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Crop Stress Biology and Molecular Breeding 3.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 26452

Special Issue Editor

1. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2. National Engineering Research Center for Sugarcane, Ministry of Science &Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: crop genetics and biotechnology; molecular interaction between crop and pathogen; gene mining and function identification; molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biotic and abiotic stresses limit variety improvement and cultivation regulation of crops, including but not limited to rice, corn, sorghum, wheat, cotton, rape, peanut, soybean,  sugarcane and beet, and thus seriously restrict the corresponding industrial developments. The response and adaptation mechanisms of crops to these stresses have remained unclear. Focusing our research efforts on crop stress biology and molecular breeding through genetic, genomics, molecular biology and other approaches is therefore vitally important. Current studies in this field seek to reveal the biological basis and processes of important crop traits, including genomics, genes and gene networks; to elucidate the signal transduction pathway of crop stress responses and its interaction mechanism with corresponding stress factors; to elaborate upon the adaptation mechanisms of crops in response to their environment (stress); and to discover and identify key genes and interacting proteins that regulate the formation of traits or adapt to the environment. The exploration of these areas will no doubt reveal gene elements or targets that can be utilized for genetic improvement of important agronomic traits and assist in enhancing crop characteristics or even creating novel germplasms.

This Special Issue, “Crop Stress Biology and Molecular Breeding 3.0”, welcomes original research and review papers considering biological process analysis of important crop traits, crop gene cloning and functional identification, the screening of linkage markers for crop target traits and all other related processes. Papers detailing bioinformatics tools and databases used for crop stress biology and molecular breeding research are also welcomed.

Prof. Dr. Youxiong Que
Guest Editor

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Keywords

  • biotic and abiotic stress
  • variety improvement
  • crop stress biology
  • molecular breeding
  • biological basis
  • signal transduction pathway
  • agronomic traits
  • excellent germplasm

Published Papers (20 papers)

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14 pages, 5346 KiB  
Article
OsMYB58 Negatively Regulates Plant Growth and Development by Regulating Phosphate Homeostasis
by Dongwon Baek, Soyeon Hong, Hye Jeong Kim, Sunok Moon, Ki Hong Jung, Won Tae Yang and Doh Hoon Kim
Int. J. Mol. Sci. 2024, 25(4), 2209; https://doi.org/10.3390/ijms25042209 - 12 Feb 2024
Viewed by 546
Abstract
Phosphate (Pi) starvation is a critical factor limiting crop growth, development, and productivity. Rice (Oryza sativa) R2R3-MYB transcription factors function in the transcriptional regulation of plant responses to various abiotic stresses and micronutrient deprivation, but little is known about their roles [...] Read more.
Phosphate (Pi) starvation is a critical factor limiting crop growth, development, and productivity. Rice (Oryza sativa) R2R3-MYB transcription factors function in the transcriptional regulation of plant responses to various abiotic stresses and micronutrient deprivation, but little is known about their roles in Pi starvation signaling and Pi homeostasis. Here, we identified the R2R3-MYB transcription factor gene OsMYB58, which shares high sequence similarity with AtMYB58. OsMYB58 expression was induced more strongly by Pi starvation than by other micronutrient deficiencies. Overexpressing OsMYB58 in Arabidopsis thaliana and rice inhibited plant growth and development under Pi-deficient conditions. In addition, the overexpression of OsMYB58 in plants exposed to Pi deficiency strongly affected root development, including seminal root, lateral root, and root hair formation. Overexpressing OsMYB58 strongly decreased the expression of the rice microRNAs OsmiR399a and OsmiR399j. By contrast, overexpressing OsMYB58 strongly increased the expression of rice PHOSPHATE 2 (OsPHO2), whose expression is repressed by miR399 during Pi starvation signaling. OsMYB58 functions as a transcriptional repressor of the expression of its target genes, as determined by a transcriptional activity assay. These results demonstrate that OsMYB58 negatively regulates OsmiR399-dependent Pi starvation signaling by enhancing OsmiR399s expression. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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15 pages, 3501 KiB  
Article
Catalase (CAT) Gene Family in Oil Palm (Elaeis guineensis Jacq.): Genome-Wide Identification, Analysis, and Expression Profile in Response to Abiotic Stress
by Lixia Zhou, Jerome Jeyakumar John Martin, Rui Li, Xianhai Zeng, Qiufei Wu, Qihong Li, Dengqiang Fu, Xinyu Li, Xiaoyu Liu, Jianqiu Ye and Hongxing Cao
Int. J. Mol. Sci. 2024, 25(3), 1480; https://doi.org/10.3390/ijms25031480 - 25 Jan 2024
Viewed by 567
Abstract
Catalases (CATs) play crucial roles in scavenging H2O2 from reactive oxygen species, controlling the growth and development of plants. So far, genome-wide identification and characterization of CAT genes in oil palm have not been reported. In the present study, five [...] Read more.
