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Crop Stress Biology and Molecular Breeding

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 (31 October 2022) | Viewed by 45998

Special Issue Editor

Prof. Dr. Youxiong Que

E-Mail Website
Guest 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”, 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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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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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 (21 papers)

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Research

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12 pages, 2739 KiB  
Article
Effect of Nickel Ions on the Physiological and Transcriptional Responses to Carbon and Nitrogen Metabolism in Tomato Roots under Low Nitrogen Levels
by Kun Zhang, Shuhao Li, Yang Xu, Yuqi Zhou, Shengxiang Ran, Huanhuan Zhao, Weiqun Huang, Ru Xu and Fenglin Zhong
Int. J. Mol. Sci. 2022, 23(19), 11398; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911398 - 27 Sep 2022
Viewed by 1209
Abstract
Nickel (Ni) is an essential trace element for plant growth and a component of the plant body that has many different functions in plants. Although it has been confirmed that nickel ions (Ni2+) havea certain regulatory effect on nitrogen (N) metabolism, [...] Read more.
Nickel (Ni) is an essential trace element for plant growth and a component of the plant body that has many different functions in plants. Although it has been confirmed that nickel ions (Ni2+) havea certain regulatory effect on nitrogen (N) metabolism, there are not enough data to prove whether exogenous Ni2+ can increase the carbon (C) and N metabolism in the roots of tomato seedlingsunder low-nitrogen (LN) conditions. Therefore, through the present experiment, we revealed the key mechanism of Ni2+-mediated tomato root tolerance to LN levels. Tomato plants were cultured at two different N levels (7.66 and 0.383 mmol L−1) and two different Ni2+ levels (0 and 0.1 mg L−1 NiSO4 6H2O) under hydroponic conditions. After nine days, we collected roots for physiological, biochemical, and transcriptome sequencing analyses and found that the activities of N assimilation-related enzymes decreased at LN levels. In contrast, Ni2+ significantly increased the activities of N assimilation-related enzymes and increased the contents of nitrate (NO3−), ammonium (NH4+), and total amino acids. Through root transcriptomic analysis, 3738 differentially expressed genes (DEGs) were identified. DEGs related to C and N metabolism were downregulated after LN application. However, after Ni2+ treatment, PK, PDHB, GAPDH, NR, NiR, GS, GOGAT, and other DEGs related to C and N metabolism were significantly upregulated. In conclusion, our results suggest that Ni2+ can regulate the C and N metabolism pathways in tomato roots to alleviate the impact of LN levels. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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20 pages, 4487 KiB  
Article
Identification and Characterization of AUXIN Response Factor Gene Family Reveals Their Regulatory Network to Respond the Multi-Hormones Crosstalk during GA-Induced Grape Parthenocarpic Berry
by Zilu Sheng, Xuxian Xuan, Fei Wang, Ehsan Sadeghnezhad, Peijie Gong, Yingke Xiao, Tianyu Dong, Peian Zhang, Xicheng Wang, Jinggui Fang and Chen Wang
Int. J. Mol. Sci. 2022, 23(19), 11108; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911108 - 21 Sep 2022
Cited by 2 | Viewed by 1750
Abstract
Exogenous gibberellin (GA) was widely used to improve berry quality through inducing parthenocarpic seedless berries in grapes. We revealed that auxin response factors (ARFs), the key transcription factors in response to auxin, might respond to GA involving modulation of grape parthenocarpy. However, the [...] Read more.
Exogenous gibberellin (GA) was widely used to improve berry quality through inducing parthenocarpic seedless berries in grapes. We revealed that auxin response factors (ARFs), the key transcription factors in response to auxin, might respond to GA involving modulation of grape parthenocarpy. However, the underlying molecular mechanism in this process remains yet unclear. Here, a total of 19 VvARF members were identified in the ovaries during GA-induced grapes’ parthenocarpy. Interestingly, almost all members were GA-responsive factors, of which 9 could be classified in plant hormone signal transduction (KO04075) and involved in the tryptophan metabolic pathway (K14486). Moreover, VvARFs were predicted to have 310 interacted proteins involved in 19 KEGG pathways. Of them, 32 interacted proteins participated in the KO04075 pathway, including auxin (IAA), salicylic acid (SA), abscisic acid (ABA), cytokinin (CTK), and ethylene signaling pathways by responding to GA-mediated multi-hormone crosstalk. Further analysis demonstrated that VvARF4-2 might be the major factor in the modulation of GA-induced parthenocarpy via the crosstalk of IAA, CTK, SA, and ethylene signaling, followed by VvARF6-1 and VvARF9 involved in SA and ABA signaling pathways, respectively. Finally, we developed a VvARFs-mediated regulatory network by responding to GA-mediated multi-hormone crosstalk during grape parthenocarpy. Collectively, our findings provided novel insights into the regulatory network of VvARFs in GA-guided multi-hormone signaling to modulate grape parthenocarpy, which has great implications for the molecular breeding of high quality seedless grape berries. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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22 pages, 7379 KiB  
Article
Transcriptome Sequencing and Metabolome Analysis Reveals the Molecular Mechanism of Drought Stress in Millet
by Xiaoning Cao, Yulu Hu, Jian Song, Hui Feng, Junjie Wang, Ling Chen, Lun Wang, Xianmin Diao, Yan Wan, Sichen Liu and Zhijun Qiao
Int. J. Mol. Sci. 2022, 23(18), 10792; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810792 - 16 Sep 2022
Cited by 14 | Viewed by 2514
Abstract
As one of the oldest agricultural crops in China, millet (Panicum miliaceum) has powerful drought tolerance. In this study, transcriptome and metabolome analyses of ‘Hequ Red millet’ (HQ) and ‘Yanshu No.10’ (YS10) millet after 6 h of drought stress were performed. [...] Read more.
