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Pang Y, Zheng K, Min Q, Wang Y, Xue X, Li W, Zhao H, Qiao F, Han S. Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots. Int J Mol Sci 2024; 25:6226. [PMID: 38892412 PMCID: PMC11172603 DOI: 10.3390/ijms25116226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca2+]i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments.
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Affiliation(s)
- Yanrong Pang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Qinyue Min
- School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Yinxing Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Xiuhua Xue
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Wanjie Li
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Feng Qiao
- School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
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Lv G, Jin X, Wang H, Wang Y, Wu Q, Wu H, Jiang F, Ma Y, An Y, Zhang M, Guo Y, Li S. Cloning a novel reduced-height ( Rht) gene TaOSCA1.4 from a QTL in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1381243. [PMID: 38817937 PMCID: PMC11137288 DOI: 10.3389/fpls.2024.1381243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
Reducing plant height (PH) is one of the core contents of the "Green Revolution", which began in the 1960s in wheat. A number of 27 reduced-height (Rht) genes have been identified and a great number of quantitative trait loci (QTLs) for PH have been mapped on all 21 chromosomes. Nonetheless, only several genes regulated PH have been cloned. In this study, we found the interval of QTL QPh-1B included an EST-SSR marker swes1079. According to the sequence of swes1079, we cloned the TaOSCA1.4 gene. We developed a CAPS marker to analyze the variation across a natural population. The result showed that the PH was significantly different between the two haplotypes of TaOSCA1.4-1B under most of the 12 environments and the average values of irrigation and rainfed conditions. This result further demonstrated that TaOSCA1.4 was associated with PH. Then, we validated the TaOSCA1.4 via RNAi technology. The average PHs of the wild-type (WT), RNAi lines 1 (Ri-1) and 2 (Ri-2) were 94.6, 83.6 and 79.2 cm, respectively, with significant differences between the WT and Ri-1 and Ri-2. This result indicated that the TaOSCA1.4 gene controls PH. TaOSCA1.4 is a constitutively expressed gene and its protein localizes to the cell membrane. TaOSCA1.4 gene is a member of the OSCA gene family, which regulates intracellular Ca2+ concentration. We hypothesized that knock down mutants of TaOSCA1.4 gene reduced regulatory ability of Ca2+, thus reducing the PH. Furthermore, the cell lengths of the knock down mutants are not significantly different than that of WT. We speculate that TaOSCA1.4 gene is not directly associated with gibberellin (GA), which should be a novel mechanism for a wheat Rht gene.
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Affiliation(s)
- Guangde Lv
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Tai’an Academy of Agricultural Science, Tai’an, China
| | - Xuemei Jin
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Rizhao Academy of Agricultural Science, Rizhao, China
| | - Hui Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yijun Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Qun Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Haimeng Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | | | - Yanming Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanrong An
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Mingxia Zhang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Ying Guo
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Sishen Li
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
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Korszun-Karbowniczak J, Krysiak ZJ, Saluk J, Niemcewicz M, Zdanowski R. The Progress in Molecular Transport and Therapeutic Development in Human Blood-Brain Barrier Models in Neurological Disorders. Cell Mol Neurobiol 2024; 44:34. [PMID: 38627312 PMCID: PMC11021242 DOI: 10.1007/s10571-024-01473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
The blood-brain barrier (BBB) is responsible for maintaining homeostasis within the central nervous system (CNS). Depending on its permeability, certain substances can penetrate the brain, while others are restricted in their passage. Therefore, the knowledge about BBB structure and function is essential for understanding physiological and pathological brain processes. Consequently, the functional models can serve as a key to help reveal this unknown. There are many in vitro models available to study molecular mechanisms that occur in the barrier. Brain endothelial cells grown in culture are commonly used to modeling the BBB. Current BBB platforms include: monolayer platforms, transwell, matrigel, spheroidal, and tissue-on-chip models. In this paper, the BBB structure, molecular characteristic, as well as its dysfunctions as a consequence of aging, neurodegeneration, or under hypoxia and neurotoxic conditions are presented. Furthermore, the current modelling strategies that can be used to study BBB for the purpose of further drugs development that may reach CNS are also described.
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Affiliation(s)
- Joanna Korszun-Karbowniczak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141, Warsaw, Poland
- BioMedChem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, 21/23 Matejki Street, 90-237, Lodz, Poland
| | - Zuzanna Joanna Krysiak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141, Warsaw, Poland.
| | - Joanna Saluk
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, Institute of Biochemistry, University of Lodz, 68 Narutowicza Street, 90-136, Lodz, Poland
| | - Marcin Niemcewicz
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, 68 Narutowicza Street, 90-136, Lodz, Poland
| | - Robert Zdanowski
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141, Warsaw, Poland
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Türkösi E, Szakács É, Ivanizs L, Farkas A, Gaál E, Said M, Darkó É, Cséplő M, Mikó P, Doležel J, Molnár-Láng M, Molnár I, Kruppa K. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:7. [PMID: 38263978 PMCID: PMC10803699 DOI: 10.1007/s11032-024-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01439-y.