Catalases (CATs) play crucial roles in scavenging H2O2 from reactive oxygen species, controlling the growth and development of plants. So far, genome-wide identification and characterization of CAT genes in oil palm have not been reported. In the present study, five EgCAT genes were obtained through a genome-wide identification approach. Phylogenetic analysis divided them into two subfamilies, with closer genes sharing similar structures. Gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the EgCAT genes. Several cis-acting elements related to hormone, stress, and defense responses were identified in the promoter regions of EgCATs. Tissue-specific expression of EgCAT genes in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Stress-responsive expression analysis showed that five EgCAT genes were significantly expressed under cold, drought, and salinity stress conditions. Collectively, this study provided valuable information on the oil palm CAT gene family and the validated EgCAT genes can be used as potential candidates for improving abiotic stress tolerance in oil palm and other related crops. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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27 pages, 6950 KiB  
Article
Characterization of the Moroccan Barley Germplasm Preserved in the Polish Genebank as a First Step towards Selecting Forms with Increased Drought Tolerance
by Maja Boczkowska, Marta Puchta-Jasińska, Paulina Bolc, Kinga Moskal, Szymon Puła, Adrian Motor, Katarzyna Bączek, Jolanta Groszyk and Wiesław Podyma
Int. J. Mol. Sci. 2023, 24(22), 16350; https://doi.org/10.3390/ijms242216350 - 15 Nov 2023
Viewed by 876
Abstract
In marginal, arid, and semi-arid areas of Morocco, crops are often exposed to multiple abiotic and biotic stresses that have a major impact on yield. Farmer-maintained Moroccan landraces have been shaped by the impact of very strong selection pressures, gradually adapting to the [...] Read more.
In marginal, arid, and semi-arid areas of Morocco, crops are often exposed to multiple abiotic and biotic stresses that have a major impact on yield. Farmer-maintained Moroccan landraces have been shaped by the impact of very strong selection pressures, gradually adapting to the local ecosystem and obsolete low-input agricultural practices without improvement towards high yield and quality. Considering the increasing threat of drought in Poland, it is necessary to introduce germplasm with tolerance to water deficit into barley breeding programs. The aim of this research was a DArTseq-based genetic characterization of a collection of germplasm of Moroccan origin, conserved in the Polish genebank. The results showed that all conserved landraces have a high level of heterogeneity and their gene pool is different from the material developed by Polish breeders. Based on the analysis of eco-geographical data, locations with extremely different intensities of drought stress were selected. A total of 129 SNPs unique to accessions from these locations were identified. In the neighborhood of the clusters of unique SNPs on chromosomes 5H and 6H, genes that may be associated with plant response to drought stress were identified. The results obtained may provide a roadmap for further research to support Polish barley breeding for increased drought tolerance. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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19 pages, 17103 KiB  
Article
Genome-Wide Identification of HSF Gene Family in Kiwifruit and the Function of AeHSFA2b in Salt Tolerance
by Chengcheng Ling, Yunyan Liu, Zuchi Yang, Jiale Xu, Zhiyin Ouyang, Jun Yang and Songhu Wang
Int. J. Mol. Sci. 2023, 24(21), 15638; https://doi.org/10.3390/ijms242115638 - 27 Oct 2023
Cited by 2 | Viewed by 814
Abstract
Heat shock transcription factors (HSFs) play a crucial role in regulating plant growth and response to various abiotic stresses. In this study, we conducted a comprehensive analysis of the AeHSF gene family at genome-wide level in kiwifruit (Actinidia eriantha), [...] Read more.
Heat shock transcription factors (HSFs) play a crucial role in regulating plant growth and response to various abiotic stresses. In this study, we conducted a comprehensive analysis of the AeHSF gene family at genome-wide level in kiwifruit (Actinidia eriantha), focusing on their functions in the response to abiotic stresses. A total of 41 AeHSF genes were identified and categorized into three primary groups, namely, HSFA, HSFB, and HSFC. Further transcriptome analysis revealed that the expression of AeHSFA2b/2c and AeHSFB1c/1d/2c/3b was strongly induced by salt, which was confirmed by qRT-PCR assays. The overexpression of AeHSFA2b in Arabidopsis significantly improved the tolerance to salt stress by increasing AtRS5, AtGolS1 and AtGolS2 expression. Furthermore, yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays demonstrated that AeHSFA2b could bind to the AeRFS4 promoter directly. Therefore, we speculated that AeHSFA2b may activate AeRFS4 expression by directly binding its promoter to enhance the kiwifruit’s tolerance to salt stress. These results will provide a new insight into the evolutionary and functional mechanisms of AeHSF genes in kiwifruit. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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15 pages, 3804 KiB  
Article
Transcriptome-Based WGCNA Analysis Reveals the Mechanism of Drought Resistance Differences in Sweetpotato (Ipomoea batatas (L.) Lam.)
by Jikai Zong, Peitao Chen, Qingqing Luo, Jilong Gao, Ruihua Qin, Chunli Wu, Qina Lv, Tengfei Zhao and Yufan Fu
Int. J. Mol. Sci. 2023, 24(18), 14398; https://doi.org/10.3390/ijms241814398 - 21 Sep 2023
Cited by 1 | Viewed by 1436
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) is a globally significant storage root crop, but it is highly susceptible to yield reduction under severe drought conditions. Therefore, understanding the mechanism of sweetpotato resistance to drought stress is helpful for the creation of outstanding germplasm [...] Read more.