As one of the oldest agricultural crops in China, millet (Panicum miliaceum) has powerful drought tolerance. In this study, transcriptome and metabolome analyses of ‘Hequ Red millet’ (HQ) and ‘Yanshu No.10’ (YS10) millet after 6 h of drought stress were performed. Transcriptome characteristics of drought stress in HQ and YS10 were characterized by Pacbio full-length transcriptome sequencing. The pathway analysis of the differentially expressed genes (DEGs) showed that the highly enriched categories were related to starch and sucrose metabolism, pyruvate metabolism, metabolic pathways, and the biosynthesis of secondary metabolites when the two millet varieties were subjected to drought stress. Under drought stress, 245 genes related to energy metabolism were found to show significant changes between the two strains. Further analysis showed that 219 genes related to plant hormone signal transduction also participated in the drought response. In addition, numerous genes involved in anthocyanin metabolism and photosynthesis were confirmed to be related to drought stress, and these genes showed significant differential expression and played an important role in anthocyanin metabolism and photosynthesis. Moreover, we identified 496 transcription factors related to drought stress, which came from 10 different transcription factor families, such as bHLH, C3H, MYB, and WRKY. Further analysis showed that many key genes related to energy metabolism, such as citrate synthase, isocitrate dehydrogenase, and ATP synthase, showed significant upregulation, and most of the structural genes involved in anthocyanin biosynthesis also showed significant upregulation in both strains. Most genes related to plant hormone signal transduction showed upregulated expression, while many JA and SA signaling pathway-related genes were downregulated. Metabolome analysis was performed on ‘Hequ red millet’ (HQ) and ‘Yanshu 10’ (YS10), a total of 2082 differential metabolites (DEMs) were identified. These findings indicate that energy metabolism, anthocyanins, photosynthesis, and plant hormones are closely related to the drought resistance of millet and adapt to adversity by precisely regulating the levels of various molecular pathways. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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21 pages, 17675 KiB  
Article
WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane
by Qibin Wu, Yong-Bao Pan, Yachun Su, Wenhui Zou, Fu Xu, Tingting Sun, Michael P. Grisham, Shaolin Yang, Liping Xu and Youxiong Que
Int. J. Mol. Sci. 2022, 23(18), 10770; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810770 - 15 Sep 2022
Cited by 20 | Viewed by 3727
Abstract
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data [...] Read more.
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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18 pages, 5862 KiB  
Article
Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient
by Zhaonian Yuan, Qiang Liu, Ziqin Pang, Nyumah Fallah, Yueming Liu, Chaohua Hu and Wenxiong Lin
Int. J. Mol. Sci. 2022, 23(18), 10303; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810303 - 07 Sep 2022
Cited by 1 | Viewed by 1737
Abstract
Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and [...] Read more.
Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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17 pages, 4192 KiB  
Article
Irrigation with Magnetized Water Alleviates the Harmful Effect of Saline–Alkaline Stress on Rice Seedlings
by Changkun Ma, Qian Li, Zhaoxin Song, Lijun Su, Wanghai Tao, Beibei Zhou and Quanjiu Wang
Int. J. Mol. Sci. 2022, 23(17), 10048; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231710048 - 02 Sep 2022
Cited by 5 | Viewed by 1637
Abstract
Saline–alkaline stress suppresses rice growth and threatens crop production. Despite substantial research on rice’s tolerance to saline–alkaline stress, fewer studies have examined the impact of magnetic water treatments on saline–alkaline-stressed rice plants. We explored the physiological and molecular mechanisms involved in saline–alkaline stress [...] Read more.
