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18 pages, 5891 KiB

Open AccessArticle

Genome-Wide Identification of NRT Gene Family and Expression Analysis of Nitrate Transporters in Response to Salt Stress in Poncirus trifoliata

by Zeqi Zhao, Mengdi Li, Weiwei Xu, Ji-Hong Liu and Chunlong Li

Genes 2022, 13(7), 1115; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13071115 - 22 Jun 2022

Cited by 8 | Viewed by 2382

Abstract

The uptake and transportation of nitrate play a crucial role in plant growth and development. These processes mostly depend on nitrate transporters (NRT), which guarantee the supplement of nutrition in the plant. In this study, genes encoding NRT with Major Facilitator Superfamily (MFS) [...] Read more.

The uptake and transportation of nitrate play a crucial role in plant growth and development. These processes mostly depend on nitrate transporters (NRT), which guarantee the supplement of nutrition in the plant. In this study, genes encoding NRT with Major Facilitator Superfamily (MFS) domain were identified in trifoliate orange (Poncirus trifoliata (L.) Raf.). Totally, 56 NRT1s, 6 NRT2s, and 2 NAR2s were explored. The bioinformation analysis, including protein characteristics, conserved domain, motif, phylogenetic relationship, cis-acting element, and synteny correlation, indicated the evolutionary conservation and functional diversity of NRT genes. Additionally, expression profiles of PtrNRTs in different tissues demonstrated that NRT genes possessed spatio-temporal expression specificity. Further, the salt condition was certified to induce the expression of some NRT members, like PtrNPF2.1, PtrNPF7.4, and PtrNAR2.1, proposing the potential role of these NRTs in salt stress response. The identification of NRT genes and the expression pattern analysis in various tissues and salt stress lay a foundation for future research between nitrogen transport and salt resistance in P. trifoliata. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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16 pages, 3997 KiB

Open AccessArticle

Genome-Wide Analysis of the GDSL Genes in Pecan (Carya illinoensis K. Koch): Phylogeny, Structure, Promoter Cis-Elements, Co-Expression Networks, and Response to Salt Stresses

by Yun Jiao, Jianhong Zhang and Cunde Pan

Genes 2022, 13(7), 1103; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13071103 - 21 Jun 2022

Cited by 6 | Viewed by 1738

Abstract

The Gly-Asp-Ser-Leu (GDSL)-lipase family is a large subfamily of lipolytic enzymes that plays an important role in plant growth and defense against environmental stress. However, little is known about their function in pecans (Carya illinoensis K. Koch). In this study, 87 CilGDSL [...] Read more.

The Gly-Asp-Ser-Leu (GDSL)-lipase family is a large subfamily of lipolytic enzymes that plays an important role in plant growth and defense against environmental stress. However, little is known about their function in pecans (Carya illinoensis K. Koch). In this study, 87 CilGDSLs were identified and divided into 2 groups and 12 subgroups using phylogenetic analysis; members of the same sub-branch had conserved gene structure and motif composition. The majority of the genes had four introns and were composed of an α-helix and a β-strand. Subcellular localization analysis revealed that these genes were localized in the extracellular matrix, chloroplasts, cytoplasm, nucleus, vacuole, and endoplasmic reticulum, and were validated by transient expression in tobacco mesophyll cells. Furthermore, the analysis of the promoter cis-elements for the CilGDSLs revealed the presence of plant anaerobic induction regulatory, abscisic acid response, light response elements, jasmonic acid (JA) response elements, etc. The qRT-PCR analysis results in “Pawnee” with salt treatment showed that the CilGDSL42.93 (leaf) and CilGDSL39.88 (root) were highly expressed in different tissues. After salt stress treatment, isobaric tags for relative and absolute quantitation (iTRAQ) analysis revealed the presence of a total of ten GDSL proteins. Moreover, the weighted gene co-expression network analysis (WGCNA) showed that one set of co-expressed genes (module), primarily CilGDSL41.11, CilGDSL39.49, CilGDSL34.85, and CilGDSL41.01, was significantly associated with salt stress in leaf. In short, some of them were shown to be involved in plant defense against salt stress in this study. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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17 pages, 5673 KiB

Open AccessArticle

Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses

by Ying Qin, Haixia Yu, Siyuan Cheng, Zhu Liu, Cheng Yu, Xiaoli Zhang, Xinjian Su, Jingwen Huang, Shuting Shi, Yangjun Zou, Fengwang Ma and Xiaoqing Gong

Genes 2022, 13(6), 1068; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13061068 - 15 Jun 2022

Cited by 12 | Viewed by 2227

Abstract

The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, [...] Read more.