Sweetpotato (Ipomoea batatas (L.) Lam.) is a globally significant storage root crop, but it is highly susceptible to yield reduction under severe drought conditions. Therefore, understanding the mechanism of sweetpotato resistance to drought stress is helpful for the creation of outstanding germplasm and the selection of varieties with strong drought resistance. In this study, we conducted a comprehensive analysis of the phenotypic and physiological traits of 17 sweetpotato breeding lines and 10 varieties under drought stress through a 48 h treatment in a Hoagland culture medium containing 20% PEG6000. The results showed that the relative water content (RWC) and vine-tip fresh-weight reduction (VTFWR) in XS161819 were 1.17 and 1.14 times higher than those for the recognized drought-resistant variety Chaoshu 1. We conducted RNA-seq analysis and weighted gene co-expression network analysis (WGCNA) on two genotypes, XS161819 and 18-12-3, which exhibited significant differences in drought resistance. The transcriptome analysis revealed that the hormone signaling pathway may play a crucial role in determining the drought resistance in sweetpotato. By applying WGCNA, we identified twenty-two differential expression modules, and the midnight blue module showed a strong positive correlation with drought resistance characteristics. Moreover, twenty candidate Hub genes were identified, including g47370 (AFP2), g14296 (CDKF), and g60091 (SPBC2A9), which are potentially involved in the regulation of drought resistance in sweetpotato. These findings provide important insights into the molecular mechanisms underlying drought resistance in sweetpotato and offer valuable genetic resources for the development of drought-resistant sweetpotato varieties in the future. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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14 pages, 8348 KiB  
Article
Transcriptome Profiling Reveals Differential Gene Expression during the Process of Microtuber Formation in Pinellia ternata
by Chen Bo, Chuandong Su, Jingtong Teng, Wei Sheng, Tao Xue, Yanfang Zhu and Jianping Xue
Int. J. Mol. Sci. 2023, 24(14), 11604; https://doi.org/10.3390/ijms241411604 - 18 Jul 2023
Cited by 1 | Viewed by 794
Abstract
Using petiole material as explants and directly inducing the formation of microtubers without going through the callus stage is an essential way to rapidly expand scarce medical plants such as Pinellia ternata. However, the early molecular mechanism underlying the formation of the [...] Read more.
Using petiole material as explants and directly inducing the formation of microtubers without going through the callus stage is an essential way to rapidly expand scarce medical plants such as Pinellia ternata. However, the early molecular mechanism underlying the formation of the microtuber is largely elusive. Here, we conducted cytology and dynamic transcriptome analyses of inchoate microtubers in Pinellia explants and identified 1092 differentially expressed genes after their cultivation in vitro for 0, 5, and 15 days. Compared with 0 day, the number and size of the microtuber cells were larger at 5 and 15 days of culture. Detailed categorization revealed that the differentially expressed genes were mainly related to responses to stimulus, biological regulation, organelles, membranes, transcription factor activity, and protein binding. Further analysis revealed that the microtuber at different incubation days exhibited quite a difference in both hormone signaling pathway transduction and the regulation pattern of transcription factors. Therefore, this study contributes to a better understanding of the early molecular regulation during the formation of the microtuber and provides new insights for the study of the rapid expansion of P. ternata and other medical plants. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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18 pages, 6782 KiB  
Article
Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family in Brassica napus and Its Role in Abiotic Stress Response
by Xiaohua Bian, Yifan Cao, Ximin Zhi and Ni Ma
Int. J. Mol. Sci. 2023, 24(14), 11242; https://doi.org/10.3390/ijms241411242 - 08 Jul 2023
Viewed by 1027
Abstract
Plant Cysteine Oxidase (PCO) is a plant O2-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were [...] Read more.