Saline–alkaline stress suppresses rice growth and threatens crop production. Despite substantial research on rice’s tolerance to saline–alkaline stress, fewer studies have examined the impact of magnetic water treatments on saline–alkaline-stressed rice plants. We explored the physiological and molecular mechanisms involved in saline–alkaline stress tolerance enhancement via irrigation with magnetized water using Nipponbare. The growth of Nipponbare plants was inhibited by saline–alkaline stress, but this inhibition was alleviated by irrigating the plants with magnetized water, as evidenced by greater plant height, biomass, chlorophyll content, photosynthetic rates, and root system in plants irrigated with magnetized water compared to those irrigated with non-magnetized water. Plants that were irrigated with magnetized water were able to acquire more total nitrogen. In addition, we proved that rice seedlings irrigated with magnetized water had a greater root NO3−-nitrogen concentration and root NH4+-nitrogen concentration than plants irrigated with non-magnetized water. These findings suggest that treatment with magnetized water could increase nitrogen uptake. To test this hypothesis, we analyzed the expression levels of genes involved in nitrogen acquisition. The expression levels of OsNRT1;1, OsNRT1;2, OsNRT2;1, OsAMT1;2, OsAMT2;1, OsAMT2;2, OsAMT2;3, OsAMT3;1, OsAMT3;2, and OsAMT3;3 were higher in plants exposed to magnetized water medium compared to those exposed to non-magnetized water media. We further demonstrated that treatment with magnetized water increases available nitrogen, NO3−-nitrogen content, and NH4+-nitrogen content in soil under saline–alkaline stress. Our results revealed that the increased resistance of rice seedlings to saline–alkaline stress may be attributable to a very effective nitrogen acquisition system enhanced by magnetized water. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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19 pages, 4982 KiB  
Article
Microscopic and Transcriptomic Comparison of Powdery Mildew Resistance in the Progenies of Brassica carinata × B. napus
by Mingzheng Zhang, Qiong Gong, Xing Su, Yaohua Cheng, Haoxue Wu, Zhen Huang, Aixia Xu, Jungang Dong and Chengyu Yu
Int. J. Mol. Sci. 2022, 23(17), 9961; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23179961 - 01 Sep 2022
Cited by 2 | Viewed by 1652
Abstract
Powdery mildew is a widespread disease in rapeseed due to a lack of resistant germplasm. We compared the foliar epidermal features and transcriptomic responses between the resistant (R) and susceptible (S) plants among the two parents and progenies of Brassica carinata × B. [...] Read more.
Powdery mildew is a widespread disease in rapeseed due to a lack of resistant germplasm. We compared the foliar epidermal features and transcriptomic responses between the resistant (R) and susceptible (S) plants among the two parents and progenies of Brassica carinata × B. napus. The amount of cuticular wax and callose deposition on the R plants was much lower than that on the S plants; hence, these chemicals are not all essential to pre-penetration resistance, although the cuticular wax on the R plants had more needle-like crystals. A total of 1049 genes involved in various defense responses were expressed differentially among the R/S plants. The expression levels of two well-known susceptibility genes, MLO6 and MLO12, were much lower in the R plant, indicating an important role in PM resistance. A set of genes related to wax biosynthesis (KCS6, LACS2, CER and MAH1), cell wall modification (PMR5, PMEI9, RWA2, PDCB1 and C/VIF2), chloroplast function (Chlorophyllase-1, OEP161, PSBO1, CP29B and CSP41b), receptor kinase activity (ERECTA, BAK1, BAM2, LYM1, LYM3, RLK902, RLP11, ERL1 and ERL2), IPCS2, GF14 lambda, RPS4 and RPS6 were highly expressed in the R plants. In the S plants, most highly expressed genes were involved in later defense responses, including CERK1, LYK4, LIK1, NIMIN-1, CHITINASE 10, PECTINESTERASE, CYP81F2 and RBOHF and the genes involved in salicylic acid-dependent systemic acquired resistance and hypersensitive responses, indicating the occurrence of severe fungal infection. The results indicate that some uncertain pre-penetration defenses are pivotal for high resistance, while post-penetration defenses are more important for the S plant survival. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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19 pages, 12735 KiB  
Article
Sugarcane ScDREB2B-1 Confers Drought Stress Tolerance in Transgenic Nicotiana benthamiana by Regulating the ABA Signal, ROS Level and Stress-Related Gene Expression
by Yufeng Chen, Zhu Li, Tingting Sun, Dongjiao Wang, Zhoutao Wang, Chang Zhang, Youxiong Que, Jinlong Guo, Liping Xu and Yachun Su
Int. J. Mol. Sci. 2022, 23(17), 9557; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23179557 - 23 Aug 2022
Cited by 8 | Viewed by 1893
Abstract
The dehydration-responsive element-binding protein (DREB) is a subgroup member of the AP2/ERF family and actively participates in the response of plants to abiotic stress. Although DREB genes have been studied in a variety of plant species, there are few reports of DREB genes [...] Read more.
