Genes

Research

15 pages, 2412 KiB

Open AccessCommunication

Hydropriming and Biopriming Improve Medicago truncatula Seed Germination and Upregulate DNA Repair and Antioxidant Genes

by Chiara Forti, Ajay Shankar, Anjali Singh, Alma Balestrazzi, Vishal Prasad and Anca Macovei

Genes 2020, 11(3), 242; https://doi.org/10.3390/genes11030242 - 25 Feb 2020

Cited by 45 | Viewed by 3883

Abstract

Seed germination is a critical parameter for the successful development of sustainable agricultural practices. While seed germination is impaired by environmental constraints emerging from the climate change scenario, several types of simple procedures, known as priming, can be used to enhance it. Seed [...] Read more.

Seed germination is a critical parameter for the successful development of sustainable agricultural practices. While seed germination is impaired by environmental constraints emerging from the climate change scenario, several types of simple procedures, known as priming, can be used to enhance it. Seed priming is defined as the process of regulating seed germination by managing a series of parameters during the initial stages of germination. Hydropriming is a highly accessible and economic technique that involves soaking of seeds in water followed by drying. Biopriming refers to the inoculation of seeds with beneficial microorganism. The present study aims to investigate whether hydropriming and biopriming could enhance seed germination. Thereby, the germination of Medicago truncatula seeds exposed to hydropriming and/or Bacillus spp. isolates was monitored for two-weeks. The seeds were sown in trays containing two types of in situ agricultural soils collected from Northern India (Karsara, Varanasi). This region is believed to be contaminated by solid waste from a nearby power plant. Phenotypic parameters had been monitored and compared to find the most appropriate combination of treatments. Additionally, qRT-PCR was used to evaluate the expression levels of specific genes used as molecular indicators of seed quality. The results show that, while hydropriming significantly enhanced seed germination percentage, biopriming resulted in improved seedling development, represented by increased biomass rather than seedling length. At a molecular level, this is reflected by the upregulation of genes involved in DNA damage repair and antioxidant defence. In conclusion, hydropriming and biopriming are efficient to improve seed germination and seedling establishment in soils collected from damaged sites of Northern India; this is reflected by morphological parameters and molecular hallmarks of seed quality. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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19 pages, 3063 KiB

Open AccessArticle

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

by Karina B. Ruiz, Jonathan Maldonado, Stefania Biondi and Herman Silva

Genes 2019, 10(12), 1042; https://doi.org/10.3390/genes10121042 - 16 Dec 2019

Cited by 17 | Viewed by 4016

Abstract

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity [...] Read more.

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a “stress-anticipatory preparedness” in this highly salt-tolerant genotype. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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27 pages, 5264 KiB

Open AccessArticle

Transcriptome Profiling, Biochemical and Physiological Analyses Provide New Insights towards Drought Tolerance in Nicotiana tabacum L.

by Rayyan Khan, Peilu Zhou, Xinghua Ma, Lei Zhou, Yuanhua Wu, Zia Ullah and Shusheng Wang

Genes 2019, 10(12), 1041; https://doi.org/10.3390/genes10121041 - 15 Dec 2019

Cited by 22 | Viewed by 4306

Abstract

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a [...] Read more.

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a comprehensive physiological, anatomical, biochemical and transcriptome analyses of three tobacco cultivars (i.e., HongHuaDaJinYuan (H), NC55 (N) and Yun Yan-100 (Y)) seedlings that had been exposed to drought stress. As a result, H maintained higher growth in term of less reduction in plant fresh weight, dry weight and chlorophyll content as compared with N and Y. Anatomical studies unveiled that drought stress had little effect on H by maintaining proper leaf anatomy while there were significant changes in the leaf anatomy of N and Y. Similarly, H among the three varieties was the least affected variety under drought stress, with more proline content accumulation and a powerful antioxidant defense system, which mitigates the negative impacts of reactive oxygen species. The transcriptomic analysis showed that the differential genes expression between HongHuaDaJinYuan, NC55 and Yun Yan-100 were enriched in the functions of plant hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism. Compared to N and Y, the differentially expressed genes of H displayed enhanced expression in the corresponding pathways under drought stress. Together, our findings offer insights that H was more tolerant than the other two varieties, as evidenced at physiological, biochemical, anatomical and molecular level. These findings can help us to enhance our understanding of the molecular mechanisms through the networks of various metabolic pathways mediating drought stress adaptation in tobacco. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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22 pages, 3733 KiB

