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19 pages, 9870 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Salt-Tolerant and -Sensitive Soybean Cultivars under Salt Stress

by Ye Cheng, Xiangqiang Cheng, Kai Wei and Yan Wang

Int. J. Mol. Sci. 2024, 25(18), 9818; https://doi.org/10.3390/ijms25189818 - 11 Sep 2024

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Abstract

Soil salinity is a major limiting factor in soybean (Glycine max (L.) Merr.) yield in Xinjiang, China. Therefore, breeding soybean to tolerate highly saline soils is crucial to improve its yield. To explore the molecular mechanisms underlying the response of soybean to [...] Read more.

Soil salinity is a major limiting factor in soybean (Glycine max (L.) Merr.) yield in Xinjiang, China. Therefore, breeding soybean to tolerate highly saline soils is crucial to improve its yield. To explore the molecular mechanisms underlying the response of soybean to salt stress, we performed a comparative transcriptome analysis of root and leaf samples collected from two local soybean cultivars. The salt-tolerant cultivar ‘Xin No. 9’ (X9) showed higher photosynthetic activity than the salt-sensitive cultivar ‘Xinzhen No. 9’ (Z9) under salt stress. In total, we identified 13,180 and 13,758 differential expression genes (DEGs) in X9 and Z9, respectively, of which the number of DEGs identified in roots was much higher than that in leaves. We constructed the co-expression gene modules and conducted Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The results suggested there were distinct differences in the mechanisms of response to salt stress between the two soybean cultivars; i.e., the salt-tolerant cultivar X9 exhibited alterations in fundamental metabolism, whereas the salt-sensitive cultivar Z9 responded to salt stress mainly through the cell cycle. The possible crosstalk among phytohormone signaling, MAPK signaling, phenylpropanoid biosynthesis, starch and sucrose metabolism, and ribosome metabolism may play crucial roles in the response to salt stress in soybean. Our results offered a comprehensive understanding of the genes and pathways involved in the response to salt stress in soybean and provided valuable molecular resources for future functional studies and the breeding of soybean varieties with enhanced tolerance to salinity. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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19 pages, 5589 KiB

Open AccessArticle

HvGSK1.1 Controls Salt Tolerance and Yield through the Brassinosteroid Signaling Pathway in Barley

by Yuliya Kloc, Marta Dmochowska-Boguta, Paulina Żebrowska-Różańska, Łukasz Łaczmański, Anna Nadolska-Orczyk and Wacław Orczyk

Int. J. Mol. Sci. 2024, 25(2), 998; https://doi.org/10.3390/ijms25020998 - 13 Jan 2024

Cited by 1 | Viewed by 1180

Abstract

Brassinosteroids (BRs) are a class of plant steroid hormones that are essential for plant growth and development. BRs control important agronomic traits and responses to abiotic stresses. Through the signaling pathway, BRs control the expression of thousands of genes, resulting in a variety [...] Read more.

Brassinosteroids (BRs) are a class of plant steroid hormones that are essential for plant growth and development. BRs control important agronomic traits and responses to abiotic stresses. Through the signaling pathway, BRs control the expression of thousands of genes, resulting in a variety of biological responses. The key effectors of the BR pathway are two transcription factors (TFs): BRASSINAZOLE RESISTANT 1 (BZR1) and BRI1-EMSSUPPRESSOR 1 (BES1). Both TFs are phosphorylated and inactivated by the Glycogen synthase kinase 3 BRASSINOSTEROID INSENSITIVE2 (BIN2), which acts as a negative regulator of the BR pathway. In our study, we describe the functional characteristics of HvGSK1.1, which is one of the GSK3/SHAGGY-like orthologs in barley. We generated mutant lines of HvGSK1.1 using CRISPR/Cas9 genome editing technology. Next Generation Sequencing (NGS) of the edited region of the HvGSK1.1 showed a wide variety of mutations. Most of the changes (frameshift, premature stop codon, and translation termination) resulted in the knock-out of the target gene. The molecular and phenotypic characteristics of the mutant lines showed that the knock-out mutation of HvGSK1.1 improved plant growth performance under salt stress conditions and increased the thousand kernel weight of the plants grown under normal conditions. The inactivation of HvGSK1.1 enhanced BR-dependent signaling, as indicated by the results of the leaf inclination assay in the edited lines. The plant traits under investigation are consistent with those known to be regulated by BRs. These results, together with studies of other GSK3 gene members in other plant species, suggest that targeted editing of these genes may be useful in creating plants with improved agricultural traits. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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11 pages, 1735 KiB