The dehydration-responsive element-binding protein (DREB) is a subgroup member of the AP2/ERF family and actively participates in the response of plants to abiotic stress. Although DREB genes have been studied in a variety of plant species, there are few reports of DREB genes in sugarcane (Saccharum spp.). In this study, a novel full-length cDNA sequence of the ScDREB2B-1 gene was cloned from the Saccharum hybrid ROC22, whose encoding protein contained only one AP2-conserved domain and was clustered into the DREB (A-2) subgroup. The diverse promoter elements in the ScDREB2B-1 gene and the accumulated transcripts of its homologous gene (SsAP2/ERF-107) in S. spontaneum under drought stress suggest that the ScDREB2B-1 gene may play a role in drought response. In addition, reverse transcription quantitative PCR analysis showed that the expression level of the ScDREB2B-1 gene was upregulated in the root and leaf of ROC22 under polyethylene glycol, sodium chloride and abscisic acid (ABA) treatments. The yeast two-hybrid experiment demonstrated that ScDREB2B-1 had transcriptional self-activation activity. Compared with wild-type plants, the overexpression of the ScDREB2B-1 gene improved the drought tolerance of the transgenic Nicotiana benthamiana by activating the ABA pathway to enhance the expression of the ABA-responsive gene (NbNCED) and ABA content, regulate the intracellular reactive oxygen species (ROS) level (enhance the transcripts of ROS synthase-related gene NbRbohB and the activities of catalase, peroxidase and superoxide dismutase) and increase the relative water content, proline content and expression level of osmotic stress-related genes (NbERD and NbLEA). Collectively, our data indicate that ScDREB2B-1 is a stress-inducible and ABA-responsive transcription factor gene that responds to drought stress by regulating ABA signaling, ROS levels and stress-related gene expression. This study contributes to a better understanding of the biological function of ScDREB2B-1, which could serve as a foundation for future resistance breeding in sugarcane. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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16 pages, 3017 KiB  
Article
Efficient Anchoring of Erianthus arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers
by Jiayun Wu, Mingxiao Zhang, Jiarui Liu, Yongji Huang, Liangnian Xu, Zuhu Deng and Xinwang Zhao
Int. J. Mol. Sci. 2022, 23(16), 9435; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23169435 - 21 Aug 2022
Cited by 1 | Viewed by 1177
Abstract
Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for [...] Read more.
Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for the development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones of E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely, Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking of the inherited status of this chromosome in a sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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19 pages, 3212 KiB  
Article
Metabolomic Analysis Revealed Distinct Physiological Responses of Leaves and Roots to Huanglongbing in a Citrus Rootstock
by Qing Chen, Ailing Min, Shu Luo, Jinwei He, Runqin Wu, Ximeng Lin, Yan Wang, Wen He, Yunting Zhang, Yuanxiu Lin, Mengyao Li, Yong Zhang, Ya Luo, Haoru Tang and Xiaorong Wang
Int. J. Mol. Sci. 2022, 23(16), 9242; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23169242 - 17 Aug 2022
Cited by 6 | Viewed by 1920
Abstract
Huanglongbing (HLB) is an obstinate disease in the citrus industry. No resistant citrus resources were currently available, but various degrees of Huanglongbing tolerance exist in different germplasm. Citrus junos is emerging as one of the popular rootstocks widely used in the citrus production. [...] Read more.
