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19 pages, 5499 KiB

Open AccessFeature PaperArticle

Transcriptome Analysis of Fusarium Root-Rot-Resistant and -Susceptible Alfalfa (Medicago sativa L.) Plants during Plant–Pathogen Interactions

by Wenyu Zhang, Zicheng Wang, Zhencuo Dan, Lixia Zhang, Ming Xu, Guofeng Yang, Maofeng Chai, Zhenyi Li, Hongli Xie and Lili Cong

Genes 2022, 13(5), 788; https://doi.org/10.3390/genes13050788 - 28 Apr 2022

Cited by 16 | Viewed by 3426

Abstract

Alfalfa (Medicago sativa L.) is a perennial leguminous forage cultivated globally. Fusarium spp.-induced root rot is a chronic and devastating disease affecting alfalfa that occurs in most production fields. Studying the disease resistance regulatory network and investigating the key genes involved in [...] Read more.

Alfalfa (Medicago sativa L.) is a perennial leguminous forage cultivated globally. Fusarium spp.-induced root rot is a chronic and devastating disease affecting alfalfa that occurs in most production fields. Studying the disease resistance regulatory network and investigating the key genes involved in plant–pathogen resistance can provide vital information for breeding alfalfa that are resistant to Fusarium spp. In this study, a resistant and susceptible clonal line of alfalfa was inoculated with Fusarium proliferatum L1 and sampled at 24 h, 48 h, 72 h, and 7 d post-inoculation for RNA-seq analysis. Among the differentially expressed genes (DEGs) detected between the two clonal lines at the four time points after inoculation, approximately 81.8% were detected at 24 h and 7 d after inoculation. Many DEGs in the two inoculated clonal lines participated in PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) mechanisms. In addition, transcription factor families such as bHLH, SBP, AP2, WRKY, and MYB were detected in response to infection. These results are an important supplement to the few existing studies on the resistance regulatory network of alfalfa against Fusarium root rot and will help to understand the evolution of host–pathogen interactions. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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18 pages, 4612 KiB

Open AccessArticle

Molecular Characterization of the miR156/MsSPL Model in Regulating the Compound Leaf Development and Abiotic Stress Response in Alfalfa

by Xueyang Min, Kai Luo, Wenxian Liu, Keyou Zhou, Junyi Li and Zhenwu Wei

Genes 2022, 13(2), 331; https://doi.org/10.3390/genes13020331 - 10 Feb 2022

Cited by 9 | Viewed by 2396

Abstract

Plant leaf patterns and shapes are spectacularly diverse. Changing the complexity of leaflet numbers is a valuable approach to increase its nutrition and photosynthesis. Alfalfa (Medicago sativa) is the most important forage legume species and has diversified compound leaf patterns, which [...] Read more.

Plant leaf patterns and shapes are spectacularly diverse. Changing the complexity of leaflet numbers is a valuable approach to increase its nutrition and photosynthesis. Alfalfa (Medicago sativa) is the most important forage legume species and has diversified compound leaf patterns, which makes it a model species for studying compound leaf development. However, transcriptomic information from alfalfa remains limited. In this study, RNA-Seq technology was used to identify 3746 differentially expressed genes (DEGs) between multifoliate and trifoliate alfalfa. Through an analysis of annotation information and expression data, SPL, one of the key regulators in modifiable plant development and abiotic stress response, was further analyzed. Here, thirty MsSPL genes were obtained from the alfalfa genome, of which 16 had the putative miR156 binding site. A tissue expression pattern analysis showed that the miR156-targeted MsSPLs were divided into two classes, namely, either tissue-specific or widely expressed in all tissues. All miR156-targeted SPLs strongly showed diversification and positive roles under drought and salt conditions. Importantly, miR156/MsSPL08 was significantly suppressed in multifoliate alfalfa. Furthermore, in the paralogous mutant of MsSPL08 isolated from Medicago truncatula, the phenotypes of mutant plants reveal that miR156/MsSPL08 is involved not only involved the branches but also especially regulates the number of leaflets. The legume is a typical compound leaf plant; the ratio of the leaflet often affects the quality of the forage. This study sheds light on new functions of SPL genes that regulate leaflet number development. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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17 pages, 7896 KiB