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Affiliation(s)
- Edina Türkösi
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Éva Szakács
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - László Ivanizs
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - András Farkas
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Eszter Gaál
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Éva Darkó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mónika Cséplő
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Péter Mikó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
| | - Márta Molnár-Láng
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - István Molnár
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Klaudia Kruppa
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
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5
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Li X, Wang X, Ma X, Cai W, Liu Y, Song W, Fu B, Li S. Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa. FRONTIERS IN PLANT SCIENCE 2023; 14:1285488. [PMID: 38023912 PMCID: PMC10655083 DOI: 10.3389/fpls.2023.1285488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Alfalfa is an excellent leguminous forage crop that is widely cultivated worldwide, but its yield and quality are often affected by drought and soil salinization. Hyperosmolality-gated calcium-permeable channel (OSCA) proteins are hyperosmotic calcium ion (Ca2+) receptors that play an essential role in regulating plant growth, development, and abiotic stress responses. However, no systematic analysis of the OSCA gene family has been conducted in alfalfa. In this study, a total of 14 OSCA genes were identified from the alfalfa genome and classified into three groups based on their sequence composition and phylogenetic relationships. Gene structure, conserved motifs and functional domain prediction showed that all MsOSCA genes had the same functional domain DUF221. Cis-acting element analysis showed that MsOSCA genes had many cis-regulatory elements in response to abiotic or biotic stresses and hormones. Tissue expression pattern analysis demonstrated that the MsOSCA genes had tissue-specific expression; for example, MsOSCA12 was only expressed in roots and leaves but not in stem and petiole tissues. Furthermore, RT-qPCR results indicated that the expression of MsOSCA genes was induced by abiotic stress (drought and salt) and hormones (JA, SA, and ABA). In particular, the expression levels of MsOSCA3, MsOSCA5, MsOSCA12 and MsOSCA13 were significantly increased under drought and salt stress, and MsOSCA7, MsOSCA10, MsOSCA12 and MsOSCA13 genes exhibited significant upregulation under plant hormone treatments, indicating that these genes play a positive role in drought, salt and hormone responses. Subcellular localization results showed that the MsOSCA3 protein was localized on the plasma membrane. This study provides a basis for understanding the biological information and further functional analysis of the MsOSCA gene family and provides candidate genes for stress resistance breeding in alfalfa.
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Affiliation(s)
- Xiaohong Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Xiaotong Wang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Xuxia Ma
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Wenqi Cai
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Yaling Liu
- Inner Mongolia Pratacultural Technology Innovation Center Co., Ltd, Hohhot, China
| | - Wenxue Song
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Bingzhe Fu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, China
| | - Shuxia Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, China
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Chelliah A, Arumugam C, Punchakkara PM, Suthanthiram B, Raman T, Subbaraya U. Genome-wide characterization of 2OGD superfamily for mining of susceptibility factors responding to various biotic stresses in Musa spp. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1319-1338. [PMID: 38024958 PMCID: PMC10678914 DOI: 10.1007/s12298-023-01380-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/29/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
Bananas are an important staple food and cash crop, but they are vulnerable to a variety of pests and diseases that substantially reduce yield and quality. Banana diseases are challenging to control and necessitate an integrated strategy, and development of resistant cultivars is one of the effective ways of managing diseases. Lasting disease resistance is the main goal in crop improvement and resistance mediated by a single resistant (R) gene mostly lack durability. However, long-term resistance can be obtained by inactivating susceptibility factors (S), which facilitate pathogen infection and proliferation. Identification and inactivation of susceptibility factors against the major pathogens like Fusarium oxysporum f. sp. cubense (Foc), Pseudocercospora eumusae and Pratylenchus coffeae in banana will be an effective way in developing banana varieties with more durable resistance. Downy mildew resistance 6 (DMR6) and DMR-like oxygenases (DLO1) are one such susceptibility factors and they belong to 2-oxoglutarate Fe(II) dependent oxygenases (2OGD) superfamily. 2OGDs are known to catalyze a plethora of reactions and also confer resistance to different pathogens in various crops, but not much is known about the 2OGD in Musa species. Through a comprehensive genome-wide analysis, 133 and 122 potential 2OGDs were systematically identified and categorized from the A and B genomes of banana, respectively. Real time expression of dmr6 and dlo1 genes showed positive correlation with transcriptome data upon Foc race1 and TR4 infection and examination of expression pattern of Macma4_04_g22670 (Ma04_g20880) and Macma4_02_g13590 (Ma02_g12040) genes revealed their involvement in Foc race1 and TR4 infections, respectively. Further the expression profile of 2OGDs, specifically Macma4_04_g25310 (Ma04_g23390), Macma4_08_g11980 (Ma08_g12090) and Macma4_04_g38910 (Ma04_g36640) shows that they may play a significant role as a susceptibility factor, particularly against P. eumusae and P. coffeae, implying that they can be exploited as a candidate gene for editing in developing resistant cultivars against these diseases. In summary, our findings contribute to a deeper comprehension of the evolutionary and functional aspects of 2OGDs in Musa spp. Furthermore, they highlight the substantial functions of these family constituents in the progression of diseases. These insights hold significance in the context of enhancing the genetic makeup of bananas to attain extended and more durable resistance against pathogens. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01380-y.