Plant Cysteine Oxidase (PCO) is a plant O2-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were analyzed. In this study, 20, 7 and 8 PCO genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the PCOs were divided into five groups: PCO1, PCO2, PCO3, PCO4 and PCO5. Gene organization and motif distribution analysis suggested that the PCO gene family was relatively conserved during evolution. According to the public expression data, PCO genes were expressed in different tissues at different developmental stages. Moreover, qRT-PCR data showed that most of the Bna/Bra/BoPCO5 members were expressed in leaves, roots, flowers and siliques, suggesting an important role in both vegetative and reproductive development. Expression of BnaPCO was induced by various abiotic stress, especially waterlogging stress, which was consistent with the result of cis-element analysis. In this study, the PCO gene family of Brassicaceae was analyzed for the first time, which contributes to a comprehensive understanding of the origin and evolution of PCO genes in Brassicaceae and the function of BnaPCO in abiotic stress responses. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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17 pages, 3755 KiB  
Article
Genome-Wide Identification and Functional Analysis of the TIFY Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (Fagopyrum tataricum)
by Zhixing Zhao, Guanghua Meng, Imran Zamin, Tao Wei, Dongdi Ma, Lizhe An and Xiule Yue
Int. J. Mol. Sci. 2023, 24(13), 10916; https://doi.org/10.3390/ijms241310916 - 30 Jun 2023
Cited by 1 | Viewed by 1047
Abstract
TIFY is a plant-specific gene family with four subfamilies: ZML, TIFY, PPD, and JAZ. Recently, this family was found to have regulatory functions in hormone stimulation, environmental response, and development. However, little is known about the roles of the [...] Read more.
TIFY is a plant-specific gene family with four subfamilies: ZML, TIFY, PPD, and JAZ. Recently, this family was found to have regulatory functions in hormone stimulation, environmental response, and development. However, little is known about the roles of the TIFY family in Tartary buckwheat (Fagopyrum tataricum), a significant crop for both food and medicine. In this study, 18 TIFY family genes (FtTIFYs) in Tartary buckwheat were identified. The characteristics, motif compositions, and evolutionary relationships of the TIFY proteins, as well as the gene structures, cis-acting elements, and synteny of the TIFY genes, are discussed in detail. Moreover, we found that most FtTIFYs responded to various abiotic stresses (cold, heat, salt, or drought) and hormone treatments (ABA, MeJA, or SA). Through yeast two-hybrid assays, we revealed that two FtTIFYs, FtTIFY1 and FtJAZ7, interacted with FtABI5, a homolog protein of AtABI5 involved in ABA-mediated germination and stress responses, implying crosstalk between ABA and JA signaling in Tartary buckwheat. Furthermore, the overexpression of FtJAZ10 and FtJAZ12 enhanced the heat stress tolerance of tobacco. Consequently, our study suggests that the FtTIFY family plays important roles in responses to abiotic stress and provides two candidate genes (FtJAZ10 and FtJAZ12) for the cultivation of stress-resistant crops. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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22 pages, 4265 KiB  
Article
An Improved Genome-Wide Association Procedure Explores Gene–Allele Constitutions and Evolutionary Drives of Growth Period Traits in the Global Soybean Germplasm Population
by Can Wang, Xiaoshuai Hao, Xueqin Liu, Yanzhu Su, Yongpeng Pan, Chunmei Zong, Wubin Wang, Guangnan Xing, Jianbo He and Junyi Gai
Int. J. Mol. Sci. 2023, 24(11), 9570; https://doi.org/10.3390/ijms24119570 - 31 May 2023
Viewed by 1122
Abstract
In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested [...] Read more.
In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested in four seasons in Nanjing, China. The ADL and AAT of DSF and DFM were calculated from daily day-lengths and temperatures provided by the Nanjing Meteorological Bureau. The improved restricted two-stage multi-locus genome-wide association study using gene–allele sequences as markers (coded GASM-RTM-GWAS) was performed. (i) For DSF and its related ADLDSF and AATDSF, 130–141 genes with 384–406 alleles were explored, and for DFM and its related ADLDFM and AATDFM, 124–135 genes with 362–384 alleles were explored, in a total of six gene–allele systems. DSF shared more ADL and AAT contributions than DFM. (ii) Comparisons between the eco-region gene–allele submatrices indicated that the genetic adaptation from the origin to the geographic sub-regions was characterized by allele emergence (mutation), while genetic expansion from primary maturity group (MG)-sets to early/late MG-sets featured allele exclusion (selection) without allele emergence in addition to inheritance (migration). (iii) Optimal crosses with transgressive segregations in both directions were predicted and recommended for breeding purposes, indicating that allele recombination in soybean is an important evolutionary drive. (iv) Genes of the six traits were mostly trait-specific involved in four categories of 10 groups of biological functions. GASM-RTM-GWAS showed potential in detecting directly causal genes with their alleles, identifying differential trait evolutionary drives, predicting recombination breeding potentials, and revealing population gene networks. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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13 pages, 2076 KiB  
Article
Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Japonica Rice under Low Nitrogen Stress
by Shupeng Xie, Hualong Liu, Tianze Ma, Shen Shen, Hongliang Zheng, Luomiao Yang, Lichao Liu, Zhonghua Wei, Wei Xin, Detang Zou and Jingguo Wang
Int. J. Mol. Sci. 2023, 24(9), 7699; https://doi.org/10.3390/ijms24097699 - 22 Apr 2023
Cited by 1 | Viewed by 1188
Abstract
Nitrogen-based nutrients are the main factors affecting rice growth and development. As the nitrogen (N) application rate increased, the nitrogen use efficiency (NUE) of rice decreased. Therefore, it is important to understand the molecular mechanism of rice plant morphological, physiological, and yield formation [...] Read more.