The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, motif and collinearity analysis. MdWRKYs are expressed in different tissues, such as seeds, flowers, stems and leaves. We analyzed seven WRKY proteins in different groups and found that all of them were localized in the nucleus. Among the 113 MdWRKYs, MdWRKY70L was induced by both drought and salt stresses. Overexpression of it in transgenic tobacco plants conferred enhanced stress tolerance to drought and salt. The malondialdehyde content and relative electrolyte leakage values were lower, while the chlorophyll content was higher in transgenic plants than in the wild-type under stressed conditions. In conclusion, this study identified the WRKY members in the apple genome GDDH13, and revealed the function of MdWRKY70L in the response to drought and salt stresses. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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18 pages, 8610 KiB

Open AccessArticle

Transcriptome Analysis Reveals Roles of Sucrose in Anthocyanin Accumulation in ‘Kuerle Xiangli’ (Pyrus sinkiangensis Yü)

by Xiangzhan Zhang, Bo Li, Ruiwei Duan, Chunhong Han, Lei Wang, Jian Yang, Long Wang, Suke Wang, Yanli Su and Huabai Xue

Genes 2022, 13(6), 1064; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13061064 - 14 Jun 2022

Cited by 5 | Viewed by 1849

Abstract

Pear (Pyrus L.) is one of the most important temperate fruit crops worldwide, with considerable economic value and significant health benefits. Red-skinned pears have an attractive appearance and relatively high anthocyanin accumulation, and are especially favored by customers. Abnormal weather conditions usually [...] Read more.

Pear (Pyrus L.) is one of the most important temperate fruit crops worldwide, with considerable economic value and significant health benefits. Red-skinned pears have an attractive appearance and relatively high anthocyanin accumulation, and are especially favored by customers. Abnormal weather conditions usually reduce the coloration of red pears. The application of exogenous sucrose obviously promotes anthocyanins accumulation in ‘Kuerle Xiangli’ (Pyrus sinkiangensis Yü); however, the underlying molecular mechanism of sucrose-mediated fruit coloration remains largely unknown. In this study, comprehensive transcriptome analysis was performed to identify the essential regulators and pathways associated with anthocyanin accumulation. The differentially expressed genes enriched in Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes items were analyzed. The transcript levels of some anthocyanin biosynthetic regulatory genes and structural genes were significantly induced by sucrose treatment. Sucrose application also stimulated the expression of some sugar transporter genes. Further RT-qPCR analysis confirmed the induction of anthocyanin biosynthetic genes. Taken together, the results revealed that sucrose promotes pear coloration most likely by regulating sugar metabolism and anthocyanin biosynthesis, and this study provides a comprehensive understanding of the complex molecular mechanisms underlying the coloration of red-skinned pear. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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19 pages, 9119 KiB

Open AccessArticle

Sorbitol Reduces Sensitivity to Alternaria by Promoting Ceramide Kinases (CERK) Expression through Transcription Factor Pswrky25 in Populus (Populus simonii Carr.)

by Meng Qi, Rui Wu, Zhihua Song, Biying Dong, Ting Chen, Mengying Wang, Hongyan Cao, Tingting Du, Shengjie Wang, Na Li, Qing Yang, Yujie Fu and Dong Meng

Genes 2022, 13(3), 405; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030405 - 24 Feb 2022

Cited by 5 | Viewed by 1950

Abstract

Sugar, acting as a signal, can regulate the production of some chemical substance during plant defense responses. However, the molecular basis and regulatory mechanisms of sugar in poplar and other forest trees are still unclear. Sorbitol is a sugar-signaling molecule associated with plant [...] Read more.

