selected SHT 120, SHT 106, and SHT 104 for stability and great performance across all environments. These findings underscored the significance of tailored hybrid recommendations and the potential of pearl millet in addressing both food security and malnutrition challenges in various agro-ecological regions. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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24 pages, 1909 KiB

Open AccessArticle

Potential of Plant-Based Extracts to Alleviate Sorbitol-Induced Osmotic Stress in Cabbage Seedlings

by Katarzyna Pacyga, Paweł Pacyga, Aleksandra Boba, Bartosz Kozak, Łukasz Wolko, Yelyzaveta Kochneva and Izabela Michalak

Plants 2024, 13(6), 843; https://doi.org/10.3390/plants13060843 - 14 Mar 2024

Viewed by 643

Abstract

In light of expected climate change, it is important to seek nature-based solutions that can contribute to the protection of our planet as well as to help overcome the emerging adverse changes. In an agricultural context, increasing plant resistance to abiotic stress seems to be crucial. Therefore, the scope of the presented research was focused on the application of botanical extracts that exerted positive effects on model plants growing under controlled laboratory conditions, as well as plants subjected to sorbitol-induced osmotic stress. Foliar spraying increased the length and fresh mass of the shoots (e.g., extracts from Taraxacum officinale, Trifolium pratense, and Pisum sativum) and the roots (e.g., Solidago gigantea, Hypericum perforatum, and Pisum sativum) of cabbage seedlings grown under stressful conditions, as well as their content of photosynthetic pigments (Pisum sativum, Lens culinaris, and Hypericum perforatum) along with total phenolic compounds (Hypericum perforatum, Taraxacum officinale, and Urtica dioica). The antioxidant activity of the shoots measured with the use of DDPH (Pisum sativum, Taraxacum officinale, Urtica dioica, and Hypericum perforatum), ABTS (Trifolium pratense, Symphytum officinale, Valeriana officinalis, Pisum sativum, and Lens culinaris), and FRAP (Symphytum officinale, Valeriana officinalis, Urtica dioica, Hypericum perforatum, and Taraxacum officinale) assays was also enhanced in plants exposed to osmotic stress. Based on these findings, the most promising formulation based on Symphytum officinale was selected and subjected to transcriptomic analysis. The modification of the expression of the following genes was noted: Bol029651 (glutathione S-transferase), Bol027348 (chlorophyll A-B binding protein), Bol015841 (S-adenosylmethionine-dependent methyltransferases), Bol009860 (chlorophyll A-B binding protein), Bol022819 (GDSL lipase/esterase), Bol036512 (heat shock protein 70 family), Bol005916 (DnaJ Chaperone), Bol028754 (pre-mRNA splicing Prp18-interacting factor), Bol009568 (heat shock protein Hsp90 family), Bol039362 (gibberellin regulated protein), Bol007693 (B-box-type zinc finger), Bol034610 (RmlC-like cupin domain superfamily), Bol019811 (myb_SHAQKYF: myb-like DNA-binding domain, SHAQKYF class), Bol028965 (DA1-like Protein). Gene Ontology functional analysis indicated that the application of the extract led to a decrease in the expression of many genes related to the response to stress and photosynthetic systems, which may confirm a reduction in the level of oxidative stress in plants treated with biostimulants. The conducted studies showed that the use of innovative plant-based products exerted positive effects on crops and can be used to supplement current cultivation practices. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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24 pages, 1810 KiB

Open AccessArticle

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

by Sanjeev Gautam, Jeewan Pandey, Douglas C. Scheuring, Jeffrey W. Koym and M. Isabel Vales

Plants 2024, 13(5), 616; https://doi.org/10.3390/plants13050616 - 23 Feb 2024

Viewed by 1129

Abstract

Heat stress during the potato growing season reduces tuber marketable yield and quality. Tuber quality deterioration includes external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, hollow heart, internal heat necrosis) tuber defects, as well as a reduction in their specific gravity and increases in reducing sugars that result in suboptimal (darker) processed products (french fries and chips). Successfully cultivating potatoes under heat-stress conditions requires planting heat-tolerant varieties that can produce high yields of marketable tubers, few external and internal tuber defects, high specific gravity, and low reducing sugars (in the case of processing potatoes). Heat tolerance is a complex trait, and understanding its genetic basis will aid in developing heat-tolerant potato varieties. A panel of 217 diverse potato clones was evaluated for yield and quality attributes in Dalhart (2019 and 2020) and Springlake (2020 and 2021), Texas, and genotyped with the Infinium 22 K V3 Potato Array. A genome-wide association study was performed to identify genomic regions associated with heat-tolerance traits using the GWASpoly package. Quantitative trait loci were identified on chromosomes 1, 3, 4, 6, 8, and 11 for external defects and on chromosomes 1, 2, 3, 10, and 11 for internal defects. Yield-related quantitative trait loci were detected on chromosomes 1, 6, and 10 pertaining to the average tuber weight and tuber number per plant. Genomic-estimated breeding values were calculated using the StageWise package. Clones with low genomic-estimated breeding values for tuber defects were identified as donors of good traits to improve heat tolerance. The identified genomic regions associated with heat-tolerance attributes and the genomic-estimated breeding values will be helpful to develop new potato cultivars with enhanced heat tolerance in potatoes. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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19 pages, 10397 KiB