Open AccessArticle

Transcriptomic Profiling Identifies Candidate Genes Involved in the Salt Tolerance of the Xerophyte Pugionium cornutum

by Yan-Nong Cui, Fang-Zhen Wang, Cheng-Hang Yang, Jian-Zhen Yuan, Huan Guo, Jin-Lin Zhang, Suo-Min Wang and Qing Ma

Genes 2019, 10(12), 1039; https://doi.org/10.3390/genes10121039 - 12 Dec 2019

Cited by 13 | Viewed by 2533

Abstract

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl⁻) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could [...] Read more.

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl⁻) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could also maintain cell membrane stability due to its prominent ROS-scavenging ability and exhibits efficient carbon assimilation capacity under salt stress. Then, the candidate genes associated with the important physiological traits of the salt tolerance of P. cornutum were identified through transcriptomic analysis. The results showed that after 50 mM NaCl treatment for 6 or 24 h, multiple genes encoding proteins facilitating Cl⁻ accumulation and NO₃⁻ homeostasis, as well as the transport of other major inorganic osmoticums, were significantly upregulated in roots and shoots, which should be favorable for enhancing osmotic adjustment capacity and maintaining the uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which might be beneficial for mitigating salt-induced oxidative damage to the cells. Meanwhile, many genes encoding components of the photosynthetic electron transport pathway and carbon fixation enzymes were significantly upregulated in shoots, possibly resulting in high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes that probably regulate the abovementioned processes were found. This work lays a preliminary foundation for clarifying the molecular mechanism underlying the adaptation of xerophytes to harsh environments. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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27 pages, 3190 KiB

Open AccessArticle

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

by Zakhar S. Mustafin, Vladimir I. Zamyatin, Dmitrii K. Konstantinov, Aleksej V. Doroshkov, Sergey A. Lashin and Dmitry A. Afonnikov

Genes 2019, 10(12), 963; https://doi.org/10.3390/genes10120963 - 22 Nov 2019

Cited by 8 | Viewed by 3205

Abstract

Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress [...] Read more.

Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution. The study of the network structure and evolution may highlight mechanisms of plants adaptation to adverse conditions, as well as their response to stresses and help in discovery and functional characterization of the stress-related genes. We performed an analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) at the network level using a phylostratigraphic approach. Our results show that a substantial fraction of genes associated with various types of abiotic stress is of ancient origin and evolves under strong purifying selection. The interaction networks of genes associated with stress response have a modular structure with a regulatory component being one of the largest for five of seven stress types. We demonstrated a positive relationship between the number of interactions of gene in the stress gene network and its age. Moreover, genes of the same age tend to be connected in stress gene networks. We also demonstrated that old stress-related genes usually participate in the response for various types of stress and are involved in numerous biological processes unrelated to stress. Our results demonstrate that the stress response genes represent the ancient and one of the fundamental molecular systems in plants. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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18 pages, 4291 KiB

Open AccessArticle

Comparative Physiological and Transcriptomic Analyses Reveal Mechanisms of Improved Osmotic Stress Tolerance in Annual Ryegrass by Exogenous Chitosan

by Junming Zhao, Ling Pan, Man Zhou, Zhongfu Yang, Yu Meng and Xinquan Zhang

Genes 2019, 10(11), 853; https://doi.org/10.3390/genes10110853 - 28 Oct 2019

Cited by 17 | Viewed by 2954

Abstract

Water deficit adversely affects the growth and productivity of annual ryegrass (Lolium multiflorum Lam.). The exogenous application of chitosan (CTS) has gained extensive interests due to its effect on improving drought resistance. This research aimed to determine the role of exogenous CTS [...] Read more.