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Affiliation(s)
- Anuradha Chelliah
- Crop Improvement Division, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Chandrasekar Arumugam
- Crop Improvement Division, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Prashina Mol Punchakkara
- Crop Improvement Division, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Backiyarani Suthanthiram
- Crop Improvement Division, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Thangavelu Raman
- Crop Improvement Division, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Uma Subbaraya
- Crop Improvement Division, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
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Du L, Ma Z, Mao H. Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2465. [PMID: 37447026 DOI: 10.3390/plants12132465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.
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Affiliation(s)
- Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Zhenbing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
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Shelden MC, Munns R. Crop root system plasticity for improved yields in saline soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1120583. [PMID: 36909408 PMCID: PMC9999379 DOI: 10.3389/fpls.2023.1120583] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Crop yields must increase to meet the demands of a growing world population. Soil salinization is increasing due to the impacts of climate change, reducing the area of arable land for crop production. Plant root systems are plastic, and their architecture can be modulated to (1) acquire nutrients and water for growth, and (2) respond to hostile soil environments. Saline soils inhibit primary root growth and alter root system architecture (RSA) of crop plants. In this review, we explore how crop root systems respond and adapt to salinity, focusing predominately on the staple cereal crops wheat, maize, rice, and barley, that all play a major role in global food security. Cereal crops are classified as glycophytes (salt-sensitive) however salt-tolerance can differ both between species and within a species. In the past, due to the inherent difficulties associated with visualising and measuring root traits, crop breeding strategies have tended to focus on optimising shoot traits. High-resolution phenotyping techniques now make it possible to visualise and measure root traits in soil systems. A steep, deep and cheap root ideotype has been proposed for water and nitrogen capture. Changes in RSA can be an adaptive strategy to avoid saline soils whilst optimising nutrient and water acquisition. In this review we propose a new model for designing crops with a salt-tolerant root ideotype. The proposed root ideotype would exhibit root plasticity to adapt to saline soils, root anatomical changes to conserve energy and restrict sodium (Na+) uptake, and transport mechanisms to reduce the amount of Na+ transported to leaves. In the future, combining high-resolution root phenotyping with advances in crop genetics will allow us to uncover root traits in complex crop species such as wheat, that can be incorporated into crop breeding programs for yield stability in saline soils.
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Affiliation(s)
- Megan C. Shelden
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Rana Munns
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
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9
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Shan F, Wu Y, Du R, Yang Q, Liu C, Wang Y, Zhang C, Chen Y. Evolutionary analysis of the OSCA gene family in sunflower ( Helianthus annuus L) and expression analysis under NaCl stress. PeerJ 2023; 11:e15089. [PMID: 37090105 PMCID: PMC10117387 DOI: 10.7717/peerj.15089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/26/2023] [Indexed: 04/25/2023] Open
Abstract
Hyperosmolality-gated calcium-permeable channels (OSCA) are Ca2 + nonselective cation channels that contain the calcium-dependent DUF221 domain, which plays an important role in plant response to stress and growth. However, the OSCA gene has not been fully identified and analyzed in sunflowers. In this study, we comprehensively analyzed the number, structure, collinearity, and phylogeny of the OSCA gene family in the sunflower, six Compositae species (Arctium lappa, Chrysanthemum morifolium, Cichorium endivia, Cichorium intybus, Lactuca sativa var. Angustata, and Carthamus tinctorius), and six other plants (soybean, Arabidopsis thaliana, rice, grape, and maize). The expression of the sunflower OSCA gene in nine different tissues, six different hormones, and NaCl stress conditions were analyzed based on transcriptome data and qRT-PCR. A total of 15 OSCA proteins, distributed on 10 chromosomes, were identified in the sunflower, and all of them were located in the endoplasmic reticulum. Using the phylogenetic tree, collinearity, gene structure, and motif analysis of the six Compositae species and six other plants, we found that the sunflower OSCA protein had only three subfamilies and lacked the Group 4 subfamily, which is conserved in the evolution of Compositae and subject to purification selection. The OSCA gene structure and motif analysis of the sunflower and six Compositae showed that there was a positive correlation between the number of motifs of most genes and the length of the gene, different subfamilies had different motifs, and the Group 4 subfamily had the smallest number of genes and the simplest gene structure. RNA-seq and qRT-PCR analysis showed that the expression levels of most OSCA genes in the sunflower changed to varying degrees under salt stress, and HaOSCA2.6 and HaOSCA3.1 were the most important in the sunflower's response to salt stress. The coexpression network of the sunflower genes under salt stress was constructed based on weighted gene co-expression network analysis (WGCNA). In conclusion, our findings suggest that the OSCA gene family is conserved during the sunflower's evolution and plays an important role in salt tolerance. These results will deepen our understanding of the evolutionary relationship of the sunflower OSCA gene family and provide a basis for their functional studies under salt stress.