Open AccessArticle

MtWRP1, a Novel Fabacean Specific Gene, Regulates Root Nodulation and Plant Growth in Medicago truncatula

by Wei Chen, Yingjun Chi, Jinglong Zhang, Binqiang Bai, Xiaomin Ji and Yixin Shen

Genes 2022, 13(2), 193; https://doi.org/10.3390/genes13020193 - 22 Jan 2022

Viewed by 2522

Abstract

Fabaceans symbiotically interact with nitrogen-fixing rhizobacteria to form root nodules. Some fabacean specific proteins play important roles in the symbiosis. WRKY-related Protein (WRP) is a novel fabacean specific protein, whose functions have not been well characterized. In this study, MtWRP1 was functionally characterized [...] Read more.

Fabaceans symbiotically interact with nitrogen-fixing rhizobacteria to form root nodules. Some fabacean specific proteins play important roles in the symbiosis. WRKY-related Protein (WRP) is a novel fabacean specific protein, whose functions have not been well characterized. In this study, MtWRP1 was functionally characterized in Medicago truncatula. It contains a WRKY domain at C-terminal and a novel transmembrane (TM) domain at N-terminal, and its WRKY domain was highly similar to the N-terminal WRKY domain of the group I WRKY proteins. The TM domain was highly homologous to the eukaryotic cytochrome b561 (Cytb561) proteins from birds. Subcellular localization revealed that MtWRP1 was targeted to the Golgi apparatus through the novel TM domain. MtWRP1 was highly expressed in roots and nodules, suggesting its possible roles in the regulation of root growth and nodulation. Both MtWRP1-overexpression transgenic M. truncatula and MtWRP1 mutants showed altered root nodulation and plant growth performance. Specifically, the formation of root nodules was significantly reduced in the absence of MtWRP1. These results demonstrated that MtWRP1 plays critical roles in root nodulation and plant growth. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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13 pages, 6108 KiB

Open AccessFeature PaperArticle

Ectopic Expression of a Salt-Inducible Gene, LcSAIN3, from Sheepgrass Improves Seed Germination and Seedling Growth under Salt Stress in Arabidopsis

by Xiaoxia Li, Weiguang Yang, Junting Jia, Pincang Zhao, Dongmei Qi, Shuangyan Chen, Li Cheng, Liqin Cheng and Gongshe Liu

Genes 2021, 12(12), 1994; https://doi.org/10.3390/genes12121994 - 16 Dec 2021

Cited by 4 | Viewed by 2377

Abstract

Sheepgrass is a perennial native grass species in China, and it can tolerate high levels of salt stress with an aggressive and vigorous rhizome system. Many salt-stress-responsive genes have been identified in sheepgrass. In this study, we report the cloning and characterization of [...] Read more.

Sheepgrass is a perennial native grass species in China, and it can tolerate high levels of salt stress with an aggressive and vigorous rhizome system. Many salt-stress-responsive genes have been identified in sheepgrass. In this study, we report the cloning and characterization of a novel salt-induced gene, LcSAIN3 (Leymus chinensis salt-induced 3), from sheepgrass. Expression analysis confirmed that LcSAIN3 was induced by PEG, ABA, and salt treatments, and the expression of LcSAIN3 was significantly increased in salt-tolerant germplasms under salt treatment. Subcellular localization analysis indicated that the GFP-LcSAIN3 protein was mainly localized in the chloroplasts. The heterologous expression of LcSAIN3 in Arabidopsis increased the seed germination rate of transgenic plants under salt, ABA, and mannitol treatments. The seedling survival rate, plant height, and fresh weight of the transgenic plants were higher than those of WT plants under salt stress. The overexpression of LcSAIN3 caused a relatively high accumulation of free proline, enhanced SOD activity, and led to the upregulation of several stress-responsive genes such as AtRD26, AtRD29B, AtSOS1, and AtP5CS1. These results suggest that LcSAIN3 could be a potential target for molecular breeding to improve plants’ salt tolerance. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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11 pages, 1728 KiB

Open AccessArticle

Transcriptome Reveals the Dynamic Response Mechanism of Pearl Millet Roots under Drought Stress

by Yang Ji, Xiaowen Lu, Huan Zhang, Dan Luo, Ailing Zhang, Min Sun, Qing Wu, Xiaoshan Wang and Linkai Huang

Genes 2021, 12(12), 1988; https://doi.org/10.3390/genes12121988 - 15 Dec 2021

Cited by 9 | Viewed by 2632

Abstract

Drought is a major threat to global agricultural production that limits the growth, development and survival rate of plants, leading to tremendous losses in yield. Pearl millet (Cenchrus americanus (L.) Morrone) has an excellent drought tolerance, and is an ideal plant material [...] Read more.

