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16 pages, 3251 KiB

Open AccessArticle

Comparative Molecular and Metabolic Profiling of Two Contrasting Wheat Cultivars under Drought Stress

by Hind Emad Fadoul, Félix Juan Martínez Rivas, Kerstin Neumann, Salma Balazadeh, Alisdair R. Fernie and Saleh Alseekh

Int. J. Mol. Sci. 2021, 22(24), 13287; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413287 - 10 Dec 2021

Cited by 4 | Viewed by 3412

Abstract

Drought is one of the most important threats to plants and agriculture; therefore, understanding of the mechanisms of drought tolerance is crucial for breeding of new tolerant varieties. Here, we assessed the effects of a long-term water deficit stress simulated on a precision [...] Read more.

Drought is one of the most important threats to plants and agriculture; therefore, understanding of the mechanisms of drought tolerance is crucial for breeding of new tolerant varieties. Here, we assessed the effects of a long-term water deficit stress simulated on a precision phenotyping system on some morphological criteria and metabolite traits, as well as the expression of drought associated transcriptional factors of two contrasting drought-responsive African wheat cultivars, Condor and Wadielniel. The current study showed that under drought stress Wadielniel exhibits significant higher tillering and height compared to Condor. Further, we used gas chromatography and ultra-high performance liquid chromatography mass-spectrometry to identify compounds that change between the two cultivars upon drought. Partial least square discriminant analysis (PLS-DA) revealed that 50 metabolites with a possible role in drought stress regulation were significantly changed in both cultivars under water deficit stress. These metabolites included several amino acids, most notably proline, some organic acids, and lipid classes PC 36:3 and TAG 56:9, which were significantly altered under drought stress. Here, the results discussed in the context of understanding the mechanisms involved in the drought response of wheat cultivars, as the phenotype parameters, metabolite content and expression of drought associated transcriptional factors could also be used for potential crop improvement under drought stress. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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22 pages, 13114 KiB

Open AccessArticle

The Laccase Gene Family Mediate Multi-Perspective Trade-Offs during Tea Plant (Camellia sinensis) Development and Defense Processes

by Yongchen Yu, Yuxian Xing, Fengjing Liu, Xin Zhang, Xiwang Li, Jin Zhang and Xiaoling Sun

Int. J. Mol. Sci. 2021, 22(22), 12554; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212554 - 21 Nov 2021

Cited by 8 | Viewed by 2095

Abstract

Laccase (LAC) plays important roles in different plant development and defense processes. In this study, we identified laccase genes (CsLACs) in Camellia sinensis cv ‘Longjing43′ cultivars, which were classified into six subclades. The expression patterns of CsLACs displayed significant spatiotemporal [...] Read more.

Laccase (LAC) plays important roles in different plant development and defense processes. In this study, we identified laccase genes (CsLACs) in Camellia sinensis cv ‘Longjing43′ cultivars, which were classified into six subclades. The expression patterns of CsLACs displayed significant spatiotemporal variations across different tissues and developmental stages. Most members in subclades II, IV and subclade I exhibited contrasting expression patterns during leaf development, consistent with a trade-off model for preferential expression in the early and late developmental stages. The extensive transcriptional changes of CsLACs under different phytohormone and herbivore treatment were observed and compared, with the expression of most genes in subclades I, II and III being downregulated but genes in subclades IV, V and VI being upregulated, suggesting a growth and defense trade-off model between these subclades. Taken together, our research reveal that CsLACs mediate multi-perspective trade-offs during tea plant development and defense processes and are involved in herbivore resistance in tea plants. More in-depth research of CsLACs upstream regulation and downstream targets mediating herbivore defense should be conducted in the future. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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22 pages, 3117 KiB

Open AccessArticle

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance

by Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka and Ellen Zuther

Int. J. Mol. Sci. 2021, 22(19), 10451; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910451 - 28 Sep 2021

Cited by 2 | Viewed by 1591

Abstract

High night temperatures (HNT) affect rice yield in the field and induce chlorosis symptoms in leaves in controlled chamber experiments. However, little is known about molecular changes in leaf segments under these conditions. Transcript and metabolite profiling were performed for leaf segments of [...] Read more.

High night temperatures (HNT) affect rice yield in the field and induce chlorosis symptoms in leaves in controlled chamber experiments. However, little is known about molecular changes in leaf segments under these conditions. Transcript and metabolite profiling were performed for leaf segments of six rice cultivars with different HNT sensitivity. The metabolite profile of the sheath revealed a lower metabolite abundance compared to segments of the leaf blade. Furthermore, pre-adaptation to stress under control conditions was detected in the sheath, whereas this segment was only slightly affected by HNT. No unique significant transcriptomic changes were observed in the leaf base, including the basal growth zone at HNT conditions. Instead, selected metabolites showed correlations with HNT sensitivity in the base. The middle part and the tip were most highly affected by HNT in sensitive cultivars on the transcriptomic level with higher expression of jasmonic acid signaling related genes, genes encoding enzymes involved in flavonoid metabolism and a gene encoding galactinol synthase. In addition, gene expression of expansins known to improve stress tolerance increased in tolerant and sensitive cultivars. The investigation of the different leaf segments indicated highly segment specific responses to HNT. Molecular key players for HNT sensitivity were identified. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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23 pages, 7309 KiB

Open AccessArticle

High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

by Yuan-Yuan Xu, Sheng-Rui Liu, Zhi-Meng Gan, Ren-Fang Zeng, Jin-Zhi Zhang and Chun-Gen Hu

Int. J. Mol. Sci. 2021, 22(11), 5723; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115723 - 27 May 2021

Cited by 7 | Viewed by 2154

Abstract

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The [...] Read more.