Nitrogen-based nutrients are the main factors affecting rice growth and development. As the nitrogen (N) application rate increased, the nitrogen use efficiency (NUE) of rice decreased. Therefore, it is important to understand the molecular mechanism of rice plant morphological, physiological, and yield formation under low N conditions to improve NUE. In this study, changes in the rice morphological, physiological, and yield-related traits under low N (13.33 ppm) and control N (40.00 ppm) conditions were performed. These results show that, compared with control N conditions, photosynthesis and growth were inhibited and the carbon (C)/N and photosynthetic nitrogen use efficiency (PNUE) were enhanced under low N conditions. To understand the post-translational modification mechanism underlying the rice response to low N conditions, comparative phosphoproteomic analysis was performed, and differentially modified proteins (DMPs) were further characterized. Compared with control N conditions, a total of 258 DMPs were identified under low N conditions. The modification of proteins involved in chloroplast development, chlorophyll synthesis, photosynthesis, carbon metabolism, phytohormones, and morphology-related proteins were differentially altered, which was an important reason for changes in rice morphological, physiological, and yield-related traits. Additionally, inconsistent changes in level of transcription and protein modification, indicates that the study of phosphoproteomics under low N conditions is also important for us to better understand the adaptation mechanism of rice to low N stress. These results provide insights into global changes in the response of rice to low N stress and may facilitate the development of rice cultivars with high NUE by regulating the phosphorylation level of carbon metabolism and rice morphology-related proteins. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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17 pages, 5110 KiB  
Article
Modifying the Expression of Cysteine Protease Gene PCP Affects Pollen Development, Germination and Plant Drought Tolerance in Maize
by Yanhua Li, Liangjie Niu, Xiaoli Zhou, Hui Liu, Fuju Tai and Wei Wang
Int. J. Mol. Sci. 2023, 24(8), 7406; https://doi.org/10.3390/ijms24087406 - 17 Apr 2023
Cited by 2 | Viewed by 1356
Abstract
Cysteine proteases (CPs) are vital proteolytic enzymes that play critical roles in various plant processes. However, the particular functions of CPs in maize remain largely unknown. We recently identified a pollen-specific CP (named PCP), which highly accumulated on the surface of maize pollen. [...] Read more.
Cysteine proteases (CPs) are vital proteolytic enzymes that play critical roles in various plant processes. However, the particular functions of CPs in maize remain largely unknown. We recently identified a pollen-specific CP (named PCP), which highly accumulated on the surface of maize pollen. Here, we reported that PCP played an important role in pollen germination and drought response in maize. Overexpression of PCP inhibited pollen germination, while mutation of PCP promoted pollen germination to some extent. Furthermore, we observed that germinal apertures of pollen grains in the PCP-overexpression transgenic lines were excessively covered, whereas this phenomenon was not observed in the wild type (WT), suggesting that PCP regulated pollen germination by affecting the germinal aperture structure. In addition, overexpression of PCP enhanced drought tolerance in maize plants, along with the increased activities of the antioxidant enzymes and the decreased numbers of the root cortical cells. Conversely, mutation of PCP significantly impaired drought tolerance. These results may aid in clarifying the precise functions of CPs in maize and contribute to the development of drought-tolerant maize materials. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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15 pages, 5237 KiB  
Article
Peach DELLA Protein PpeDGYLA Is Not Degraded in the Presence of Active GA and Causes Dwarfism When Overexpressed in Poplar and Arabidopsis
by Yun Chen, Mengmeng Zhang, Xiaofei Wang, Yun Shao, Xinyue Hu, Jun Cheng, Xianbo Zheng, Bin Tan, Xia Ye, Wei Wang, Jidong Li, Ming Li, Langlang Zhang and Jiancan Feng
Int. J. Mol. Sci. 2023, 24(7), 6789; https://doi.org/10.3390/ijms24076789 - 06 Apr 2023
Cited by 1 | Viewed by 1624
Abstract
Controlling the tree size of fruit species such as peach can reduce the amount of labor and input needed for orchard management. The phytohormone gibberellin (GA) positively regulates tree size by inducing degradation of the GA signaling repressor DELLA. The N-terminal DELLA domain [...] Read more.