Sugar, acting as a signal, can regulate the production of some chemical substance during plant defense responses. However, the molecular basis and regulatory mechanisms of sugar in poplar and other forest trees are still unclear. Sorbitol is a sugar-signaling molecule associated with plant defense. In this study, the pathogen-infested status of poplar was alleviated after exogenous feeding of 50 mM sorbitol. We sequenced and analyzed the transcriptome of poplar leaves before and after inoculation. The results showed that the genes PR1, WRKY, ceramide kinases (CERK) and so on responded to sorbitol feeding and pathogen infestation. We screened for genes related to disease resistance such as PsWRKY25 and PsCERK1 and found that significant disease spots occurred on day six of strep throat infestation. Under sorbitol feeding conditions, the appearance of spots was delayed after the pathogen inoculation. Due to the overexpression of PsWRKY25, the overexpression of PsCERK1 triggered the defense response in poplar. This was also confirmed by PsWRKY25 overexpression experiments. These findings present new insights into the influence of sorbitol on Populus simonii Carr. disease resistance. These results emphasize the value of molecular phenotypes in predicting physiological changes. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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12 pages, 3292 KiB

Open AccessArticle

Chitinase Chi 2 Positively Regulates Cucumber Resistance against Fusarium oxysporum f. sp. cucumerinum

by Jun Xu, Ningyuan Zhang, Ke Wang, Qianqian Xian, Jingping Dong, Xiaohua Qi and Xuehao Chen

Genes 2022, 13(1), 62; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010062 - 27 Dec 2021

Cited by 6 | Viewed by 2575

Abstract

Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide, and Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), severely restricts cucumber growth and yield. Accumulating lines of evidence indicate that chitinases play important roles in attacking [...] Read more.

Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide, and Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), severely restricts cucumber growth and yield. Accumulating lines of evidence indicate that chitinases play important roles in attacking the invading fungal pathogens through catalyzing their cell wall degradation. Here, we identified the chitinase (Chi) genes in cucumber and further screened the FW-responsive genes via a comparative transcriptome analysis and found that six common genes were predominantly expressed in roots but also significantly upregulated after Foc infection. Expression verification further conformed that Chi2 and Chi14 were obviously induced by Foc as well as by hormone treatments, compared with the controls. The purified Chi2 and Chi14 proteins significantly affected the growth of Foc in vitro, compared with the controls. Knockdown of Chi2 in cucumber by virus-induced gene silencing (VIGS) increased susceptibility to FW, compared with the Chi14-silenced and control plants, and silencing of Chi2 drastically impaired gene activation in the jasmonic acid pathway, suggesting that the Chi2 gene might play positive roles in cucumber FW defense and, therefore, can provide a gene resource for developing cucumber-FW-resistance breeding programs. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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15 pages, 2742 KiB

Open AccessArticle

Polyamines Involved in Regulating Self-Incompatibility in Apple

by Jie Yu, Baoan Wang, Wenqi Fan, Songbo Fan, Ya Xu, Chunsheng Liu, Tianxing Lv, Wanda Liu, Ling Wu, Linfeng Xian and Tianzhong Li

Genes 2021, 12(11), 1797; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111797 - 15 Nov 2021

Cited by 7 | Viewed by 2384

Abstract

Apple exhibits typical gametophytic self-incompatibility, in which self-S-RNase can arrest pollen tube growth, leading to failure of fertilization. To date, there have been few studies on how to resist the toxicity of self-S-RNase. In this study, pollen tube polyamines were found to respond [...] Read more.

Apple exhibits typical gametophytic self-incompatibility, in which self-S-RNase can arrest pollen tube growth, leading to failure of fertilization. To date, there have been few studies on how to resist the toxicity of self-S-RNase. In this study, pollen tube polyamines were found to respond to self-S-RNase and help pollen tubes defend against self-S-RNase. In particular, the contents of putrescine, spermidine, and spermine in the pollen tube treated with self-S-RNase were substantially lower than those treated with non-self-S-RNase. Further analysis of gene expression of key enzymes in the synthesis and degradation pathways of polyamines found that the expression of DIAMINE OXIDASE 4 (MdDAO4) as well as several polyamine oxidases such as POLYAMINE OXIDASES 3 (MdPAO3), POLYAMINE OXIDASES 4 (MdPAO4), and POLYAMINE OXIDASES 6 (MdPAO6) were significantly up-regulated under self-S-RNase treatment, resulting in the reduction of polyamines. Silencing MdPAO6 in pollen tubes alleviates the inhibitory effect of self-S-RNase on pollen tube growth. In addition, exogenous polyamines also enhance pollen tube resistance to self-S-RNase. Transcriptome sequencing data found that polyamines may communicate with S-RNase through the calcium signal pathway, thereby regulating the growth of the pollen tubes. To summarize, our results suggested that polyamines responded to the self-incompatibility reaction and could enhance pollen tube tolerance to S-RNase, thus providing a potential way to break self-incompatibility in apple. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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12 pages, 2155 KiB