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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21 pages, 4389 KiB

Open AccessArticle

Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation

by Romina Beleggia, Nooshin Omranian, Yan Holtz, Tania Gioia, Fabio Fiorani, Franca M. Nigro, Nicola Pecchioni, Pasquale De Vita, Ulrich Schurr, Jacques L. David, Zoran Nikoloski and Roberto Papa

Int. J. Mol. Sci. 2021, 22(9), 4790; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22094790 - 30 Apr 2021

Cited by 4 | Viewed by 3522

Abstract

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two [...] Read more.

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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18 pages, 3899 KiB

Open AccessArticle

Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens

by Xiaoyang Chen, Zhangxin Pei, Pingping Li, Xiabing Li, Yuhang Duan, Hao Liu, Xiaolin Chen, Lu Zheng, Chaoxi Luo and Junbin Huang

Int. J. Mol. Sci. 2021, 22(8), 4069; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22084069 - 15 Apr 2021

Cited by 10 | Viewed by 2139

Abstract

Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but [...] Read more.

Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but the functions of ketone cyclases such as SnoaL in plant fungal pathogens remain unclear. Deletion of UvEC1 caused defects in vegetative growth and conidiation. UvEC1 was also required for response to hyperosmotic and oxidative stresses and for maintenance of cell wall integrity. Importantly, ΔUvEC1 mutants exhibited reduced virulence. We performed a tandem mass tag (TMT)-based quantitative proteomic analysis to identify differentially accumulating proteins (DAPs) between the ΔUvEC1-1 mutant and the wild-type isolate HWD-2. Proteomics data revealed that UvEC1 has a variety of effects on metabolism, protein localization, catalytic activity, binding, toxin biosynthesis and the spliceosome. Taken together, our findings suggest that UvEC1 is critical for the development and virulence of U. virens. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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Review

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25 pages, 2166 KiB

Open AccessReview

The Role of Membrane Transporters in Plant Growth and Development, and Abiotic Stress Tolerance

by Rafaqat Ali Gill, Sunny Ahmar, Basharat Ali, Muhammad Hamzah Saleem, Muhammad Umar Khan, Weijun Zhou and Shengyi Liu

Int. J. Mol. Sci. 2021, 22(23), 12792; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312792 - 26 Nov 2021

Cited by 30 | Viewed by 4288

Abstract

The proteins of membrane transporters (MTs) are embedded within membrane-bounded organelles and are the prime targets for improvements in the efficiency of water and nutrient transportation. Their function is to maintain cellular homeostasis by controlling ionic movements across cellular channels from roots to [...] Read more.

The proteins of membrane transporters (MTs) are embedded within membrane-bounded organelles and are the prime targets for improvements in the efficiency of water and nutrient transportation. Their function is to maintain cellular homeostasis by controlling ionic movements across cellular channels from roots to upper plant parts, xylem loading and remobilization of sugar molecules from photosynthesis tissues in the leaf (source) to roots, stem and seeds (sink) via phloem loading. The plant’s entire source-to-sink relationship is regulated by multiple transporting proteins in a highly sophisticated manner and driven based on different stages of plant growth and development (PG&D) and environmental changes. The MTs play a pivotal role in PG&D in terms of increased plant height, branches/tiller numbers, enhanced numbers, length and filled panicles per plant, seed yield and grain quality. Dynamic climatic changes disturbed ionic balance (salt, drought and heavy metals) and sugar supply (cold and heat stress) in plants. Due to poor selectivity, some of the MTs also uptake toxic elements in roots negatively impact PG&D and are later on also exported to upper parts where they deteriorate grain quality. As an adaptive strategy, in response to salt and heavy metals, plants activate plasma membranes and vacuolar membrane-localized MTs that export toxic elements into vacuole and also translocate in the root’s tips and shoot. However, in case of drought, cold and heat stresses, MTs increased water and sugar supplies to all organs. In this review, we mainly review recent literature from Arabidopsis, halophytes and major field crops such as rice, wheat, maize and oilseed rape in order to argue the global role of MTs in PG&D, and abiotic stress tolerance. We also discussed gene expression level changes and genomic variations within a species as well as within a family in response to developmental and environmental cues. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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24 pages, 2792 KiB

Open AccessReview

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

by Fabio Palumbo, Alessandro Vannozzi and Gianni Barcaccia

Int. J. Mol. Sci. 2021, 22(18), 9713; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22189713 - 08 Sep 2021

Cited by 7 | Viewed by 3022

Abstract

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for [...] Read more.

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family. Full article

(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)

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