Editorial

6 pages, 1874 KiB

Open AccessEditorial

by Nicolò G. M. Cultrera

Int. J. Mol. Sci. 2023, 24(8), 6890; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24086890 - 07 Apr 2023

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This Special Issue is aimed to collect scientific papers that support holistic methodological approaches, both top-down and horizontal, for the correct application of various omics sciences because, when well-integrated, they can contribute to our understanding of the genotypic plasticity of plant species [...] [...] Read more.

This Special Issue is aimed to collect scientific papers that support holistic methodological approaches, both top-down and horizontal, for the correct application of various omics sciences because, when well-integrated, they can contribute to our understanding of the genotypic plasticity of plant species [...] Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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Research

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15 pages, 10014 KiB

Open AccessArticle

Mutation in OsFWL7 Affects Cadmium and Micronutrient Metal Accumulation in Rice

by Qingsong Gao, Lei Liu, Haiying Zhou, Xi Liu, Wei Li, Yu Min, Yurong Yan, Jianhui Ji, Hao Zhang and Xiangxiang Zhao

Int. J. Mol. Sci. 2021, 22(22), 12583; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212583 - 22 Nov 2021

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Abstract

Micronutrient metals, such as Mn, Cu, Fe, and Zn, are essential heavy metals for plant growth and development, while Cd is a nonessential heavy metal that is highly toxic to both plants and humans. Our understanding of the molecular mechanisms underlying Cd and [...] Read more.

Micronutrient metals, such as Mn, Cu, Fe, and Zn, are essential heavy metals for plant growth and development, while Cd is a nonessential heavy metal that is highly toxic to both plants and humans. Our understanding of the molecular mechanisms underlying Cd and micronutrient metal accumulation in plants remains incomplete. Here, we show that OsFWL7, an FW2.2-like (FWL) family gene in Oryza sativa, is preferentially expressed in the root and encodes a protein localized to the cell membrane. The osfwl7 mutation reduces both the uptake and the root-to-shoot translocation of Cd in rice plants. Additionally, the accumulation of micronutrient metals, including Mn, Cu, and Fe, was lower in osfwl7 mutants than in the wildtype plants under normal growth conditions. Moreover, the osfwl7 mutation affects the expression of several heavy metal transporter genes. Protein interaction analyses reveal that rice FWL proteins interact with themselves and one another, and with several membrane microdomain marker proteins. Our results suggest that OsFWL7 is involved in Cd and micronutrient metal accumulation in rice. Additionally, rice FWL proteins may form oligomers and some of them may be located in membrane microdomains. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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22 pages, 4014 KiB

Open AccessArticle

Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties

by Qionghou Li, Xin Qiao, Luting Jia, Yuxin Zhang and Shaoling Zhang

Int. J. Mol. Sci. 2021, 22(17), 9622; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22179622 - 06 Sep 2021

Cited by 5 | Viewed by 3518

Abstract

Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, [...] Read more.

Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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22 pages, 2971 KiB

Open AccessArticle

Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea

by Shulin Shen, Yunshan Tang, Chao Zhang, Nengwen Yin, Yuanyi Mao, Fujun Sun, Si Chen, Ran Hu, Xueqin Liu, Guoxia Shang, Liezhao Liu, Kun Lu, Jiana Li and Cunmin Qu

Int. J. Mol. Sci. 2021, 22(13), 7215; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22137215 - 05 Jul 2021

Cited by 13 | Viewed by 3123

Abstract

The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops; the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and [...] Read more.