Water deficit adversely affects the growth and productivity of annual ryegrass (Lolium multiflorum Lam.). The exogenous application of chitosan (CTS) has gained extensive interests due to its effect on improving drought resistance. This research aimed to determine the role of exogenous CTS on annual ryegrass in response to water stress. Here, we investigated the impact of exogenous CTS on the physiological responses and transcriptome changes of annual ryegrass variety “Tetragold” under osmotic stress induced by exposing them to 20% polyethylene glycol (PEG)-6000. Our experimental results demonstrated that 50 mg/L exogenous CTS had the optimal effect on promoting seed germination under osmotic stress. Pre-treatment of annual ryegrass seedlings with 500 mg/L CTS solution reduced the level of electrolyte leakage (EL) as well as the contents of malondialdehyde (MDA) and proline and enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) under osmotic stress. In addition, CTS increased soluble sugars and chlorophyll (Chl) content, net photosynthetic rate (A), stomatal conductance (gs), water use efficiency (WUE), and transpiration rate (E) in annual ryegrass seedlings in response to three and six days of osmotic stress. Transcriptome analysis further provided a comprehensive understanding of underlying molecular mechanisms of CTS impact. To be more specific, in contrast of non-treated seedlings, the distinct changes of gene expressions of CTS-treated seedlings were shown to be tightly related to carbon metabolism, photosynthesis, and plant hormone. Altogether, exogenous CTS could elicit drought-related genes in annual ryegrass, leading to resistance to osmotic stress via producing antioxidant enzymes and maintaining intact cell membranes and photosynthetic rates. This robust evidence supports the potential of the application of exogenous CTS, which will be helpful for determining the suitability and productivity of agricultural crops. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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22 pages, 7131 KiB

Open AccessArticle

Transcriptomic Revelation of Phenolic Compounds Involved in Aluminum Toxicity Responses in Roots of Cunninghamia lanceolata (Lamb.) Hook

by Zhihui Ma and Sizu Lin

Genes 2019, 10(11), 835; https://doi.org/10.3390/genes10110835 - 23 Oct 2019

Cited by 12 | Viewed by 2470

Abstract

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is one of the most important coniferous evergreen tree species in South China due to its desirable attributes of fast growth and production of strong and hardy wood. However, the yield of Chinese fir is often [...] Read more.

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is one of the most important coniferous evergreen tree species in South China due to its desirable attributes of fast growth and production of strong and hardy wood. However, the yield of Chinese fir is often inhibited by aluminum (Al) toxicity in acidic soils of South China. Understanding the molecular mechanisms of Chinese fir root responses to Al toxicity might help to further increase its productivity. Here we used the Illumina Hiseq4000 platform to carry out transcriptome analysis of Chinese fir roots subjected to Al toxicity conditions. A total of 88.88 Gb of clean data was generated from 12 samples and assembled into 105,732 distinct unigenes. The average length and N50 length of these unigenes were 839 bp and 1411 bp, respectively. Among them, 58362 unigenes were annotated through searches of five public databases (Nr: NCBI non-redundant protein sequences, Swiss-Prot: A manually annotated and reviewed protein sequence database, GO: Gene Ontology, KOG/COG: Clusters of Orthologous Groups of proteins, and KEGG: the Kyoto Encyclopedia of Genes and Genomes database), which led to association of unigenes with 44 GO terms. Plus, 1615 transcription factors (TFs) were functionally classified. Then, differentially expressed genes (DEGs, |log₂(fold change)| ≥ 1 and FDR ≤ 0.05) were identified in comparisons labelled TC1 (CK-72 h/CK-1 h) and TC2 (Al-72 h/Al-1 h). A large number of TC2 DEGs group were identified, with most being down-regulated under Al stress, while TC1 DEGs were primarily up-regulated. Combining GO, KEGG, and MapMan pathway analysis indicated that many DEGs are involved in primary metabolism, including cell wall metabolism and lipid metabolism, while other DEGs are associated with signaling pathways and secondary metabolism, including flavonoids and phenylpropanoids metabolism. Furthermore, TFs identified in TC1 and TC2 DEGs represented 21 and 40 transcription factor families, respectively. Among them, expression of bHLH, C2H2, ERF, bZIP, GRAS, and MYB TFs changed considerably under Al stress, which suggests that these TFs might play crucial roles in Chinese fir root responses to Al toxicity. These differentially expressed TFs might act in concert with flavonoid and phenylpropanoid pathway genes in fulfilling of key roles in Chinese fir roots responding to Al toxicity. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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13 pages, 1518 KiB

Open AccessArticle

Overexpression of OsPT8 Increases Auxin Content and Enhances Tolerance to High-Temperature Stress in Nicotiana tabacum

by Zhaopeng Song, Ningbo Fan, Guizhen Jiao, Minghong Liu, Xiaoyan Wang and Hongfang Jia

Genes 2019, 10(10), 809; https://doi.org/10.3390/genes10100809 - 14 Oct 2019

Cited by 14 | Viewed by 3310

Abstract

Temperature is a primary factor affecting the rate of plant development; as the climate warms, extreme temperature events are likely to increasingly affect agriculture. Understanding how to improve crop tolerance to heat stress is a key concern. Wild plants have evolved numerous strategies [...] Read more.