Drought is a major threat to global agricultural production that limits the growth, development and survival rate of plants, leading to tremendous losses in yield. Pearl millet (Cenchrus americanus (L.) Morrone) has an excellent drought tolerance, and is an ideal plant material for studying the drought resistance of cereal crops. The roots are crucial organs of plants that experience drought stress, and the roots can sense and respond to such conditions. In this study, we explored the mechanism of drought tolerance of pearl millet by comparing transcriptomic data under normal conditions and drought treatment at four time points (24 h, 48 h, 96 h, and 144 h) in the roots during the seedling stage. A total of 1297, 2814, 7401, and 14,480 differentially expressed genes (DEGs) were found at 24 h, 48 h, 96 h, and 144 h, respectively. Based on Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses, we found that many DEGs participated in plant hormone-related signaling pathways and the “oxidoreductase activity” pathway. These results should provide a theoretical basis to enhance drought resistance in other plant species. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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14 pages, 2070 KiB

Open AccessArticle

Combined Transcriptome and Metabolome Analysis of Alfalfa Response to Thrips Infection

by Zhiqiang Zhang, Qi Chen, Yao Tan, Shuang Shuang, Rui Dai, Xiaohong Jiang and Buhe Temuer

Genes 2021, 12(12), 1967; https://doi.org/10.3390/genes12121967 - 10 Dec 2021

Cited by 32 | Viewed by 4276

Abstract

Thrips (Thysanoptera: Thripidae) is a major insect pest for alfalfa which can result in decreased plant nutrients, low yields, and even plant death. To identify the differentially expressed genes and metabolites in response to thrips in alfalfa, a combination of metabolomics and transcriptomics [...] Read more.

Thrips (Thysanoptera: Thripidae) is a major insect pest for alfalfa which can result in decreased plant nutrients, low yields, and even plant death. To identify the differentially expressed genes and metabolites in response to thrips in alfalfa, a combination of metabolomics and transcriptomics was employed using alfalfa (Caoyuan No. 2) with and without thrips infestation. The results showed that the flavonoid biosynthesis and isoflavonoid biosynthesis pathways were the most significantly enriched pathways in response to thrips infection, as shown by the combined transcriptome and metabolome analysis. The transcriptome results showed that SA and JA signal transduction and PAPM-triggered immunity and the MAPK signaling pathway–plant pathways played a crucial role in thrips-induced plant resistance in alfalfa. In addition, we found that thrips infestation could also induce numerous changes in plant primary metabolism, such as carbohydrate and amino acid metabolism as compared to the control. Overall, our results described here should improve fundamental knowledge of molecular responses to herbivore-inducible plant defenses and contribute to the design of strategies against thrips in alfalfa. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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16 pages, 3435 KiB

Open AccessArticle

Genome-Wide Identification of the Q-type C2H2 Transcription Factor Family in Alfalfa (Medicago sativa) and Expression Analysis under Different Abiotic Stresses

by Jun Pu, Mingyu Li, Pei Mao, Qiang Zhou, Wenxian Liu and Zhipeng Liu

Genes 2021, 12(12), 1906; https://doi.org/10.3390/genes12121906 - 27 Nov 2021

Cited by 11 | Viewed by 2678

Abstract

Q-type C2H2 zinc-finger protein (C2H2-ZFP) transcription factors are associated with many plant growth development and environmental stress responses. To date, there have been few analyses of the Q-type C2H2-ZFP gene family in alfalfa (Medicago sativa subsp. sativa). In this study, we [...] Read more.