The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops; the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and dark-seeded B. juncea seeds. In this study, we identified 236 compounds, including 31 phenolic acids, 47 flavonoids, 17 glucosinolates, 38 lipids, 69 other hydroxycinnamic acid compounds, and 34 novel unknown compounds. Of these, 36 compounds (especially epicatechin and its derivatives) accumulated significantly different levels during the development of yellow- and dark-seeded B. juncea. In addition, the transcript levels of BjuDFR, BjuANS,BjuBAN, BjuTT8, and BjuTT19 were closely associated with changes to epicatechin and its derivatives during seed development, implicating this pathway in the seed coat color determinant in B. juncea. Furthermore, we found numerous variations of sequences in the TT8A genes that may be associated with the stability of seed coat color in B. rapa, B. napus, and B. juncea, which might have undergone functional differentiation during polyploidization in the Brassica species. The results provide valuable information for understanding the accumulation of metabolites in the seed coat color of B. juncea and lay a foundation for exploring the underlying mechanism. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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18 pages, 13262 KiB

Open AccessArticle

The BAG2 and BAG6 Genes Are Involved in Multiple Abiotic Stress Tolerances in Arabidopsis Thaliana

by Muhammad Arif, Zitong Li, Qiong Luo, Luhua Li, Yuequan Shen and Shuzhen Men

Int. J. Mol. Sci. 2021, 22(11), 5856; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115856 - 29 May 2021

Cited by 16 | Viewed by 4190

Abstract

The BAG proteins are a family of multi-functional co-chaperones. In plants, BAG proteins were found to play roles both in abiotic and biotic stress tolerance. However, the function of Arabidopsis BAG2 remains largely unknown, whereas BAG6 is required for plants’ defense to pathogens, [...] Read more.

The BAG proteins are a family of multi-functional co-chaperones. In plants, BAG proteins were found to play roles both in abiotic and biotic stress tolerance. However, the function of Arabidopsis BAG2 remains largely unknown, whereas BAG6 is required for plants’ defense to pathogens, although it remains unknown whether BAG6 is involved in plants’ tolerance to abiotic stresses. Here, we show that both BAG2 and BAG6 are expressed in various tissues and are upregulated by salt, mannitol, and heat treatments and by stress-related hormones including ABA, ethylene, and SA. Germination of bag2, bag6 and bag2 bag6 seeds is less sensitive to ABA compared to the wild type (WT), whereas BAG2 and BAG6 overexpression lines are hypersensitive to ABA. bag2, bag6, and bag2 bag6 plants show higher survival rates than WT in drought treatment but display lower survival rates in heat-stress treatment. Consistently, these mutants showed differential expression of several stress- and ABA-related genes such as RD29A, RD29B, NCED3 and ABI4 compared to the WT. Furthermore, these mutants exhibit lower levels of ROS after drought and ABA treatment but higher ROS accumulation after heat treatment than the WT. These results suggest that BAG2 and BAG6 are negatively involved in drought stress but play a positive role in heat stress in Arabidopsis. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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22 pages, 3594 KiB

Open AccessArticle

Integrating Transcriptome and Coexpression Network Analyses to Characterize Salicylic Acid- and Jasmonic Acid-Related Genes in Tolerant Poplars Infected with Rust

by Qiaoli Chen, Ruizhi Zhang, Danlei Li and Feng Wang

Int. J. Mol. Sci. 2021, 22(9), 5001; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22095001 - 08 May 2021

Cited by 12 | Viewed by 2620

Abstract

Melampsora larici-populina causes serious poplar foliar diseases called rust worldwide. Salicylic acid (SA) and jasmonic acid (JA) are important phytohormones that are related to plant defence responses. To investigate the transcriptome profiles of SA- and JA-related genes involved in poplar rust interaction, two [...] Read more.