Temperature is a primary factor affecting the rate of plant development; as the climate warms, extreme temperature events are likely to increasingly affect agriculture. Understanding how to improve crop tolerance to heat stress is a key concern. Wild plants have evolved numerous strategies to tolerate environmental conditions, notably the regulation of root architecture by phytohormones, but the molecular mechanisms of stress resistance are unclear. In this study, we showed that high temperatures could significantly reduce tobacco biomass and change its root architecture, probably through changes in auxin content and distribution. Overexpression of the OsPT8 phosphate transporter enhanced tobacco tolerance to high-temperature stress by changing the root architecture and increased the antioxidant ability. Molecular assays suggested that overexpression of OsPT8 in tobacco significantly increased the expression of auxin synthesis genes NtYUCCA 6, 8 and auxin efflux carriers genes NtPIN 1,2 under high-temperature stress. We also found that the expression levels of auxin response factors NtARF1 and NtARF2 were increased in OsPT8 transgenic tobacco under high-temperature stress, suggesting that OsPT8 regulates auxin signaling in response to high-temperature conditions. Our findings provided new insights into the molecular mechanisms of plant stress signaling and showed that OsPT8 plays a key role in regulating plant tolerance to stress conditions. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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20 pages, 3405 KiB

Open AccessArticle

Overexpression of a Novel Cytochrome P450 Promotes Flavonoid Biosynthesis and Osmotic Stress Tolerance in Transgenic Arabidopsis

by Naveed Ahmad, Liu Jianyu, Tian Xu, Muhammad Noman, Aysha Jameel, Yao Na, Dong Yuanyuan, Wang Nan, Li Xiaowei, Wang Fawei, Liu Xiuming and Li Haiyan

Genes 2019, 10(10), 756; https://doi.org/10.3390/genes10100756 - 26 Sep 2019

Cited by 35 | Viewed by 4492

Abstract

Flavonoids are mainly associated with growth, development, and responses to diverse abiotic stresses in plants. A growing amount of data have demonstrated the biosynthesis of flavonoids through multienzyme complexes of which the membrane-bounded cytochrome P450 supergene family shares a crucial part. However, the [...] Read more.

Flavonoids are mainly associated with growth, development, and responses to diverse abiotic stresses in plants. A growing amount of data have demonstrated the biosynthesis of flavonoids through multienzyme complexes of which the membrane-bounded cytochrome P450 supergene family shares a crucial part. However, the explicit regulation mechanism of Cytochrome P450s related to flavonoid biosynthesis largely remains elusive. In the present study, we reported the identification of a stress-tolerant flavonoid biosynthetic CtCYP82G24 gene from Carthamus tinctorius. The transient transformation of CtCYP82G24 determined the subcellular localization to the cytosol. Heterologously expressed CtCYP82G24 was effective to catalyze the substrate-specific conversion, promoting the de novo biosynthesis of flavonoids in vitro. Furthermore, a qRT-PCR assay and the accumulation of metabolites demonstrated that the expression of CtCYP82G24 was effectively induced by Polyethylene glycol stress in transgenic Arabidopsis. In addition, the overexpression of CtCYP82G24 could also trigger expression levels of several other flavonoid biosynthetic genes in transgenic plants. Taken together, our findings suggest that CtCYP82G24 overexpression plays a decisive regulatory role in PEG-induced osmotic stress tolerance and alleviates flavonoid accumulation in transgenic Arabidopsis. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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24 pages, 2841 KiB

Open AccessArticle

Physiological and Transcriptomic Analysis Reveals Distorted Ion Homeostasis and Responses in the Freshwater Plant Spirodela polyrhiza L. under Salt Stress

by Lili Fu, Zehong Ding, Xuepiao Sun and Jiaming Zhang

Genes 2019, 10(10), 743; https://doi.org/10.3390/genes10100743 - 24 Sep 2019

Cited by 13 | Viewed by 3044

Abstract

Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly [...] Read more.

Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly to their nutrient suppliers (waters), therefore, their responses to salinity may be distinct. In this research, we found that the duckweed Spirodela polyrhiza L. accumulated high content of sodium and reduced potassium and calcium contents in large amounts under salt stress. Fresh weight, Rubisco and AGPase activities, and starch content were significantly decreaseded in the first day but recovered gradually in the following days and accumulated more starch than control from Day 3 to Day 5 when treated with 100 mM and 150 mM NaCl. A total of 2156 differentially expressed genes were identified. Overall, the genes related to ethylene metabolism, major CHO degradation, lipid degradation, N-metabolism, secondary metabolism of flavonoids, and abiotic stress were significantly increased, while those involved in cell cycle and organization, cell wall, mitochondrial electron transport of ATP synthesis, light reaction of photosynthesis, auxin metabolism, and tetrapyrrole synthesis were greatly inhibited. Moreover, salt stress also significantly influenced the expression of transcription factors that are mainly involved in abiotic stress and cell differentiation. However, most of the osmosensing calcium antiporters (OSCA) and the potassium inward channels were downregulated, Na⁺/H⁺ antiporters (SOS1 and NHX) and a Na⁺/Ca²⁺ exchanger were slightly upregulated, but most of them did not respond significantly to salt stress. These results indicated that the ion homeostasis was strongly disturbed. Finally, the shared and distinct regulatory networks of salt stress responses between duckweeds and other plants were intensively discussed. Taken together, these findings provide novel insights into the underlying mechanisms of salt stress response in duckweeds, and can be served as a useful foundation for salt tolerance improvement of duckweeds for the application in salinity conditions. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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17 pages, 3097 KiB

Open AccessArticle

Comparison between the Transcriptomes of ‘KDML105’ Rice and a Salt-Tolerant Chromosome Segment Substitution Line

by Nopphawitchayaphong Khrueasan, Panita Chutimanukul, Kitiporn Plaimas, Teerapong Buaboocha, Meechai Siangliw, Theerayut Toojinda, Luca Comai and Supachitra Chadchawan

Genes 2019, 10(10), 742; https://doi.org/10.3390/genes10100742 - 24 Sep 2019

Cited by 6 | Viewed by 2800

Abstract

‘KDML105’ rice, known as jasmine rice, is grown in northeast Thailand. The soil there has high salinity, which leads to low productivity. Chromosome substitution lines (CSSLs) with the ‘KDML105’ rice genetic background were evaluated for salt tolerance. CSSL18 showed the highest salt tolerance [...] Read more.

‘KDML105’ rice, known as jasmine rice, is grown in northeast Thailand. The soil there has high salinity, which leads to low productivity. Chromosome substitution lines (CSSLs) with the ‘KDML105’ rice genetic background were evaluated for salt tolerance. CSSL18 showed the highest salt tolerance among the four lines tested. Based on a comparison between the CSSL18 and ‘KDML105’ transcriptomes, more than 27,000 genes were mapped onto the rice genome. Gene ontology enrichment of the significantly differentially expressed genes (DEGs) revealed that different mechanisms were involved in the salt stress responses between these lines. Biological process and molecular function enrichment analysis of the DEGs from both lines revealed differences in the two-component signal transduction system, involving LOC_Os04g23890, which encodes phototropin 2 (PHOT2), and LOC_Os07g44330, which encodes pyruvate dehydrogenase kinase (PDK), the enzyme that inhibits pyruvate dehydrogenase in respiration. OsPHOT2 expression was maintained in CSSL18 under salt stress, whereas it was significantly decreased in ‘KDML105’, suggesting OsPHOT2 signaling may be involved in salt tolerance in CSSL18. PDK expression was induced only in ‘KDML105’. These results suggested respiration was more inhibited in ‘KDML105’ than in CSSL18, and this may contribute to the higher salt susceptibility of ‘KDML105’ rice. Moreover, the DEGs between ‘KDML105’ and CSSL18 revealed the enrichment in transcription factors and signaling proteins located on salt-tolerant quantitative trait loci (QTLs) on chromosome 1. Two of them, OsIRO2 and OsMSR2, showed the potential to be involved in salt stress response, especially, OsMSR2, whose orthologous genes in Arabidopsis had the potential role in photosynthesis adaptation under salt stress. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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16 pages, 3614 KiB

Open AccessCommunication

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

by Mingdong Zhu, Hongjun Xie, Xiangjin Wei, Komivi Dossa, Yaying Yu, Suozhen Hui, Guohua Tang, Xiaoshan Zeng, Yinghong Yu, Peisong Hu and Jianlong Wang

Genes 2019, 10(9), 719; https://doi.org/10.3390/genes10090719 - 17 Sep 2019

Cited by 56 | Viewed by 8985

Abstract

Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, [...] Read more.

Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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15 pages, 4719 KiB

Open AccessArticle

Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress

by Shuangcheng Ding, Fengyu He, Wenlin Tang, Hewei Du and Hongwei Wang

Genes 2019, 10(8), 610; https://doi.org/10.3390/genes10080610 - 12 Aug 2019

Cited by 16 | Viewed by 3618

Abstract

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. [...] Read more.

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. We performed a TBLASTN search to identify ZmGRXCCs in the maize genome and verified the identified sequences using the NCBI conservative domain database (CDD). We further established a phylogenetic tree using Mega7 and surveyed known cis-elements in the promoters of ZmGRXCCs using the PlantCARE database. We found twenty-one ZmGRXCCs in the maize genome by a genome-wide investigation and compared their phylogenetic relationships with rice, maize, and Arabidopsis. The analysis of their redox active sites showed that most of the 21 ZmGRXCCs share similar structures with their homologs. We assessed their expression at young seedlings and adult leaves under drought stress and their expression profiles in 15 tissues, and found that they were differentially expressed, indicating that different ZmGRXCC genes have different functions. Notably, ZmGRXCC14 is up-regulated at seedling, V12, V14, V16, and R1 stages. Importantly, significant associations between genetic variation in ZmGRXCC14 and drought tolerance are found at the seedling stage. These results will help to advance the study of the function of ZmGRXCCs genes under drought stress and understand the mechanism of drought resistance in maize. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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21 pages, 4620 KiB

Open AccessArticle

Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut

by Xiaomei Luo and Juncheng Liu

Genes 2019, 10(8), 605; https://doi.org/10.3390/genes10080605 - 10 Aug 2019

Cited by 5 | Viewed by 3631

Abstract

We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH [...] Read more.

We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH 4–5 and pH 5–6 treatments than for the pH 3–4 and pH 6–7 treatments. A total of 2768 differentially expressed genes were detected and categorized into 12 clusters by Short Time-series Expression Miner (STEM). The 994 low-expression genes in cluster III and 255 high-expression genes in cluster X were classified as acid-responsive genes on the basis of the relationships between phenotype, physiology, and STEM clustering, and the two gene clusters were analyzed by a maximum likelihood (ML) evolutionary tree with the greatest log likelihood values. No prominent sub-clusters occurred in cluster III, but three occurred in cluster X. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that acid-responsive genes were related primarily to arginine biosynthesis and the arginine/proline metabolism pathway, implying that polyamine accumulation may enhance iron walnut acid stress tolerance. Overall, our results revealed 1249 potentially acid-responsive genes in iron walnut, indicating that its response to acid stress involves different pathways and activated genes. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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14 pages, 9547 KiB

Open AccessArticle

Potassium Transporter LrKUP8 Is Essential for K⁺ Preservation in Lycium ruthenicum, A Salt-Resistant Desert Shrub

by Fengbin Dai, Aijia Li, Shupei Rao and Jinhuan Chen

Genes 2019, 10(8), 600; https://doi.org/10.3390/genes10080600 - 09 Aug 2019

Cited by 16 | Viewed by 3199

Abstract

Salt stress is a major constraint for many crops and trees. A wild species of Goji named Lycium ruthenicum is an important economic halophyte in China and has an extremely high tolerance to salinity. L. ruthenicum grows in saline soil and is known [...] Read more.