Controlling the tree size of fruit species such as peach can reduce the amount of labor and input needed for orchard management. The phytohormone gibberellin (GA) positively regulates tree size by inducing degradation of the GA signaling repressor DELLA. The N-terminal DELLA domain in this protein is critical for its GA-dependent interaction with the GA receptor GID1 and the resulting degradation of the DELLA protein, which allows for growth-promoting GA signaling. In this study, a DELLA family member, PpeDGYLA, contains a DELLA domain but has amino acid changes in three conserved motifs (DELLA into DGYLA, LEQLE into LERLE, and TVHYNP into AVLYNP). In the absence or presence of GA3, the PpeDGYLA protein did not interact with PpeGID1c and was stable in 35S-PpeDGYLA peach transgenic callus. The overexpression of PpeDGYLA in both polar and Arabidopsis showed an extremely dwarfed phenotype, and these transgenic plants were insensitive to GA3 treatment. PpeDGYLA could interact with PpeARF6-1 and -2, supposed growth-promoting factors. It is suggested that the changes in the DELLA domain of PpeDGYLA may, to some extent, account for the severe dwarf phenotype of poplar and Arabidopsis transgenic plants. In addition, our study showed that the DELLA family contained three clades (DELLA-like, DELLA, and DGLLA). PpeDGYLA clustered into the DGLLA clade and was expressed in all of the analyzed tissues. These results lay the foundation for the further study of the repression of tree size by PpeDGYLA. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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17 pages, 2429 KiB  
Article
Development of Highly Efficient Resistance to Beet Curly Top Iran Virus (Becurtovirus) in Sugar Beet (B. vulgaris) via CRISPR/Cas9 System
by Kubilay Yıldırım, Musa Kavas, İlkay Sevgen Küçük, Zafer Seçgin and Çiğdem Gökcek Saraç
Int. J. Mol. Sci. 2023, 24(7), 6515; https://doi.org/10.3390/ijms24076515 - 30 Mar 2023
Cited by 4 | Viewed by 1841
Abstract
Beet Curly Top Iran Virus (BCTIV, Becurtovirus) is a dominant and widespread pathogen responsible for great damage and yield reduction in sugar beet production in the Mediterranean and Middle East. CRISPR-based gene editing is a versatile tool that has been successfully used [...] Read more.
Beet Curly Top Iran Virus (BCTIV, Becurtovirus) is a dominant and widespread pathogen responsible for great damage and yield reduction in sugar beet production in the Mediterranean and Middle East. CRISPR-based gene editing is a versatile tool that has been successfully used in plants to improve resistance against many viral pathogens. In this study, the efficiency of gRNA/Cas9 constructs targeting the expressed genes of BCTIV was assessed in sugar beet leaves by their transient expression. Almost all positive control sugar beets revealed systemic infection and severe disease symptoms (90%), with a great biomass reduction (68%) after BCTIV agroinoculation. On the other hand, sugar beets co-agronioculated with BCTIV and gRNA/Cas9 indicated much lower systemic infection (10–55%), disease symptoms and biomass reduction (13–45%). Viral inactivation was also verified by RCA and qPCR assays for gRNA/Cas9 treated sugar beets. PCR-RE digestion and sequencing assays confirmed the gRNA/Cas9-mediated INDEL mutations at the target sites of the BCTIV genome and represented high efficiencies (53–88%), especially for those targeting BCTIV’s movement gene and its overlapping region between capsid and ssDNA regulator genes. A multiplex CRISPR approach was also tested. The most effective four gRNAs targeting all the genes of BCTIV were cloned into a Cas9-containing vector and agroinoculated into virus-infected sugar beet leaves. The results of this multiplex CRISPR system revealed almost complete viral resistance with inhibition of systemic infection and mutant escape. This is the first report of CRSIPR-mediated broad-spectrum resistance against Becurtovirus in sugar beet. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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17 pages, 6290 KiB  
Article
The MdmiR156n Regulates Drought Tolerance and Flavonoid Synthesis in Apple Calli and Arabidopsis
by Guo Chen, Yaping Wang, Xueli Liu, Siyue Duan, Shenghui Jiang, Jun Zhu, Yugang Zhang and Hongmin Hou
Int. J. Mol. Sci. 2023, 24(7), 6049; https://doi.org/10.3390/ijms24076049 - 23 Mar 2023
Cited by 6 | Viewed by 1276
Abstract
Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in [...] Read more.
Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in response to abiotic stress. To better understand the functions of MdmiR156 in abiotic stress tolerance, we constructed the overexpression (OE) and short tandem target mimic (STTM) vector of MdmiR156n and performed its functional analysis through the characterization of transgenic apple calli and Arabidopsis thaliana plants. In this study, MdmiR156n overexpression significantly increased the length of primary roots and the number of lateral roots in transgenic Arabidopsis plants under drought stress. In addition, MdmiR156n transgenic Arabidopsis and apple calli had a lower electrolyte leakage rate and less cell membrane damage than WT and STTM156 after drought stress. Further studies showed that MdmiR156n overexpression promoted the accumulation of flavonoids and scavenging of reactive oxygen species (ROS) under drought conditions in transgenic apple calli and A. thaliana plants. Taken together, overexpression MdmiR156n enhances drought tolerance by regulating flavonoid synthesis and ROS signaling cascades in apple calli and A. thaliana. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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19 pages, 11364 KiB  
Article
Rhizosphere Fungal Dynamics in Sugarcane during Different Growth Stages
by Qiang Liu, Ziqin Pang, Yueming Liu, Nyumah Fallah, Chaohua Hu, Wenxiong Lin and Zhaonian Yuan
Int. J. Mol. Sci. 2023, 24(6), 5701; https://doi.org/10.3390/ijms24065701 - 16 Mar 2023
Cited by 4 | Viewed by 1625
Abstract
Understanding the normal variation of the sugarcane rhizosphere fungal community throughout its life cycle is essential for the development of agricultural practices for fungal and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using [...] Read more.
Understanding the normal variation of the sugarcane rhizosphere fungal community throughout its life cycle is essential for the development of agricultural practices for fungal and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using the Illumina sequencing platform for correlation analysis of rhizosphere fungal community time series, covering information from 84 samples in four growth periods. The results revealed that the sugarcane rhizosphere fungi possessed the maximum fungal richness in Tillering. Rhizosphere fungi were closely associated with sugarcane growth, including Ascomycota, Basidiomycota, and Chytridiomycota, which showed high abundance in a stage-specific manner. Through the Manhattan plots, 10 fungal genera showed a decreasing trend throughout the sugarcane growth, and two fungal genera were significantly enriched at three stages of sugarcane growth (p < 0.05) including Pseudallescheria (Microascales, Microascaceae) and Nectriaceae (Hypocreales, Nectriaceae). In addition, soil pH, soil temperature, total nitrogen, and total potassium were critical drivers of fungal community structure at different stages of sugarcane growth. We also found that sugarcane disease status showed a significant and strong negative effect on selected soil properties by using structural equation modeling (SEM), suggesting that poor soil increases the likelihood of sugarcane disease. In addition, the assembly of sugarcane rhizosphere fungal community structure was mainly influenced by stochastic factors, but after the sugarcane root system became stable (Maturity), the stochastic contribution rate decreased to the lowest value. Our work provides a more extensive and solid basis for the biological control of sugarcane potential fungal diseases. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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14 pages, 2971 KiB  
Article
GmGSTU23 Encoding a Tau Class Glutathione S-Transferase Protein Enhances the Salt Tolerance of Soybean (Glycine max L.)
by Xingang Li, Yuanting Pang, Yiwang Zhong, Zhandong Cai, Qibin Ma, Ke Wen and Hai Nian
Int. J. Mol. Sci. 2023, 24(6), 5547; https://doi.org/10.3390/ijms24065547 - 14 Mar 2023
Cited by 6 | Viewed by 1490
Abstract
Salt stress has a detrimental impact on crop yield, quality, and profitability. The tau-like glutathione transferases (GSTs) represent a significant group of enzymes that play a crucial role in plant stress responses, including salt stress. In this study, we identified a tau-like glutathione [...] Read more.
Salt stress has a detrimental impact on crop yield, quality, and profitability. The tau-like glutathione transferases (GSTs) represent a significant group of enzymes that play a crucial role in plant stress responses, including salt stress. In this study, we identified a tau-like glutathione transferase family gene from soybean named GmGSTU23. Expression pattern analysis revealed that GmGSTU23 was predominantly expressed in the roots and flowers and exhibited a concentration–time-specific pattern in response to salt stress. Transgenic lines were generated and subjected to phenotypic characterization under salt stress. The transgenic lines exhibited increased salt tolerance, root length, and fresh weight compared to the wild type. Antioxidant enzyme activity and malondialdehyde content were subsequently measured, and the data revealed no significant differences between the transgenic and wild-type plants in the absence of salt stress. However, under salt stress, the wild-type plants exhibited significantly lower activities of SOD, POD, and CAT than the three transgenic lines, whereas the activity of APX and the content of MDA showed the opposite trend. We identified changes in glutathione pools and associated enzyme activity to gain insights into the underlying mechanisms of the observed phenotypic differences. Notably, under salt stress, the transgenic Arabidopsis’s GST activity, GR activity, and GSH content were significantly higher than those of the wild type. In summary, our findings suggest that GmGSTU23 mediates the scavenging of reactive oxygen species and glutathione by enhancing the activity of glutathione transferase, thereby conferring enhanced tolerance to salt stress in plants. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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13 pages, 2425 KiB  
Article
SiMYBS3, Encoding a Setaria italica Heterosis-Related MYB Transcription Factor, Confers Drought Tolerance in Arabidopsis
by Xin Liu, Shuai Zhang, Mengbo Sun, Yurong Guo, Shaoxing Zhao, Xutao Zhou, Xionghui Bai, Keli Dai, Huixia Li, Xiangyang Yuan, Weiping Shi, Pingyi Guo and Jie Guo
Int. J. Mol. Sci. 2023, 24(6), 5418; https://doi.org/10.3390/ijms24065418 - 12 Mar 2023
Cited by 3 | Viewed by 1481
Abstract
Drought is a major limiting factor affecting grain production. Drought-tolerant crop varieties are required to ensure future grain production. Here, 5597 DEGs were identified using transcriptome data before and after drought stress in foxtail millet (Setaria italica) hybrid Zhangza 19 and [...] Read more.