Huanglongbing (HLB) is an obstinate disease in the citrus industry. No resistant citrus resources were currently available, but various degrees of Huanglongbing tolerance exist in different germplasm. Citrus junos is emerging as one of the popular rootstocks widely used in the citrus production. However, its responses to the HLB causal agent, Candidatus Liberibacter asiaticus (CLas), were still elusive. In the current study, we investigated the physiological, anatomical, and metabolomic responses of a C. junos rootstock ‘Pujiang Xiangcheng’ by a controlled CLas grafting inoculation. The summer flushes and roots were impaired at 15 weeks after inoculation, although typical leaf symptomatic phenotypes were not obvious. The chlorophyll pigments and the photosynthetic rate were compromised. The phloem sieve tubes were still working, despite the fact that the callose was deposited and the starch granules were accumulated in the phloem cells. A wide, targeted metabolomic analysis was carried out to explore the systematic alterations of the metabolites at this early stage of infection in the leaves and root system. The differentially accumulated metabolites in the CLas-affected leaves and roots compared with the mock-inoculation control tissues revealed that distinct responses were obvious. Besides the commonly observed alteration of sugar and amino acids, the active break down of starch in the roots was discovered. The different types of fatty acids were altered in the two tissues, with a more pronounced content decline in the roots. Our results not only provided fundamental knowledge about the response of the C. junos rootstock to the HLB disease, but also presented new insights into the host–pathogen interaction in the early stages. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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20 pages, 16799 KiB  
Article
Genome-Wide Expression Profiling Analysis of Kiwifruit GolS and RFS Genes and Identification of AcRFS4 Function in Raffinose Accumulation
by Jun Yang, Chengcheng Ling, Yunyan Liu, Huamin Zhang, Quaid Hussain, Shiheng Lyu, Songhu Wang and Yongsheng Liu
Int. J. Mol. Sci. 2022, 23(16), 8836; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23168836 - 09 Aug 2022
Cited by 9 | Viewed by 2075
Abstract
The raffinose synthetase (RFS) and galactinol synthase (GolS) are two critical enzymes for raffinose biosynthesis, which play an important role in modulating plant growth and in response to a variety of biotic or abiotic stresses. Here, we comprehensively analyzed [...] Read more.
The raffinose synthetase (RFS) and galactinol synthase (GolS) are two critical enzymes for raffinose biosynthesis, which play an important role in modulating plant growth and in response to a variety of biotic or abiotic stresses. Here, we comprehensively analyzed the RFS and GolS gene families and their involvement in abiotic and biotic stresses responses at the genome-wide scale in kiwifruit. A total of 22 GolS and 24 RFS genes were identified in Actinidia chinensis and Actinidia eriantha genomes. Phylogenetic analysis showed that the GolS and RFS genes were clustered into four and six groups, respectively. Transcriptomic analysis revealed that abiotic stresses strongly induced some crucial genes members including AcGolS1/2/4/8 and AcRFS2/4/8/11 and their expression levels were further confirmed by qRT-PCR. The GUS staining of AcRFS4Pro::GUS transgenic plants revealed that the transcriptionlevel of AcRFS4 was significantly increased by salt stress. Overexpression of AcRFS4 in Arabidopsis demonstrated that this gene enhanced the raffinose accumulation and the tolerance to salt stress. The co-expression networks analysis of hub transcription factors targeting key AcRFS4 genes indicated that there was a strong correlation between AcNAC30 and AcRFS4 expression under salt stress. Furthermore, the yeast one-hybrid assays showed that AcNAC30 could bind the AcRFS4 promoter directly. These results may provide insights into the evolutionary and functional mechanisms of GolS and RFS genes in kiwifruit. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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18 pages, 4555 KiB  
Article
miR3633a-GA3ox2 Module Conducts Grape Seed-Embryo Abortion in Response to Gibberellin
by Yunhe Bai, Xiaowen Zhang, Xuxian Xuan, Ehsan Sadeghnezhad, Fei Liu, Tianyu Dong, Dan Pei, Jinggui Fang and Chen Wang
Int. J. Mol. Sci. 2022, 23(15), 8767; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158767 - 07 Aug 2022
Cited by 3 | Viewed by 1636
Abstract
Seedlessness is one of the important quality and economic traits favored by grapevine consumers, which are mainly affected by phytohormones, especially gibberellin (GA). GA is widely utilized in seedless berry production and could effectively induce grape seed embryo abortion. However, the molecular mechanism [...] Read more.
Seedlessness is one of the important quality and economic traits favored by grapevine consumers, which are mainly affected by phytohormones, especially gibberellin (GA). GA is widely utilized in seedless berry production and could effectively induce grape seed embryo abortion. However, the molecular mechanism underlying this process, like the role of RNA silencing in the biosynthesis pathway of GA remains elusive. Here, Gibberellin 3-β dioxygenase2 (GA3ox2) as the last key enzyme in GA biosynthesis was predicated as a potential target gene for miR3633a, and two of them were identified as a GA response in grape berries. We also analyzed the promoter regions of genes encoding GA biosynthesis and found the hormone-responsive elements to regulate grape growth and development. The cleavage interaction between VvmiR3633a and VvGA3ox2 was validated by RLM-RACE and the transient co-transformation technique in tobacco in vivo. Interestingly, during GA-induced grape seed embryo abortion, exogenous GA promoted the expression of VvmiR3633a, thereby mainly repressing the level of VvGA3ox2 in seed embryos. We also observed a negative correlation between down-regulated VvGA20ox2/VvGA3ox2 and up-regulated VvGA2ox3/VvGA2ox1, of which GA inactivation was greater than GA synthesis, inhibited active GA content, accompanied by the reduction of VvSOD and VvCAT expression levels and enzymatic activities. These series of changes might be the main causes of grape seed embryo abortion. In conclusion, we have preliminarily drawn a schematic mode of GA-mediated VvmiR3633a and related genes regulatory network during grape seed abortion induced by exogenous GA. Our findings provide novel insights into the GA-responsive roles of the VvmiR3633a-VvGA3ox2 module in the modulation of grape seed-embryo abortion, which has implications for the molecular breeding of high-quality seedless grape berries. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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17 pages, 11173 KiB  
Article
Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.)