Salt stress is a major constraint for many crops and trees. A wild species of Goji named Lycium ruthenicum is an important economic halophyte in China and has an extremely high tolerance to salinity. L. ruthenicum grows in saline soil and is known as a potash-rich species. However, its salt adaptation strategies and ion balance mechanism remains poorly understood. Potassium (K⁺) is one of the essential macronutrients for plant growth and development. In this study, a putative salt stress-responsive gene encoding a HAK (high-affinity K⁺)/KUP (K⁺ uptake)/KT (K⁺ transporter) transporter was cloned and designated as LrKUP8. This gene belongs to the cluster II group of the KT/HAK/KUP family. The expression of LrKUP8 was strongly induced under high NaCl concentrations. The OE-LrKUP8 calli grew significantly better than the vector control calli under salt stress conditions. Further estimation by ion content and micro-electrode ion flux indicated a relative weaker K⁺ efflux in the OE-LrKUP8 calli than in the control. Thus, a key gene involved in K⁺ uptake under salt condition was functionally characterized using a newly established L. ruthenicum callus transformation system. The importance of K⁺ regulation in L. ruthenicum under salt tolerance was highlighted. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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20 pages, 3206 KiB

Open AccessArticle

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress

by Chakkree Lekklar, Duangjai Suriya-arunroj, Monnat Pongpanich, Luca Comai, Boonthida Kositsup, Supachitra Chadchawan and Teerapong Buaboocha

Genes 2019, 10(8), 562; https://doi.org/10.3390/genes10080562 - 25 Jul 2019

Cited by 17 | Viewed by 4408

Abstract

Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the [...] Read more.

Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (P_N) and intercellular CO₂ concentration (C_i) under salt stress, P_N was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two “high-yield rice” varieties and two “low-yield rice” varieties with contrasting photosynthesis and grain yield characteristics. A total of 2089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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21 pages, 2054 KiB

Open AccessArticle

Complex Gene Regulation Underlying Mineral Nutrient Homeostasis in Soybean Root Response to Acidity Stress

by Qianqian Chen, Weiwei Wu, Tong Zhao, Wenqi Tan, Jiang Tian and Cuiyue Liang

Genes 2019, 10(5), 402; https://doi.org/10.3390/genes10050402 - 27 May 2019

Cited by 9 | Viewed by 3135

Abstract

Proton toxicity is one of the major environmental stresses limiting crop production and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrients accumulation, and global transcriptome changes in soybean (Glycine max) in response [...] Read more.

Proton toxicity is one of the major environmental stresses limiting crop production and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrients accumulation, and global transcriptome changes in soybean (Glycine max) in response to long-term acidity stress were investigated. Results showed that acidity stress significantly inhibited soybean root growth but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acidity stress, mainly differing among soybean organs and mineral nutrient types. Concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N), and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased by acidity stress, respectively. Whereas, concentrations of calcium (Ca), sulfate (S), and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identification of 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrients transportation. Among them, all the detected five GmPTs, four GmZIPs, two GmAMTs, and GmKUPs, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5, and GmHKT1, were significantly down-regulated by acidity stress. Moreover, the transcription of genes encoding transcription factors (e.g., GmSTOP2s) and associated with pH stat metabolic pathways was significantly up-regulated by acidity stress. Taken together, it strongly suggests that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acidity stress, which might be regulated by a complex signaling network. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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16 pages, 2020 KiB

Open AccessArticle

Protein Changes in Response to Lead Stress of Lead-Tolerant and Lead-Sensitive Industrial Hemp Using SWATH Technology

by Cheng Xia, Li Hong, Yang Yang, Xu Yanping, Huang Xing and Deng Gang

Genes 2019, 10(5), 396; https://doi.org/10.3390/genes10050396 - 22 May 2019

Cited by 20 | Viewed by 3322

Abstract

Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) [...] Read more.

Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) technology to study the difference in proteomics between the leaves of Pb-tolerant seed-type hemp variety Bamahuoma (BM) and the Pb-sensitive fiber-type hemp variety Yunma 1 (Y1) under Pb stress (3 g/kg soil). A total of 63 and 372 proteins differentially expressed under Pb stress relative to control conditions were identified with liquid chromatography electro spray ionization tandem mass spectrometry in BM and Y1, respectively; with each of these proteins being classified into 14 categories. Hemp adapted to Pb stress by: accelerating adenosine triphosphate (ATP) metabolism; enhancing respiration, light absorption and light energy transfer; promoting assimilation of intercellular nitrogen (N) and carbon (C); eliminating reactive oxygen species; regulating stomatal development and closure; improving exchange of water and CO₂ in leaves; promoting intercellular transport; preventing aggregation of unfolded proteins; degrading misfolded proteins; and increasing the transmembrane transport of ATP in chloroplasts. Our results provide an important reference protein and gene information for future molecular studies into the resistance and accumulation of Pb in hemp. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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