Open AccessArticle

Genome-Wide Identification and Comprehensive Analysis of the GASA Gene Family in Peanuts (Arachis hypogaea L.) under Abiotic Stress

by Rizwana Begum Syed Nabi, Myoung Hee Lee, Kwang-Soo Cho, Rupesh Tayade, Sungup Kim, Jung-In Kim, Min-Young Kim, Eunsoo Lee, Jungeun Lee, Sang-Woo Kim and Eunyoung Oh

Int. J. Mol. Sci. 2023, 24(23), 17117; https://doi.org/10.3390/ijms242317117 - 4 Dec 2023

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Abstract

Peanut (Arachis hypogaea L.) is a globally cultivated crop of significant economic and nutritional importance. The role of gibberellic-acid-stimulated Arabidopsis (GASA) family genes is well established in plant growth, development, and biotic and abiotic stress responses. However, there is a gap in [...] Read more.

Peanut (Arachis hypogaea L.) is a globally cultivated crop of significant economic and nutritional importance. The role of gibberellic-acid-stimulated Arabidopsis (GASA) family genes is well established in plant growth, development, and biotic and abiotic stress responses. However, there is a gap in understanding the function of GASA proteins in cultivated peanuts, particularly in response to abiotic stresses such as drought and salinity. Thus, we conducted comprehensive in silico analyses to identify and verify the existence of 40 GASA genes (termed AhGASA) in cultivated peanuts. Subsequently, we conducted biological experiments and performed expression analyses of selected AhGASA genes to elucidate their potential regulatory roles in response to drought and salinity. Phylogenetic analysis revealed that AhGASA genes could be categorized into four distinct subfamilies. Under normal growth conditions, selected AhGASA genes exhibited varying expressions in young peanut seedling leaves, stems, and roots tissues. Notably, our findings indicate that certain AhGASA genes were downregulated under drought stress but upregulated under salt stress. These results suggest that specific AhGASA genes are involved in the regulation of salt or drought stress. Further functional characterization of the upregulated genes under both drought and salt stress will be essential to confirm their regulatory roles in this context. Overall, our findings provide compelling evidence of the involvement of AhGASA genes in the mechanisms of stress tolerance in cultivated peanuts. This study enhances our understanding of the functions of AhGASA genes in response to abiotic stress and lays the groundwork for future investigations into the molecular characterization of AhGASA genes. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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20 pages, 2642 KiB

Open AccessArticle

The Identification of a Quantative Trait Loci-Allele System of Antixenosis against the Common Cutworm (Spodoptera litura Fabricius) at the Seedling Stage in the Chinese Soybean Landrace Population

by Lin Pan, Junyi Gai and Guangnan Xing

Int. J. Mol. Sci. 2023, 24(22), 16089; https://doi.org/10.3390/ijms242216089 - 8 Nov 2023

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Abstract

Common cutworm (CCW) is an omnivorous insect causing severe yield losses in soybean crops. The seedling-stage mini-tray identification system with the damaged leaf percentage (DLP) as an indicator was used to evaluate antixenosis against CCW in the Chinese soybean landrace population (CSLRP) under [...] Read more.

Common cutworm (CCW) is an omnivorous insect causing severe yield losses in soybean crops. The seedling-stage mini-tray identification system with the damaged leaf percentage (DLP) as an indicator was used to evaluate antixenosis against CCW in the Chinese soybean landrace population (CSLRP) under three environments. Using the innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS), 86 DLP QTLs with 243 alleles (2–11/QTL) were identified, including 66 main-effect loci with 203 alleles and 57 QTL-environment interaction loci with 172 alleles. Among the main-effect loci, 12 large-contribution loci (R² ≥ 1%) explained 25.45% of the phenotypic variation (PV), and 54 small-contribution loci (R² < 1%) explained 16.55% of the PV. This indicates that the CSLRP can be characterized with a DLP QTL-allele system complex that has not been found before, except for a few individual QTLs without alleles involved. From the DLP QTL-allele matrix, the recombination potentials expressed in the 25th percentile of the DLP of all possible crosses were predicted to be reduced by 41.5% as the maximum improvement and 14.2% as the maximum transgression, indicating great breeding potential in the antixenosis of the CSLRP. From the QTLs, 62 candidate genes were annotated, which were involved in eight biological function categories as a gene network of the DLP. Changing from susceptible to moderate plus resistant varieties in the CSLRP, 26 QTLs had 32 alleles involved, in which 19 genes were annotated from 25 QTL-alleles, including eight increased negative alleles on seven loci and 11 decreased positive alleles on 11 loci, showing the major genetic constitution changes for the antixenosis enhancement at the seedling stage in the CSLRP. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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22 pages, 12196 KiB

Open AccessArticle

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya

by Yunsu Dai, Yu Wang, Liwang Zeng, Ruizong Jia, Linwen He, Xueying Huang, Hui Zhao, Difa Liu, Haixu Zhao, Shuai Hu, Ling Gao, Anping Guo, Wei Xia and Changmian Ji

Int. J. Mol. Sci. 2023, 24(18), 14039; https://doi.org/10.3390/ijms241814039 - 13 Sep 2023

Cited by 3 | Viewed by 1284

Abstract

MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their [...] Read more.

MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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Review

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22 pages, 2014 KiB

Open AccessReview

Surviving a Double-Edged Sword: Response of Horticultural Crops to Multiple Abiotic Stressors

by Wenjing Yan, Rahat Sharif, Hamza Sohail, Yu Zhu, Xuehao Chen and Xuewen Xu

Int. J. Mol. Sci. 2024, 25(10), 5199; https://doi.org/10.3390/ijms25105199 - 10 May 2024

Cited by 1 | Viewed by 1016

Abstract

Climate change-induced weather events, such as extreme temperatures, prolonged drought spells, or flooding, pose an enormous risk to crop productivity. Studies on the implications of multiple stresses may vary from those on a single stress. Usually, these stresses coincide, amplifying the extent of [...] Read more.

Climate change-induced weather events, such as extreme temperatures, prolonged drought spells, or flooding, pose an enormous risk to crop productivity. Studies on the implications of multiple stresses may vary from those on a single stress. Usually, these stresses coincide, amplifying the extent of collateral damage and contributing to significant financial losses. The breadth of investigations focusing on the response of horticultural crops to a single abiotic stress is immense. However, the tolerance mechanisms of horticultural crops to multiple abiotic stresses remain poorly understood. In this review, we described the most prevalent types of abiotic stresses that occur simultaneously and discussed them in in-depth detail regarding the physiological and molecular responses of horticultural crops. In particular, we discussed the transcriptional, posttranscriptional, and metabolic responses of horticultural crops to multiple abiotic stresses. Strategies to breed multi-stress-resilient lines have been presented. Our manuscript presents an interesting amount of proposed knowledge that could be valuable in generating resilient genotypes for multiple stressors. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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23 pages, 1845 KiB

Open AccessReview

Calcium Signaling and the Response to Heat Shock in Crop Plants

by Xinmiao Kang, Liqun Zhao and Xiaotong Liu

Int. J. Mol. Sci. 2024, 25(1), 324; https://doi.org/10.3390/ijms25010324 - 26 Dec 2023

Cited by 2 | Viewed by 1817

Abstract

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca²⁺), a versatile [...] Read more.

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca²⁺), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca²⁺ is detected by Ca²⁺-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca²⁺ in plant cells increases rapidly, making Ca²⁺ signals the earliest response to HS. In this review, we discuss the crucial role of Ca²⁺ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR). Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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25 pages, 1415 KiB

Open AccessReview

Drought Stress Tolerance in Vegetables: The Functional Role of Structural Features, Key Gene Pathways, and Exogenous Hormones

by Kumail Abbas, Jingrui Li, Binbin Gong, Yusong Lu, Xiaolei Wu, Guiyun Lü and Hongbo Gao

Int. J. Mol. Sci. 2023, 24(18), 13876; https://doi.org/10.3390/ijms241813876 - 9 Sep 2023

Cited by 10 | Viewed by 3155

Abstract

The deleterious effects of drought stress have led to a significant decline in vegetable production, ultimately affecting food security. After sensing drought stress signals, vegetables prompt multifaceted response measures, eventually leading to changes in internal cell structure and external morphology. Among them, it [...] Read more.

The deleterious effects of drought stress have led to a significant decline in vegetable production, ultimately affecting food security. After sensing drought stress signals, vegetables prompt multifaceted response measures, eventually leading to changes in internal cell structure and external morphology. Among them, it is important to highlight that the changes, including changes in physiological metabolism, signal transduction, key genes, and hormone regulation, significantly influence drought stress tolerance in vegetables. This article elaborates on vegetable stress tolerance, focusing on structural adaptations, key genes, drought stress signaling transduction pathways, osmotic adjustments, and antioxidants. At the same time, the mechanisms of exogenous hormones such as abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) toward improving the adaptive drought tolerance of vegetables were also reviewed. These insights can enhance the understanding of vegetable drought tolerance, supporting vegetable tolerance enhancement by cultivation technology improvements under changing climatic conditions, which provides theoretical support and technical reference for innovative vegetable stress tolerance breeding and food security. Full article

(This article belongs to the Special Issue Crop Biotic and Abiotic Stress Tolerance: 3rd Edition)

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