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Affiliation(s)
- Feibiao Shan
- Hetao College, Bayannur, China
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot, China
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
| | - Yue Wu
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
| | - Ruixia Du
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
| | - Qinfang Yang
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
| | - Chunhui Liu
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
| | - Yongxing Wang
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
| | | | - Yang Chen
- Hetao College, Bayannur, China
- Bayannur Institute of Agricultural and Animal Sciences, Bayannur, China
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10
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Kaur A, Sharma A, Dixit S, Singh K, Upadhyay SK. OSCA Genes in Bread Wheat: Molecular Characterization, Expression Profiling, and Interaction Analyses Indicated Their Diverse Roles during Development and Stress Response. Int J Mol Sci 2022; 23:ijms232314867. [PMID: 36499199 PMCID: PMC9737358 DOI: 10.3390/ijms232314867] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals the close clustering of the OSCA proteins of Arabidopsis thaliana, Oryza sativa, and T. aestivum in all the clades, suggesting their origin before the divergence of dicots and monocots. Furthermore, evolutionary analyses suggest the role of segmental and tandem duplication events (Des) and purifying selection pressure in the expansion of the OSCA gene family in T. aestivum. Expression profiling in various tissue developmental stages and under abiotic and biotic stress treatments reveals the probable functioning of OSCA genes in plant development and the stress response in T. aestivum. In addition, protein-protein and protein-chemical interactions reveal that OSCA proteins might play a putative role in Ca2+-mediated developmental processes and adaptive responses. The miRNA interaction analysis strengthens the evidence for their functioning in various biological processes and stress-induced signaling cascades. The current study could provide a foundation for the functional characterization of TaOSCA genes in future studies.
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Affiliation(s)
- Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Sameer Dixit
- Department of Biology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Santosh Kumar Upadhyay
- Department of Botany, Panjab University, Chandigarh 160014, India
- Correspondence: or ; Tel.: +91-172-2534001; Fax: +91-172-2779510
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11
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Shelake RM, Kadam US, Kumar R, Pramanik D, Singh AK, Kim JY. Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100417. [PMID: 35927945 PMCID: PMC9700172 DOI: 10.1016/j.xplc.2022.100417] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 07/27/2022] [Indexed: 05/10/2023]
Abstract
Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one of the major abiotic stresses that severely affect crop health and agricultural production. Plant responses to drought and salinity involve multiple processes that operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, and post-translational changes. Consequently, drought and salinity stress tolerance are polygenic traits influenced by genome-environment interactions. One of the ideal solutions to these challenges is the development of high-yielding crop varieties with enhanced stress tolerance, together with improved agricultural practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied to elucidate how plants deal with drought and saline environments. In this work, we aim to portray that the combined use of CRISPR-based genome engineering tools and modern genomic-assisted breeding approaches are gaining momentum in identifying genetic determinants of complex traits for crop improvement. This review provides a synopsis of plant responses to drought and salinity stresses at the morphological, physiological, and molecular levels. We also highlight recent advances in CRISPR-based tools and their use in understanding the multi-level nature of plant adaptations to drought and salinity stress. Integrating CRISPR tools with modern breeding approaches is ideal for identifying genetic factors that regulate plant stress-response pathways and for the introgression of beneficial traits to develop stress-resilient crops.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Ulhas Sopanrao Kadam
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Ritesh Kumar
- Department of Agronomy & Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea.