Open AccessArticle

Identification of Susceptibility Genes for Fusarium oxysporum in Cucumber via Comparative Proteomic Analysis

by Jun Xu, Ke Wang, Qianqian Xian, Ningyuan Zhang, Jingping Dong and Xuehao Chen

Genes 2021, 12(11), 1781; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111781 - 10 Nov 2021

Cited by 3 | Viewed by 1901

Abstract

Fusarium wilt (FW) in cucumber (Cucumis sativus L.), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), poses a major threat to cucumber growth and productivity. However, lack of available natural resistance resources for FW restricts the breeding of resistant cultivars [...] Read more.

Fusarium wilt (FW) in cucumber (Cucumis sativus L.), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), poses a major threat to cucumber growth and productivity. However, lack of available natural resistance resources for FW restricts the breeding of resistant cultivars via conventional approaches. Susceptibility (S) genes in susceptible host plants facilitate infection by the pathogen and contribute to susceptibility. Loss of function of these S genes might provide broad-spectrum and durable disease resistance. Here, we screened S genes via comparative proteomic analysis between cucumber cultivars Rijiecheng and Superina, which exhibited resistance and high -susceptibility to FW, respectively. We identified 210 and 243 differentially regulated proteins (DRPs) in the Rijiecheng and Superina, respectively, and further found that 32 DRPs were predominantly expressed in Superina and significantly up-regulated after Foc inoculation. Expression verification found that TMEM115 (CsaV3_5G025750), encoding a transmembrane protein, TET8 (CsaV3_2G007840), encoding function as a tetraspanin, TPS10 (CsaV3_2G017980) encoding a terpene synthase, and MGT2 (CsaV3_7G006660), encoding a glycosyltransferase, were significantly induced in both cultivars after Foc infection but were induced to a higher expression level in Superina. These candidate genes might act as negative regulators of FW resistance in cucumber and provide effective FW-susceptibility gene resources for improving cucumber FW resistance through breeding programs. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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14 pages, 3571 KiB

Open AccessArticle

Genome-Wide Analysis of the Glutathione S-Transferase (GST) Genes and Functional Identification of MdGSTU12 Reveals the Involvement in the Regulation of Anthocyanin Accumulation in Apple

by Yu-Wen Zhao, Chu-Kun Wang, Xiao-Yu Huang and Da-Gang Hu

Genes 2021, 12(11), 1733; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111733 - 29 Oct 2021

Cited by 17 | Viewed by 2305

Abstract

Anthocyanins have essential biological functions, affecting the development of horticultural production. They are synthesized in the cytoplasm through flavonoid metabolic pathways and finally transported into vacuoles for storage. Plant glutathione S-transferases (GSTs) are multifunctional enzymes involved in anthocyanin transportation. In this study, we [...] Read more.

Anthocyanins have essential biological functions, affecting the development of horticultural production. They are synthesized in the cytoplasm through flavonoid metabolic pathways and finally transported into vacuoles for storage. Plant glutathione S-transferases (GSTs) are multifunctional enzymes involved in anthocyanin transportation. In this study, we identified 38 GSTs from the apple (Malus domestica) genome (HFTH1 Whole Genome v1.0) based on the sequence similarity with the GST family proteins of Arabidopsis. These MdGST genes could be grouped into nine chief subclasses: U, F, L, Z, T, GHR, EF1Bγ, TCHQD, and DHAR. The structures, motifs, three-dimensional models, and chromosomal distribution of MdGST genes were further analyzed. Elements which are responsive for some hormones and stress, and others that involve genes related to flavonoid biosynthesis were forecast in the promoter of MdGST. In addition, we identified 32 orthologous gene pairs between apple and Arabidopsis. These genes indicated that numerous apple and Arabidopsis counterparts appeared to be derived from a common ancestor. Amongst the 38 MdGST genes, MdGSTU12 was considerably correlated with anthocyanin variation in terms of extracting expression profiles from reported. Finally, further functional identification in apple transgenic calli and subcellular localization confirmed that MdGSTU12 was of great significance in anthocyanin accumulation in apple. Full article

(This article belongs to the Special Issue Frontiers in Horticultural Genetics and Breeding)

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