Q-type C2H2 zinc-finger protein (C2H2-ZFP) transcription factors are associated with many plant growth development and environmental stress responses. To date, there have been few analyses of the Q-type C2H2-ZFP gene family in alfalfa (Medicago sativa subsp. sativa). In this study, we identified 58 Q-type C2H2-ZFPs across the entire alfalfa genome, and the gene structure, motif composition, chromosomal mapping, and cis-regulatory elements were explored, as well as the expression profiles of specific tissues and the response under different abiotic stresses. According to their phylogenetic features, these 58 MsZFPs were divided into 12 subgroups. Synteny analysis showed that duplication events play a vital role in the expansion of the MsZFP gene family. The collinearity results showed that a total of 26 and 42 of the 58 MsZFP genes were homologous with Arabidopsis and M. truncatula, respectively. The expression profiles showed that C2H2-ZFP genes played various roles in different tissues and abiotic stresses. The results of subsequent quantitative real-time polymerase chain reaction (qRT-PCR) showed that the nine selected MsZFP genes were rapidly induced under different abiotic stresses, indicating that C2H2-ZFP genes are closely related to abiotic stress. This study provides results on MsZFP genes, their response to various abiotic stresses, and new information on the C2H2 family in alfalfa. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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15 pages, 2234 KiB

Open AccessArticle

Overexpression of a Voltage-Dependent Anion-Selective Channel (VDAC) Protein-Encoding Gene, MsVDAC, from Medicago sativa Confers Cold and Drought Tolerance to Transgenic Tobacco

by Mei Yang, Xinhang Duan, Zhaoyu Wang, Hang Yin, Junrui Zang, Kai Zhu, Yumeng Wang and Pan Zhang

Genes 2021, 12(11), 1706; https://doi.org/10.3390/genes12111706 - 27 Oct 2021

Cited by 10 | Viewed by 2667

Abstract

Voltage-dependent anion channels (VDACs) are highly conserved proteins that are involved in the translocation of tRNA and play a key role in modulating plant senescence and multiple pathways. However, the functions of VDACs in plants are still poorly understood. Here, a novel VDAC [...] Read more.

Voltage-dependent anion channels (VDACs) are highly conserved proteins that are involved in the translocation of tRNA and play a key role in modulating plant senescence and multiple pathways. However, the functions of VDACs in plants are still poorly understood. Here, a novel VDAC gene was isolated and identified from alfalfa (Medicago sativa L.). MsVDAC localized to the mitochondria, and its expression was highest in alfalfa roots and was induced in response to cold, drought and salt treatment. Overexpression of MsVDAC in tobacco significantly increased MDA, GSH, soluble sugars, soluble protein and proline contents under cold and drought stress. However, the activities of SOD and POD decreased in transgenic tobacco under cold stress, while the O₂^- content increased. Stress-responsive genes including LTP1, ERD10B and Hxk3 were upregulated in the transgenic plants under cold and drought stress. However, GAPC, CBL1, BI-1, Cu/ZnSOD and MnSOD were upregulated only in the transgenic tobacco plants under cold stress, and GAPC, CBL1, and BI-1 were downregulated under drought stress. These results suggest that MsVDAC provides cold tolerance by regulating ROS scavenging, osmotic homeostasis and stress-responsive gene expression in plants, but the improved drought tolerance via MsVDAC may be mainly due to osmotic homeostasis and stress-responsive genes. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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Review

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9 pages, 455 KiB

Open AccessReview

Leaf Development in Medicago truncatula

by Liren Du, Samuel Adkins and Mingli Xu

Genes 2022, 13(7), 1203; https://doi.org/10.3390/genes13071203 - 5 Jul 2022

Cited by 3 | Viewed by 2666

Abstract

Forage yield is largely dependent on leaf development, during which the number of leaves, leaflets, leaf size, and shape are determined. In this mini-review, we briefly summarize recent studies of leaf development in Medicago truncatula, a model plant for legumes, with a [...] Read more.

Forage yield is largely dependent on leaf development, during which the number of leaves, leaflets, leaf size, and shape are determined. In this mini-review, we briefly summarize recent studies of leaf development in Medicago truncatula, a model plant for legumes, with a focus on factors that could affect biomass of leaves. These include: floral development and related genes, lateral organ boundary genes, auxin biosynthesis, transportation and signaling genes, and WOX related genes. Full article

(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)

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