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12
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She K, Pan W, Yan Y, Shi T, Chu Y, Cheng Y, Ma B, Song W. Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley ( Hordeum vulgare L.). Int J Mol Sci 2022; 23:13027. [PMID: 36361820 PMCID: PMC9653715 DOI: 10.3390/ijms232113027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 09/06/2023] Open
Abstract
The hyperosmolality-gated calcium-permeable channel gene family (OSCA) is one kind of conserved osmosensors, playing a crucial role in maintaining ion and water homeostasis and protecting cellular stability from the damage of hypertonic stress. Although it has been systematically characterized in diverse plants, it is necessary to explore the role of the OSCA family in barley, especially its importance in regulating abiotic stress response. In this study, a total of 13 OSCA genes (HvOSCAs) were identified in barley through an in silico genome search method, which were clustered into 4 clades based on phylogenetic relationships with members in the same clade showing similar protein structures and conserved motif compositions. These HvOSCAs had many cis-regulatory elements related to various abiotic stress, such as MBS and ARE, indicating their potential roles in abiotic stress regulation. Furthermore, their expression patterns were systematically detected under diverse stresses using RNA-seq data and qRT-PCR methods. All of these 13 HvOSCAs were significantly induced by drought, cold, salt and ABA treatment, demonstrating their functions in osmotic regulation. Finally, the genetic variations of the HvOSCAs were investigated using the re-sequencing data, and their nucleotide diversity in wild barley and landrace populations were 0.4966 × 10-3 and 0.391 × 10-3, respectively, indicating that a genetic bottleneck has occurred in the OSCA family during the barley evolution process. This study evaluated the genomic organization, evolutionary relationship and genetic expression of the OSCA family in barley, which not only provides potential candidates for further functional genomic study, but also contributes to genetically improving stress tolerance in barley and other crops.
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Affiliation(s)
- Kuijun She
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Ying Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tingrui Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yingqi Chu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yue Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Bo Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
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13
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Liu C, Wang H, Zhang Y, Cheng H, Hu Z, Pei ZM, Li Q. Systematic Characterization of the OSCA Family Members in Soybean and Validation of Their Functions in Osmotic Stress. Int J Mol Sci 2022; 23:ijms231810570. [PMID: 36142482 PMCID: PMC9500692 DOI: 10.3390/ijms231810570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 12/31/2022] Open
Abstract
Since we discovered OSCA1, a hyperosmolarity-gated calcium-permeable channel that acted as an osmosensor in Arabidopsis, the OSCA family has been identified genome-wide in several crops, but only a few OSCA members' functions have been experimentally demonstrated. Osmotic stress seriously restricts the yield and quality of soybean. Therefore, it is essential to decipher the molecular mechanism of how soybean responds to osmotic stress. Here, we first systematically studied and experimentally demonstrated the role of OSCA family members in the osmotic sensing of soybean. Phylogenetic relationships, gene structures, protein domains and structures analysis revealed that 20 GmOSCA members were divided into four clades, of which members in the same cluster may have more similar functions. In addition, GmOSCA members in clusters III and IV may be functionally redundant and diverged from those in clusters I and II. Based on the spatiotemporal expression patterns, GmOSCA1.6, GmOSCA2.1, GmOSCA2.6, and GmOSCA4.1 were extremely low expressed or possible pseudogenes. The remaining 16 GmOSCA genes were heterologously overexpressed in an Arabidopsis osca1 mutant, to explore their functions. Subcellular localization showed that most GmOSCA members could localize to the plasma membrane (PM). Among 16 GmOSCA genes, only overexpressing GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, and GmOSCA1.5 in cluster I could fully complement the reduced hyperosmolality-induced [Ca2+]i increase (OICI) in osca1. The expression profiles of GmOSCA genes against osmotic stress demonstrated that most GmOSCA genes, especially GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, GmOSCA1.5, GmOSCA3.1, and GmOSCA3.2, strongly responded to osmotic stress. Moreover, overexpression of GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, GmOSCA1.5, GmOSCA3.1, and GmOSCA3.2 rescued the drought-hypersensitive phenotype of osca1. Our findings provide important clues for further studies of GmOSCA-mediated calcium signaling in the osmotic sensing of soybean and contribute to improving soybean drought tolerance through genetic engineering and molecular breeding.
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Affiliation(s)
- Congge Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hong Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311401, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Haijing Cheng
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhangli Hu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhen-Ming Pei
- Department of Biology, Duke University, Durham, NC 27708, USA
- Correspondence: (Z.-M.P.); or (Q.L.)
| | - Qing Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311401, China
- Correspondence: (Z.-M.P.); or (Q.L.)
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14
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Corona-Gomez JA, Coss-Navarrete EL, Garcia-Lopez IJ, Klapproth C, Pérez-Patiño JA, Fernandez-Valverde SL. Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana. Sci Rep 2022; 12:14063. [PMID: 35982083 PMCID: PMC9388643 DOI: 10.1038/s41598-022-18254-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.