by Shaoming Liang, Shanbin Xu, Di Qu, Luomiao Yang, Jingguo Wang, Hualong Liu, Wei Xin, Detang Zou and Hongliang Zheng
Int. J. Mol. Sci. 2022, 23(15), 8491; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158491 - 31 Jul 2022
Cited by 16 | Viewed by 2527
Abstract
Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and [...] Read more.
Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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21 pages, 9014 KiB  
Article
Characterization and Functional Implications of the Nonexpressor of Pathogenesis-Related Genes 1 (NPR1) in Saccharum
by Shoujian Zang, Liqian Qin, Zhennan Zhao, Jing Zhang, Wenhui Zou, Dongjiao Wang, Aoyin Feng, Shaolin Yang, Youxiong Que and Yachun Su
Int. J. Mol. Sci. 2022, 23(14), 7984; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23147984 - 20 Jul 2022
Cited by 3 | Viewed by 2044
Abstract
Sugarcane (Saccharum spp.) is an important sugar and energy crop worldwide. As a core regulator of the salicylic acid (SA) signaling pathway, nonexpressor of pathogenesis-related genes 1 (NPR1) plays a significant role in the response of the plant to biotic [...] Read more.
Sugarcane (Saccharum spp.) is an important sugar and energy crop worldwide. As a core regulator of the salicylic acid (SA) signaling pathway, nonexpressor of pathogenesis-related genes 1 (NPR1) plays a significant role in the response of the plant to biotic and abiotic stresses. However, there is currently no report on the NPR1-like gene family in sugarcane. In this study, a total of 18 NPR1-like genes were identified in Saccharum spontaneum and classified into three clades (clade I, II, and III). The cis-elements predicted in the promotors revealed that the sugarcane NPR1-like genes may be involved in various phytohormones and stress responses. RNA sequencing and quantitative real-time PCR analysis demonstrated that NPR1-like genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, a novel ShNPR1 gene from Saccharum spp. hybrid ROC22 was isolated by homologous cloning and validated to be a nuclear-localized clade II member. The ShNPR1 gene was constitutively expressed in all the sugarcane tissues, with the highest expression level in the leaf and the lowest in the bud. The expression level of ShNPR1 was decreased by the plant hormones salicylic acid (SA) and abscisic acid (ABA). Additionally, the transient expression showed that the ShNPR1 gene plays a positive role in Nicotiana benthamiana plants’ defense response to Ralstonia solanacearum and Fusarium solani var. coeruleum. This study provided comprehensive information for the NPR1-like family in sugarcane, which should be helpful for functional characterization of sugarcane NPR1-like genes in the future. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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17 pages, 3568 KiB  
Article
MdMKK9-Mediated the Regulation of Anthocyanin Synthesis in Red-Fleshed Apple in Response to Different Nitrogen Signals
by Xiaohong Sun, Xinxin Li, Yanbo Wang, Jihua Xu, Shenghui Jiang and Yugang Zhang
Int. J. Mol. Sci. 2022, 23(14), 7755; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23147755 - 14 Jul 2022
Cited by 10 | Viewed by 2192
Abstract
The mitogen-activated protein kinase (MAPK) signaling cascade is a widely existing signal transduction system in eukaryotes, and plays an important role in the signal transduction processes of plant cells in response to environmental stress. In this study, we screened MdMKK9, a gene [...] Read more.