Melampsora larici-populina causes serious poplar foliar diseases called rust worldwide. Salicylic acid (SA) and jasmonic acid (JA) are important phytohormones that are related to plant defence responses. To investigate the transcriptome profiles of SA- and JA-related genes involved in poplar rust interaction, two tolerant poplars and one intolerant poplar were selected for this study. Weighted gene coexpression network analysis (WGCNA) was applied to characterize the changes in the transcriptome profiles and contents of SA and JA after infection with the virulent E4 race of M. larici-populina. In response to infection with the E4 race of M. larici-populina, tolerant symptoms were correlated with the expression of genes related to SA and JA biosynthesis, the levels of SA and JA, and the expression of defence-related genes downstream of SA and JA. Tolerant poplars could promptly regulate the occurrence of defence responses by activating or inhibiting SA or JA pathways in a timely manner, including regulating the expression of genes related to programmed cell death, such as Kunitz-type trypsin inhibitor (KTI), to limit the growth of E4 and protect themselves. WGCNA suggested that KTI might be regulated by a Cytochrome P450 family (CYP) gene. Some CYPs should play an important role in both JA- and SA-related pathways. In contrast, in intolerant poplar, the inhibition of SA-related defence signalling through increasing JA levels in the early stage led to continued inhibition of a large number of plant–pathogen interaction-related and signalling-related genes, including NBS-LRRs, EDS1, NDR1, WRKYs, and PRs. Therefore, timely activation or inhibition of the SA or JA pathways is the key difference between tolerant and intolerant poplars. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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Review

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21 pages, 1610 KiB

Open AccessReview

Dissection of Crop Metabolome Responses to Nitrogen, Phosphorus, Potassium, and Other Nutrient Deficiencies

by Yingbin Xue, Shengnan Zhu, Rainer Schultze-Kraft, Guodao Liu and Zhijian Chen

Int. J. Mol. Sci. 2022, 23(16), 9079; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23169079 - 13 Aug 2022

Cited by 2 | Viewed by 1656

Abstract

Crop growth and yield often face sophisticated environmental stresses, especially the low availability of mineral nutrients in soils, such as deficiencies of nitrogen, phosphorus, potassium, and others. Thus, it is of great importance to understand the mechanisms of crop response to mineral nutrient [...] Read more.

Crop growth and yield often face sophisticated environmental stresses, especially the low availability of mineral nutrients in soils, such as deficiencies of nitrogen, phosphorus, potassium, and others. Thus, it is of great importance to understand the mechanisms of crop response to mineral nutrient deficiencies, as a basis to contribute to genetic improvement and breeding of crop varieties with high nutrient efficiency for sustainable agriculture. With the advent of large-scale omics approaches, the metabolome based on mass spectrometry has been employed as a powerful and useful technique to dissect the biochemical, molecular, and genetic bases of metabolisms in many crops. Numerous metabolites have been demonstrated to play essential roles in plant growth and cellular stress response to nutrient limitations. Therefore, the purpose of this review was to summarize the recent advances in the dissection of crop metabolism responses to deficiencies of mineral nutrients, as well as the underlying adaptive mechanisms. This review is intended to provide insights into and perspectives on developing crop varieties with high nutrient efficiency through metabolite-based crop improvement. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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22 pages, 3168 KiB

Open AccessReview

Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways

by Muhammad Anwar, Liu Chen, Yibo Xiao, Jinsong Wu, Lihui Zeng, Hui Li, Qingyu Wu and Zhangli Hu

Int. J. Mol. Sci. 2021, 22(17), 9544; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22179544 - 03 Sep 2021

Cited by 23 | Viewed by 4378

Abstract

The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, [...] Read more.

The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, plant defense against various stresses and cell morphology. R2R3 MYB TFs contained a conserved N-terminal domain, but the domain at C-terminal sorts them different regarding their structures and functions. MYB TFs suppressors generally possess particular repressive motifs, such as pdLNLD/ELxiG/S and TLLLFR, which contribute to their suppression role through a diversity of complex regulatory mechanisms. A novel flower specific “NF/YWSV/MEDF/LW” conserved motif has a great potential to understand the mechanisms of flower development. In the current review, we summarize recent advanced progress of MYB TFs on transcription regulation, posttranscriptional, microRNA, conserved motif and propose directions to future prospective research. We further suggest there should be more focus on the investigation for the role of MYB TFs in microalgae, which has great potential for heterologous protein expression system for future perspectives. Full article

(This article belongs to the Special Issue Genetics of Plant Metabolism)

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