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Affiliation(s)
| | | | | | - Christopher Klapproth
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.,ScaDS.AI Leipzig (Center for Scalable Data Analytics and Artificial Intelligence), Humboldstrasse 25, 04105, Leipzig, Germany
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15
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Yang S, Zhu C, Chen J, Zhao J, Hu Z, Liu S, Zhou Y. Identification and Expression Profile Analysis of the OSCA Gene Family Related to Abiotic and Biotic Stress Response in Cucumber. BIOLOGY 2022; 11:biology11081134. [PMID: 36009761 PMCID: PMC9404750 DOI: 10.3390/biology11081134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Hyperosmolality-gated calcium-permeable channels (OSCAs) are calcium nonselective cation channel proteins involved in multiple biological processes. In this work, the members of the OSCA family in cucumber were systematically analyzed, including their sequence characteristics, phylogenetic relationships, conserved motifs, gene structures, promoter regions, and tissue expression patterns. In addition, the effects of different osmotic-related abiotic stresses [salt (NaCl), drought (PEG), and abscisic acid (ABA)] and three biotic stresses [powdery mildew (PM), downy mildew (DM), and root-knot nematode (RKN)] on OSCA family genes were also determined. The results indicated that cucumber OSCA genes play important roles in response to osmotic-related abiotic stresses and pathogen invasion. Overall, this study lays a foundation for research on the biological function and evolutionary process of OSCA family genes in cucumber. Abstract Calcium ions are important second messengers, playing an important role in the signal transduction pathways. Hyperosmolality gated calcium-permeable channels (OSCA) gene family members play critical modulating roles in response to osmotic-related abiotic stress as well as other abiotic and biotic stresses, which has been reported in many plant species such as Arabidopsis, rice, maize, and wheat. However, there has been no report about the identification and expression profile of the OSCA genes in cucumber. In this study, a total of nine OSCA genes were identified, which are unevenly distributed on the six chromosomes of cucumber. Phylogenetic analysis revealed that the OSCAs of cucumber, Arabidopsis, rice and maize were clustered into four clades. The motif arrangement of CsOSCAs was strongly conserved, and the CsOSCA genes in each group had similar genetic structure. A total of 11 and 10 types of cis-elements related to hormone and stress, respectively, were identified in the promoter regions of CsOSCA genes. Gene expression analysis indicated that the CsOSCA genes have different expression patterns in various tissues, and some of them were regulated by three osmotic-related abiotic stresses (salt, drought and ABA) and three biotic stresses (powdery mildew, downy mildew, and root-knot nematode). As the first genome-wide identification and characterization of the OSCA gene family in cucumber, this study lays a foundation for research on the biological function and evolutionary process of this gene family, which is of great significance for exploiting stress resistant cucumber varieties.
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Affiliation(s)
- Shuting Yang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
| | - Chuxia Zhu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
| | - Jingju Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
| | - Jindong Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
| | - Zhaoyang Hu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
| | - Shiqiang Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
- Correspondence: (S.L.); (Y.Z.)
| | - Yong Zhou
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (S.Y.); (C.Z.); (J.C.); (J.Z.); (Z.H.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (S.L.); (Y.Z.)
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16
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Moran C, Xu ZY, Mehta H, Gillies M, Karayiannis C, Beare R, Chen C, Srikanth V. Neuroimaging and cognitive correlates of retinal Optical Coherence Tomography (OCT) measures at late middle age in a twin sample. Sci Rep 2022; 12:9562. [PMID: 35688899 PMCID: PMC9187769 DOI: 10.1038/s41598-022-13662-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/26/2022] [Indexed: 11/09/2022] Open
Abstract
Sharing in embryology and function between the eye and brain has led to interest in whether assessments of the eye reflect brain changes seen in neurodegeneration. We aimed to examine the associations between measures of retinal layer thickness using optical coherence tomography (OCT) and multimodal measures of brain structure and function. Using a convenient sample of twins discordant for type 2 diabetes, we performed cognitive testing, structural brain MRI (tissue volumetry), diffusion tensor imaging (white matter microstructure), and arterial spin labelling (cerebral blood flow). OCT images were recorded and retinal thickness maps generated. We used mixed level modelling to examine the relationship between retinal layer thicknesses and brain measures. We enrolled 35 people (18 pairs, mean age 63.8 years, 63% female). Ganglion cell layer thickness was positively associated with memory, speed, gray matter volume, and altered mean diffusivity. Ganglion cell layer thickness was strongly positively associated with regional cerebral blood flow. We found only a limited number of associations between other retinal layer thickness and measures of brain structure or function. Ganglion cell layer thickness showed consistent associations with a range of brain measures suggesting it may have utility as a marker for future dementia risk.