The mitogen-activated protein kinase (MAPK) signaling cascade is a widely existing signal transduction system in eukaryotes, and plays an important role in the signal transduction processes of plant cells in response to environmental stress. In this study, we screened MdMKK9, a gene in the MAPK family. This gene is directly related to changes in anthocyanin synthesis in the ‘Daihong’ variety of red-fleshed apple (Malus sieversii f neidzwetzkyana (Dieck) Langenf). MdMKK9 expression was up-regulated in ‘Daihong’ tissue culture seedlings cultured at low levels of nitrogen. This change in gene expression up-regulated the expression of genes related to anthocyanin synthesis and nitrogen transport, thus promoting anthocyanin synthesis and causing the tissue culture seedlings to appear red in color. To elucidate the function of MdMKK9, we used the CRISPR/Cas9 system to construct a gene editing vector for MdMKK9 and successfully introduced it into the calli of the ‘Orin’ apple. The MdMKK9 deletion mutants (MUT) calli could not respond to the low level of nitrogen signal, the expression level of anthocyanin synthesis-related genes was down-regulated, and the anthocyanin content was lower than that of the wild type (WT). In contrast, the MdMKK9-overexpressed calli up-regulated the expression level of anthocyanin synthesis-related genes and increased anthocyanin content, and appeared red in conditions of low level of nitrogen or nitrogen deficiency. These results show that MdMKK9 plays a role in the adaptation of red-fleshed apple to low levels of nitrogen by regulating the nitrogen status and anthocyanin accumulation. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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14 pages, 3422 KiB  
Article
Expression of Pinellia pedatisecta Agglutinin PPA Gene in Transgenic Sugarcane Led to Stomata Patterning Change and Resistance to Sugarcane Woolly Aphid, Ceratovacuna lanigera Zehntner
by Mengyu Zhao, Yuming Zhou, Liangyinan Su, Guomeng Li, Zizhou Huang, Dunyou Huang, Weimin Wu and Yang Zhao
Int. J. Mol. Sci. 2022, 23(13), 7195; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23137195 - 28 Jun 2022
Cited by 1 | Viewed by 2071
Abstract
The sugarcane woolly aphid is one of the main pests of sugarcane worldwide. The Pinellia pedatisecta agglutinin (PPA) gene has been demonstrated to function towards aphid resistance in other crops. In our study, in order to investigate the PPA function towards [...] Read more.
The sugarcane woolly aphid is one of the main pests of sugarcane worldwide. The Pinellia pedatisecta agglutinin (PPA) gene has been demonstrated to function towards aphid resistance in other crops. In our study, in order to investigate the PPA function towards aphid control in sugarcane and its underlying mechanism, the PPA gene was overexpressed in a sugarcane Zhongzhe 1 (ZZ1) cultivar in independent transgenic sugarcane lines. It was confirmed in this study that PPA transgenic sugarcane can resist aphids via detecting the aphids’ development and tracing the survival number on PPA−transgenic sugarcane lines as well as PPA negative control lines. The mechanism of PPA lectin−associated defense against aphids was preliminarily explored. Stomatal patterning differences of sugarcane leaves between PPA−transgenic sugarcane lines and negative control lines were found. PPA overexpression led to an increase in stomata number and a decrease in stomata size that might have changed the transpiration status, which is critical for aphids’ passive feeding. Moreover, the antioxidant enzyme, sugar, tannin and chlorophyll content in sugarcane leaves before and after aphid infestation was determined. The results indicated that PPA overexpression in sugarcane resulted in an increase in antioxidant enzyme activity and tannin content, as well as a reduction in the decline of certain sugars. These together may improve sugarcane resistance against the sugarcane woolly aphid. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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20 pages, 4438 KiB  
Article
A NAC Transcription Factor from ‘Sea Rice 86′ Enhances Salt Tolerance by Promoting Hydrogen Sulfide Production in Rice Seedlings
by Yan Sun, Kaiqiang Song, Miaomiao Guo, Hao Wu, Xuan Ji, Lixia Hou, Xin Liu and Songchong Lu
Int. J. Mol. Sci. 2022, 23(12), 6435; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126435 - 09 Jun 2022
Cited by 8 | Viewed by 1896
Abstract
Soil salinity severely threatens plant growth and crop performance. Hydrogen sulfide (H2S), a plant signal molecule, has been implicated in the regulation of plant responses to salinity stress. However, it is unclear how the transcriptional network regulates H2S biosynthesis [...] Read more.