Open AccessArticle

Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

by Haroon Rashid Hakla, Shubham Sharma, Mohammad Urfan, Rushil Mandlik, Surbhi Kumawat, Prakriti Rajput, Bhubneshwari Khajuria, Rehana Chowdhary, Rupesh Deshmukh, Rajib Roychowdhury and Sikander Pal

Plants 2024, 13(3), 457; https://doi.org/10.3390/plants13030457 - 5 Feb 2024

Viewed by 1463

Abstract

Phosphate (P) is a crucial macronutrient for normal plant growth and development. The P availability in soils is a limitation factor, and understanding genetic factors playing roles in plant adaptation for improving P uptake is of great biological importance. Genome-wide association studies (GWAS) have become indispensable tools in unraveling the genetic basis of complex traits in various plant species. In this study, a comprehensive GWAS was conducted on diverse tomato (Solanum lycopersicum L.) accessions grown under normal and low P conditions for two weeks. Plant traits such as shoot height, primary root length, plant biomass, shoot inorganic content (SiP), and root inorganic content (RiP) were measured. Among several models of GWAS tested, the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) models were used for the identification of single nucleotide polymorphisms (SNPs). Among all the traits analyzed, significantly associated SNPs were recorded for PB, i.e., 1 SNP (SSL4.0CH10_49261145) under control P, SiP, i.e., 1 SNP (SSL4.0CH08_58433186) under control P and 1 SNP (SSL4.0CH08_51271168) under low P and RiP i.e., 2 SNPs (SSL4.0CH04_37267952 and SSL4.0CH09_4609062) under control P and 1 SNP (SSL4.0CH09_3930922) under low P condition. The identified SNPs served as genetic markers pinpointing regions of the tomato genome linked to P-responsive traits. The novel candidate genes associated with the identified SNPs were further analyzed for their protein-protein interactions using STRING. The study provided novel candidate genes, viz. Solyc10g050370 for PB under control, Solyc08g062490, and Solyc08g062500 for SiP and Solyc09g010450, Solyc09g010460, Solyc09g010690, and Solyc09g010710 for RiP under low P condition. These findings offer a glimpse into the genetic diversity of tomato accessions’ responses to P uptake, highlighting the potential for tailored breeding programs to develop P-efficient tomato varieties that could adapt to varying soil conditions, making them crucial for sustainable agriculture and addressing global challenges, such as soil depletion and food security. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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15 pages, 1089 KiB

Open AccessArticle

Optimization of Low-Tech Protected Structure and Irrigation Regime for Cucumber Production under Hot Arid Regions of India

by Pradeep Kumar, Pratapsingh S. Khapte, Akath Singh and Anurag Saxena

Plants 2024, 13(1), 146; https://doi.org/10.3390/plants13010146 - 4 Jan 2024

Viewed by 986

Abstract

Water scarcity and climate variability impede the realization of satisfactory vegetable yields in arid regions. It is imperative to delve into high-productivity and water-use-efficient protected cultivation systems for the sustained supply of vegetables in harsh arid climates. A strenuous effort was made to find suitable protected structures and levels of irrigation for greenhouse cucumber production in hot arid zones of India. In this endeavor, the effects of three low-tech passively ventilated protected structures, i.e., naturally ventilated polyhouse (NVP), insect-proof screenhouse (IPS) and shade screenhouse (SHS), as well as three levels of irrigation (100%, 80% and 60% of evapotranspiration, ET) were assessed for different morpho-physiological, yield and quality traits of the cucumber in a two-year study. Among the low-tech protected structures, NVP was found superior to IPS and SHS for cucumber performance, as evidenced by distinctly higher fruit yields (i.e., 31% and 121%, respectively) arising as a result of higher fruit number/plants and mean fruit weights under NVP. The fruit yield decreased in response to the degree of water shortage in deficit irrigation across all protected structures. However, the interaction effect of the protected structure and irrigation regime reveals that plants grown under moderate deficit (MD, 20% deficit) inside NVP could provide higher yields than those obtained under well-watered (WW, 100% of ET) conditions inside IPS or SHS. Plant growth indices such as vine length, node number/plant, and shoot dry mass were also measured higher under NVP. The greater performance of cucumber under NVP was attributed to a better plant physiological status (i.e., higher photosystem II efficiency, leaf relative water content and lower leaf water potential). The water deficit increased water productivity progressively with its severity; it remained higher in NVP, as reflected by 20% and 94% higher water productivity than those recorded in IPS and SHS, respectively, across different irrigation levels. With the exception of total soluble solids and fruit dry matter content (which were recorded higher), fruit quality parameters were reduced under water deficit conditions. The findings of this study emphasize the importance of considering suitable low-tech protected structures (i.e., NVP) and irrigation levels (i.e., normal rates for higher yields and moderate deficit (−20%) for satisfactory yields) for cucumber in hot arid regions. The results provide valuable insights for growers as well as researchers aiming to increase vegetable production under harsh climates and the water-limiting conditions of arid regions. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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20 pages, 997 KiB