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Affiliation(s)
- Chris Moran
- National Centre for Healthy Ageing, Melbourne, Australia.,Department of Geriatric Medicine, Peninsula Health and Central Clinical School, Monash University, Melbourne, Australia.,Department of Aged Care, Alfred Health, Melbourne, Australia
| | - Zheng Yang Xu
- Royal Free London NHS Foundation Trust, London, UK.,UCL Medical School, London, UK
| | - Hemal Mehta
- Royal Free London NHS Foundation Trust, London, UK.,Macular Research Group, University of Sydney, Sydney, Australia
| | - Mark Gillies
- Macular Research Group, University of Sydney, Sydney, Australia
| | - Chris Karayiannis
- National Centre for Healthy Ageing, Melbourne, Australia.,Department of Geriatric Medicine, Peninsula Health and Central Clinical School, Monash University, Melbourne, Australia
| | - Richard Beare
- National Centre for Healthy Ageing, Melbourne, Australia.,Department of Geriatric Medicine, Peninsula Health and Central Clinical School, Monash University, Melbourne, Australia
| | - Christine Chen
- Department of Ophthalmology, Monash Health, Melbourne, Australia
| | - Velandai Srikanth
- National Centre for Healthy Ageing, Melbourne, Australia. .,Department of Geriatric Medicine, Peninsula Health and Central Clinical School, Monash University, Melbourne, Australia.
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17
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Chen SQ, Chen XY, Cui YZ, Yan BX, Zhou Y, Wang ZY, Xu F, Huang YZ, Zheng YX, Man XY. Cutaneous nerve fibers participate in the progression of psoriasis by linking epidermal keratinocytes and immunocytes. Cell Mol Life Sci 2022; 79:267. [PMID: 35488965 PMCID: PMC11072315 DOI: 10.1007/s00018-022-04299-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 12/11/2022]
Abstract
Recent studies have illustrated that psoriatic lesions are innervated by dense sensory nerve fibers. Psoriatic plaques appeared to improve after central or peripheral nerve injury. Therefore, the nervous system may play a vital role in psoriasis. We aimed to clarify the expression of nerve fibers in psoriasis and their relationship with immune cells and keratinocytes, and to explore the effect of skin nerve impairment. Our results illustrated that nerve fibers in psoriatic lesions increased and were closely innervated around immune cells and keratinocytes. RNA-seq analysis showed that peripheral sensory nerve-related genes were disrupted in psoriasis. In spinal cord hemi-section mice, sensory impairment improved psoriasiform dermatitis and inhibited the abnormal proliferation of keratinocytes. Botulinum toxin A alleviated psoriasiform dermatitis by inhibiting the secretion of calcitonin gene-related peptide. Collectively, cutaneous nerve fibers participate in the progression of psoriasis by linking epidermal keratinocytes and immunocytes. Neurological intervention may be a new treatment strategy for psoriasis.
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Affiliation(s)
- Si-Qi Chen
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Xue-Yan Chen
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Ying-Zhe Cui
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Bing-Xi Yan
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Yuan Zhou
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Zhao-Yuan Wang
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Fan Xu
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Yan-Zhou Huang
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Yu-Xin Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China
| | - Xiao-Yong Man
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, China.
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18
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Huang H, Huo Z, Jiao J, Ji W, Huang J, Bian Z, Xu B, Shao J, Sun J. HOXC6 impacts epithelial-mesenchymal transition and the immune microenvironment through gene transcription in gliomas. Cancer Cell Int 2022; 22:170. [PMID: 35488304 PMCID: PMC9052479 DOI: 10.1186/s12935-022-02589-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gliomas are the most common primary malignant tumours of the central nervous system (CNS). To improve the prognosis of glioma, it is necessary to identify molecular markers that may be useful for glioma therapy. HOXC6, an important transcription factor, is involved in multiple cancers. However, the role of HOXC6 in gliomas is not clear. METHODS Bioinformatic and IHC analyses of collected samples (n = 299) were performed to detect HOXC6 expression and the correlation between HOXC6 expression and clinicopathological features of gliomas. We collected clinical information from 177 to 299 patient samples and estimated the prognostic value of HOXC6. Moreover, cell proliferation assays were performed. We performed Gene Ontology (GO) analysis and gene set enrichment analysis (GSEA) based on ChIP-seq and public datasets to explore the biological characteristics of HOXC6 in gliomas. RNA-seq was conducted to verify the relationship between HOXC6 expression levels and epithelial-mesenchymal transition (EMT) biomarkers. Furthermore, the tumour purity, stromal and immune scores were evaluated. The relationship between HOXC6 expression and infiltrating immune cell populations and immune checkpoint proteins was also researched. RESULTS HOXC6 was overexpressed and related to the clinicopathological features of gliomas. In addition, knockdown of HOXC6 inhibited the proliferation of glioma cells. Furthermore, increased HOXC6 expression was associated with clinical progression. The biological role of HOXC6 in gliomas was primarily associated with EMT and the immune microenvironment in gliomas. High HOXC6 expression was related to high infiltration by immune cells, a low tumour purity score, a high stromal score, a high immune score and the expression of a variety of immune checkpoint genes, including PD-L1, B7-H3 and CLTA-4. CONCLUSIONS These results indicated that HOXC6 might be a key factor in promoting tumorigenesis and glioma progression by regulating the EMT signalling pathway and might represent a novel immune therapeutic target in gliomas.