Soil salinity severely threatens plant growth and crop performance. Hydrogen sulfide (H2S), a plant signal molecule, has been implicated in the regulation of plant responses to salinity stress. However, it is unclear how the transcriptional network regulates H2S biosynthesis during salt stress response. In this study, we identify a rice NAC (NAM, ATAF and CUC) transcription factor, OsNAC35-like (OsNACL35), from a salt-tolerant cultivar ‘Sea Rice 86′ (SR86) and further show that it may have improved salt tolerance via enhanced H2S production. The expression of OsNACL35 was significantly upregulated by high salinity and hydrogen peroxide (H2O2). The OsNACL35 protein was localized predominantly in the nucleus and was found to have transactivation activity in yeast. The overexpression of OsNACL35 (OsNACL35-OE) in japonica cultivar Nipponbare ramatically increased resistance to salinity stress, whereas its dominant-negative constructs (SUPERMAN repression domain, SRDX) conferred hypersensitivity to salt stress in the transgenic lines at the vegetative stage. Moreover, the quantitative real-time PCR analysis showed that many stress-associated genes were differentially expressed in the OsNACL35-OE and OsNACL35-SRDX lines. Interestingly, the ectopic expression of OsNACL35 triggered a sharp increase in H2S content by upregulating the expression of a H2S biosynthetic gene, OsDCD1, upon salinity stress. Furthermore, the dual luciferase and yeast one-hybrid assays indicated that OsNACL35 directly upregulated the expression of OsDCD1 by binding to the promoter sequence of OsDCD1. Taken together, our observations illustrate that OsNACL35 acts as a positive regulator that links H2S production to salt stress tolerance, which may hold promising utility in breeding salt-tolerant rice cultivar. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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19 pages, 6948 KiB  
Article
A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress
by Ying Liu, Xiaolan Liu, Dandan Yang, Ze Yin, Yaolan Jiang, Hui Ling, Ning Huang, Dawei Zhang, Jinfeng Wu, Lili Liu, Liping Xu, Mingli Yan, Youxiong Que and Dinggang Zhou
Int. J. Mol. Sci. 2022, 23(11), 6334; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116334 - 06 Jun 2022
Cited by 10 | Viewed by 1996
Abstract
The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum [...] Read more.
The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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14 pages, 8475 KiB  
Article
A TIR-NBS-LRR Gene MdTNL1 Regulates Resistance to Glomerella Leaf Spot in Apple
by Lingling Lv, Yingshuang Liu, Suhua Bai, Khurshid Sadullaevich Turakulov, Chaohua Dong and Yugang Zhang
Int. J. Mol. Sci. 2022, 23(11), 6323; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116323 - 05 Jun 2022
Cited by 6 | Viewed by 2180
Abstract
Glomerella leaf spot (GLS), caused by the fungus Colletotrichum fructicola, is one of the most devastating apple diseases. Our previous study reported that the GLS resistance locus was defined on the chromosome 15 region. Here, we further found a single-nucleotide polymorphism (SNP) [...] Read more.
Glomerella leaf spot (GLS), caused by the fungus Colletotrichum fructicola, is one of the most devastating apple diseases. Our previous study reported that the GLS resistance locus was defined on the chromosome 15 region. Here, we further found a single-nucleotide polymorphism (SNP) site (SNP7309212) in the GLS resistance that was able to distinguish resistant cultivars (lines) from susceptible ones. On the basis of the SNP site, we cloned a TNL gene from the GLS resistant locus and named it MdTNL1 (NCBI Accession Number: ON402514). This gene contains a toll/interleukin-1 receptor transmembrane domain (TIR), nucleotide-binding sites (NBS), and leucine-rich repeat (LRR) domain. Subcellular location indicated that MdTNL1 was expressed in the nucleus and cell membrane. Ectopic overexpression of MdTNL1 in Nicotiana benthamiana caused cell death. We further demonstrated allelic polymorphisms in MdTNL1. It is noteworthy that NBS and LRR domains of the MdTNL1 protein serve as the repository for generating allelic diversity. Quantitative real-time PCR (qRT-PCR) assay revealed that MdTNL1 was highly expressed in resistant apple cultivar ‘Fuji’ after inoculation with C. fructicola, whereas susceptible cultivar ‘Golden Delicious’ exhibited low expression after inoculation. Over-expression of MdTNL1-1 in susceptible apple fruits and leaves improved disease resistance, while in ‘Orin’ calli, silencing the MdTNL1-1 gene conversely decreased GLS resistance. In conclusion, we identified a GLS associated with SNP7309212 and demonstrated that a TIR-NBS-LRR gene MdTNL1-1 positively regulates GLS resistance in apple. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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Review

Jump to: Research

20 pages, 382 KiB  
Review
Current Status and Future Perspectives of Genomics Research in the Rust Fungi
by Chongjing Xia, Age Qiu, Meinan Wang, Taiguo Liu, Wanquan Chen and Xianming Chen
Int. J. Mol. Sci. 2022, 23(17), 9629; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23179629 - 25 Aug 2022
Cited by 3 | Viewed by 2266
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of [...] Read more.
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
18 pages, 3246 KiB  
Review
Long Non-Coding RNAs: New Players in Plants
by Zhennan Zhao, Shoujian Zang, Wenhui Zou, Yong-Bao Pan, Wei Yao, Cuihuai You and Youxiong Que
Int. J. Mol. Sci. 2022, 23(16), 9301; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23169301 - 18 Aug 2022
Cited by 22 | Viewed by 3375
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules [...] Read more.
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding)
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