Open AccessArticle

Genotype-by-Environment Interaction Analysis for Quantity and Quality Traits in Faba Beans Using AMMI, GGE Models, and Stability Indices

by Vasileios Greveniotis, Elisavet Bouloumpasi, Stylianos Zotis, Athanasios Korkovelos, Dimitrios Kantas and Constantinos G. Ipsilandis

Plants 2023, 12(21), 3769; https://doi.org/10.3390/plants12213769 - 4 Nov 2023

Cited by 3 | Viewed by 1120

Abstract

Faba beans are considered one of the most important crops for animal feed. The genotype × environment interaction (GEI) has a considerable effect on faba bean seed production. The objectives of this study included assessing multiple locations and genotypes to understand how various ecosystems and faba bean genotypes relate to one another, and suggesting the ideal climatic conditions, crop management system, and genotypes so that they are carefully chosen for their stability. A 2-year experiment was conducted in order to define the stability across four environments based on stability indices for certain characteristics: moisture (%), ash content (%), crude protein content (%), crude fat (%), total starch (%), and crude fiber content (%). Statistically significant differences indicated that GEIs were present. The heritability was generally high for qualitative traits in comparison with quantitative traits. The crude protein content, plant height, and thousand-seed weight were all positively correlated with the seed yield; however, the other qualitative variables were adversely correlated. The crude protein content of the cultivar Tanagra displayed a high stability index, followed by Ste1. Under conventional management, Tanagra demonstrated high values for the seed yield in Giannitsa and Florina. Ste1 and Ste2 are particularly promising genetic materials that showed high values under low-input conditions. The best genotypes to use and the most favorable environments/types of cultivation were the Tanagra cultivar, followed by the Ste2 genotype, according to the additive main effects and multiplicative interaction (AMMI) and genotype plus genotype-by-environment (GGE) biplot models. Earliness showed significant heritability values and very high stability indices, again indicating qualitative behavior according to genetic parameters. With the exception of the number of pods per plant, which demonstrated low heritability while having excellent index values, traits like seed yield showed relatively low-stability-based heritability values. Global efforts aimed at improving the genetics of faba beans might benefit from genotypes that exhibit consistent yields in various conditions. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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15 pages, 4872 KiB

Open AccessArticle

Characterization of Pre-Breeding Wheat (Triticum aestivum L.) Germplasm for Stripe Rust Resistance Using Field Phenotyping and Genotyping

by Basharat Ul Islam, Saba Mir, Mohammad Saleem Dar, Gazala H. Khan, Asif B. Shikari, Najeeb ul Rehman Sofi, Fayaz Mohiddin, Mohammad Ashraf Ahangar, Intikhab Aalum Jehangir, Satish Kumar, Gyanendra Singh and Shabir H. Wani

Plants 2023, 12(18), 3239; https://doi.org/10.3390/plants12183239 - 12 Sep 2023

Viewed by 1034

Abstract

Wheat is highly affected by stripe rust disease, particularly under cooler environments, and the losses can reach up to 100 percent depending on the intensity of infection and the susceptibility of the genotype. The most effective method to manage this disease is the use of resistant varieties. In the present study, 192 wheat genotypes were evaluated for stripe rust resistance under field conditions and also in a laboratory using molecular markers. These lines included pre-breeding germplasm developed for rust resistance and some high-yielding commercially grown wheat varieties. Out of 192 genotypes, 53 were found to be resistant, and 29 showed moderate resistance reaction under field conditions, whereas the remaining genotypes were all either moderately susceptible or susceptible. Under controlled conditions, out of 109 genotypes, only 12 were found to be resistant to all the six virulent/pathogenic pathotypes. Additionally, a selection of 97 genotypes were found resistant in field screening and were subjected to molecular validation using the markers linked to major R-genes, viz., Yr5, Yr10, Yr15 and Yr17. Nine genotypes possessed the Yr5 gene, twelve had the Yr10 gene, fourteen had the Yr15 gene and thirty-two had the Yr17 gene. The resistance genes studied in the current study are effective in conferring resistance against stripe rust disease. The genotypes identified as resistant under both field and controlled conditions can be used as sources in stripe rust resistance breeding programs. Full article

(This article belongs to the Special Issue Crop Improvement under a Changing Climate)

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