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Affiliation(s)
- Hui Huang
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Zhengyuan Huo
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Jiantong Jiao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Wei Ji
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Jin Huang
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Zheng Bian
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Bin Xu
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China
| | - Junfei Shao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China.
| | - Jun Sun
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023, Wuxi, Jiangsu, China.
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Du J, Liu B, Zhao T, Xu X, Lin H, Ji Y, Li Y, Li Z, Lu C, Li P, Zhao H, Li Y, Yin Z, Ding X. Silica nanoparticles protect rice against biotic and abiotic stresses. J Nanobiotechnology 2022; 20:197. [PMID: 35459250 PMCID: PMC9034512 DOI: 10.1186/s12951-022-01420-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND By 2050, the world population will increase to 10 billion which urged global demand for food production to double. Plant disease and land drought will make the situation more dire, and safer and environment-friendly materials are thus considered as a new countermeasure. The rice blast fungus, Magnaporthe oryzae, causes one of the most destructive diseases of cultivated rice worldwide that seriously threatens rice production. Unfortunately, traditional breeding nor chemical approaches along control it well. Nowadays, nanotechnology stands as a new weapon against these mounting challenges and silica nanoparticles (SiO2 NPs) have been considered as potential new safer agrochemicals recently but the systematically studies remain limited, especially in rice. RESULTS Salicylic acid (SA) is a key plant hormone essential for establishing plant resistance to several pathogens and its further affected a special form of induced resistance, the systemic acquired resistance (SAR), which considered as an important aspect of plant innate immunity from the locally induced disease resistance to the whole plant. Here we showed that SiO2 NPs could stimulate plant immunity to protect rice against M. oryzae through foliar treatment that significantly decreased disease severity by nearly 70% within an appropriate concentration range. Excessive concentration of foliar treatment led to disordered intake and abnormal SA responsive genes expressions which weaken the plant resistance and even aggravated the disease. Importantly, this SA-dependent fungal resistance could achieve better results with root treatment through a SAR manner with no phytotoxicity since the orderly and moderate absorption. What's more, root treatment with SiO2 NPs could also promote root development which was better to deal with drought. CONCLUSIONS Taken together, our findings not only revealed SiO2 NPs as a potential effective and safe strategy to protect rice against biotic and abiotic stresses, but also identify root treatment for the appropriate application method since it seems not causing negative effects and even have promotion on root development.
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Affiliation(s)
- Jianfeng Du
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Baoyou Liu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.,Yantai Academy of Agricultural Sciences, Yantai, China.,College of Life Sciences, Yantai University, Yantai, China
| | - Tianfeng Zhao
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Xinning Xu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Han Lin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Yatai Ji
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Yue Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Zhiwei Li
- College of Life Sciences, Yantai University, Yantai, China
| | - Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Pengan Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Haipeng Zhao
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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Huang L, Li Z, Sun C, Yin S, Wang B, Duan T, Liu Y, Li J, Pu G. Genome-wide identification, molecular characterization, and gene expression analyses of honeysuckle NHX antiporters suggest their involvement in salt stress adaptation. PeerJ 2022; 10:e13214. [PMID: 35462769 PMCID: PMC9029436 DOI: 10.7717/peerj.13214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/12/2022] [Indexed: 01/12/2023] Open
Abstract
Background Ion homeostasis is an essential process for the survival of plants under salt stress. Na+/H+ antiporters (NHXs) are secondary ion transporters that regulate Na+ compartmentalization or efflux reduce Na+ toxicity and play a critical role during plant development and stress responses. Methods and Results To gain insight into the functional divergence of NHX genes in honeysuckle, a total of seven LjNHX genes were identified on the whole genome level and were renamed according to their chromosomal positions. All LjNHXs possessed the Na+/H+ exchanger domain and the amiloride-binding site was presented in all NHX proteins except LjNHX4. The phylogenetic analysis divided the seven NHX genes into Vac-clade (LjNHX1/2/3/4/5/7) and PM-clade (LjNHX6) based on their subcellular localization and validated by the distribution of conserved protein motifs and exon/intron organization analysis. The protein-protein interaction network showed that LjNHX4/5/6/7 shared the same putatively interactive proteins, including SOS2, SOS3, HKT1, and AVP1. Cis-acting elements and gene ontology (GO) analysis suggested that most LjNHXs involve in the response to salt stress through ion transmembrane transport. The expression profile analysis revealed that the expression levels of LjNHX3/7 were remarkably affected by salinity. These results suggested that LjNHXs play significant roles in honeysuckle development and response to salt stresses. Conclusions The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in honeysuckle.
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Affiliation(s)
- Luyao Huang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | | | - Chunyong Sun
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shijie Yin
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bin Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tongyao Duan
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yang Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jia Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Gaobin Pu
- Shandong University of Traditional Chinese Medicine, Jinan, China
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