Drought is a major limiting factor affecting grain production. Drought-tolerant crop varieties are required to ensure future grain production. Here, 5597 DEGs were identified using transcriptome data before and after drought stress in foxtail millet (Setaria italica) hybrid Zhangza 19 and its parents. A total of 607 drought-tolerant genes were screened through WGCNA, and 286 heterotic genes were screened according to the expression level. Among them, 18 genes overlapped. One gene, Seita.9G321800, encoded MYBS3 transcription factor and showed upregulated expression after drought stress. It is highly homologous with MYBS3 in maize, rice, and sorghum and was named SiMYBS3. Subcellular localization analysis showed that the SiMYBS3 protein was located in the nucleus and cytoplasm, and transactivation assay showed SiMYBS3 had transcriptional activation activity in yeast cells. Overexpression of SiMYBS3 in Arabidopsis thaliana conferred drought tolerance, insensitivity to ABA, and earlier flowering. Our results demonstrate that SiMYBS3 is a drought-related heterotic gene and it can be used for enhancing drought resistance in agricultural crop breeding. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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18 pages, 6950 KiB  
Article
Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions
by Weiping Wang, Wei Xin, Ning Chen, Fan Yang, Jia Li, Guize Qu, Xingdong Jiang, Lu Xu, Shijiao Zhao, Hualong Liu, Luomiao Yang, Hongliang Zheng, Detang Zou and Jingguo Wang
Int. J. Mol. Sci. 2023, 24(6), 5290; https://doi.org/10.3390/ijms24065290 - 09 Mar 2023
Cited by 1 | Viewed by 1588
Abstract
Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time [...] Read more.
Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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17 pages, 2908 KiB  
Article
Transcription Factor ZmNAC20 Improves Drought Resistance by Promoting Stomatal Closure and Activating Expression of Stress-Responsive Genes in Maize
by Hui Liu, Songbo Song, Mengyao Liu, Yangwei Mu, Ying Li, Yuxin Xuan, Liangjie Niu, Hui Zhang and Wei Wang
Int. J. Mol. Sci. 2023, 24(5), 4712; https://doi.org/10.3390/ijms24054712 - 01 Mar 2023
Cited by 3 | Viewed by 1613
Abstract
Drought is a major environmental threat that limits crop growth, development, and productivity worldwide. Improving drought resistance with genetic engineering methods is necessary to tackle global climate change. It is well known that NAC (NAM, ATAF and CUC) transcription factors play a critical [...] Read more.
Drought is a major environmental threat that limits crop growth, development, and productivity worldwide. Improving drought resistance with genetic engineering methods is necessary to tackle global climate change. It is well known that NAC (NAM, ATAF and CUC) transcription factors play a critical role in coping with drought stress in plants. In this study, we identified an NAC transcription factor ZmNAC20, which regulates drought stress response in maize. ZmNAC20 expression was rapidly upregulated by drought and abscisic acid (ABA). Under drought conditions, the ZmNAC20-overexpressing plants had higher relative water content and survival rate than the wild-type maize inbred B104, suggesting that overexpression of ZmNAC20 improved drought resistance in maize. The detached leaves of ZmNAC20-overexpressing plants lost less water than those of wild-type B104 after dehydration. Overexpression of ZmNAC20 promoted stomatal closure in response to ABA. ZmNAC20 was localized in the nucleus and regulated the expression of many genes involved in drought stress response using RNA-Seq analysis. The study indicated that ZmNAC20 improved drought resistance by promoting stomatal closure and activating the expression of stress-responsible genes in maize. Our findings provide a valuable gene and new clues on improving crop drought resistance. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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Review

Jump to: Research

17 pages, 2433 KiB  
Review
Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors
by Ao-Mei Li, Fen Liao, Miao Wang, Zhong-Liang Chen, Cui-Xian Qin, Ruo-Qi Huang, Krishan K. Verma, Yang-Rui Li, You-Xiong Que, You-Qiang Pan and Dong-Liang Huang
Int. J. Mol. Sci. 2023, 24(10), 8913; https://doi.org/10.3390/ijms24108913 - 17 May 2023
Cited by 5 | Viewed by 1539
Abstract
Sugarcane, a C4 plant, provides most of the world’s sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the [...] Read more.
Sugarcane, a C4 plant, provides most of the world’s sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane’s response to various stresses will provide targets and resources for sugarcane crop improvement. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding 3.0)
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