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Gan Y, Ping J, Liu X, Peng C. Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides. Biochem Genet 2024:10.1007/s10528-024-10874-7. [PMID: 38954211 DOI: 10.1007/s10528-024-10874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Annonaceae is the largest family in Magnoliales, exhibiting the greatest diversity among and within genera. In this study, we conducted an analysis of repetitive sequences and codon usage bias in the previously acquired plastome of Miliusa glochidioides. Using a concatenated dataset of shared genes, we constructed the phylogenetic relationships among 27 Annonaceae species. The results showed that the size of the plastomes in the Annonaceae ranged from 159 to 202 kb, with the size of the inverted repeat region ranging from 40 to 65 kb. Within the plastome of M. glochidioides, we identified 42 SSRs, 36 tandem repeats, and 9 dispersed repeats. These SSRs consist of three nucleotide types and eight motif types, with a preference for A/T bases, primarily located in the large single-copy regions and intergenic spacers. Tandem and dispersed repeat sequences were predominantly detected in the IR region. Through codon usage bias analysis, we identified 30 high-frequency codons and 11 optimal codons. The plastome of M. glochidioides demonstrated relatively weak codon usage bias, favoring codons with A/T endings, primarily influenced by natural selection. Phylogenetic analysis revealed that all four subfamilies formed monophyletic groups, with Cananga odorata (Ambavioideae) and Anaxagorea javanica (Anaxagoreoideae) successively nested outside Annonoideae + Malmeoideae. These findings improve our understanding of the plastome of M. glochidioides and provide additional insights for studying plastome evolution in Annonaceae.
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Affiliation(s)
- Yangying Gan
- Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Economics and Information, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jingyao Ping
- College of Life Sciences, Sun Yet-sen University, Guangzhou, 510275, China
| | - Xiaojing Liu
- Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Economics and Information, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Caixia Peng
- Horticulture Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Arriola ÍA, Costa EC, de Oliveira DC, Isaias RMDS. Soil-plant-gall relationships: from gall development to ecological patterns. Biol Rev Camb Philos Soc 2024. [PMID: 38888220 DOI: 10.1111/brv.13106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
The adaptive nature of the galler habit has been tentatively explained by the nutrition, microenvironment, and enemy hypotheses. Soil attributes have direct relationships with these three hypotheses at the cellular and macroecological scales, but their influence has been restricted previously to effects on the nutritional status of the host plant on gall richness and abundance. Herein, we discuss the ionome patterns within gall tissues and their significance for gall development, physiology, structure, and for the nutrition of the gallers. Previous ecological and chemical quantification focused extensively on nitrogen and carbon contents, evoking the carbon-nutrient defence hypothesis as an explanation for establishing the plant-gall interaction. Different elements are involved in cell wall composition dynamics, antioxidant activity, and regulation of plant-gall water dynamics. An overview of the different soil-plant-gall relationships highlights the complexity of the nutritional requirements of gallers, which are strongly influenced by environmental soil traits. Soil and plant chemical profiles interact to determine the outcome of plant-herbivore interactions and need to be addressed by considering not only the soil features and galler nutrition but also the host plant's physiological traits. The quantitative and qualitative results for iron metabolism in gall tissues, as well as the roles of iron as an essential element in the physiology and reproduction of gallers suggest that it may represent a key nutritional resource, aligning with the nutrition hypothesis, and providing an integrative explanation for higher gall diversity in iron-rich soils.
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Affiliation(s)
- Ígor Abba Arriola
- Department of Botany, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CP 486, Belo Horizonte, Brazil
| | - Elaine Cotrim Costa
- Institute of Biological Sciences/Botany, Universidade Federal do Rio Grande, Av. Itália Km 8, Campus Carreiros, Rio Grande, Brazil
| | - Denis Coelho de Oliveira
- Institute of Biology, Universidade Federal de Uberlândia, Campus Umuarama, Rua Ceará s/n, Uberlândia, Brazil
| | - Rosy Mary Dos Santos Isaias
- Department of Botany, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CP 486, Belo Horizonte, Brazil
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Ashraf U, Anjum SA, Naseer S, Abbas A, Abrar M, Nawaz M, Luo K. Gamma amino butyric acid (GABA) application modulated the morpho-physiological and yield traits of fragrant rice under well-watered and drought conditions. BMC PLANT BIOLOGY 2024; 24:569. [PMID: 38886652 PMCID: PMC11184787 DOI: 10.1186/s12870-024-05272-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Changing climate is causing erratic rainfall and prolonged drought periods, thus posing serious threats to crop productivity. Owing to severity of drought events, it is imperative to take proactive measures to enhance the resilience of drought sensitive crops like rice. Therefore, the present study was carried out to improve the drought stress tolerance in rice through gamma amino butyric acid (GABA) application. METHODS The experiment was included four GABA concentrations i.e., 0 mM as control, 1 mM, 1.5 mM, and 2 mM, two water levels i.e., 100% and 50% field capacity (referred as FC100 for well-watered and FC50 for drought conditions, respectively), and two fragrant rice cultivars i.e., Super Basmati and Basmati-515. RESULTS The findings unveiled a comprehensive improvement in various parameters with GABA application in fragrant rice under both well-watered (FC100) and water-limited (FC50) conditions, compared to the control. Specifically, GABA induced enhancements were observed in plant height, root length, fresh weight, dry weight, total soluble protein content, and total free amino acid content across both cultivars. Moreover, GABA application significantly improved peroxidase (POD) and catalase (CAT) enzyme activities, alongside elevating anthocyanin levels, while concurrently reducing H2O2 contents in both FC100 and FC50 treatments. Furthermore, the positive impact of GABA extended to morphological traits, with notable increases in panicle length, total tillers and productive tillers per hill, branch and grain numbers per panicle, and 1000-grain weight for Super Basmati and Basmati 515 cultivars under both water regimes, compared to Ck. Similarly, the grain yield increased by 31.01% and 27.32% under FC100 and 36.85% and 27.71% under FC50 in Super Basmati and Basmati-515, respectively, in response to GABA application, compared to Ck. Additionally, principal component analysis (PCA) revealed significant variances attributed to Dim1 and Dim2, with 86.1% and 4.0% of the variance, respectively, across three bi-plots encompassing rice cultivars, water levels, and GABA treatments. Notably, all tested indices, except for H2O2 and non-productive tillers per hill, exhibited positive correlations amongst themselves and with rice yield, further emphasizing the beneficial effects of GABA application on fragrant rice under well-watered and drought conditions. CONCLUSIONS GABA significantly improved fragrant rice performance under both well-watered (FC100) and water-limited (FC50) conditions. Moreover, integrating GABA application into rice cultivation practices could not only improve the crop resilience to drought stress but also potentially benefiting the future food and nutritional security globally. However, however; further research is needed to understand the cellular and molecular mechanisms of the functionality of GABA in fragrant rice, particularly under drought conditions.
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Affiliation(s)
- Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Punjab, 54770, Pakistan.
| | - Shakeel Ahmad Anjum
- Department of Agronomy, University of Agriculture, Faisalabad, Punjab, 38040, Pakistan
| | - Sidra Naseer
- Department of Botany, Faculty of Sciences, University of Agriculture, Faisalabad, Punjab, 38040, Pakistan
| | - Anees Abbas
- Department of Agronomy, University of Agriculture, Faisalabad, Punjab, 38040, Pakistan
| | - Muhammad Abrar
- State Key Laboratory of Grassland Agroecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Kebo Luo
- Jieyang Research Institute of Agricultural Sciences, Jieyang, China.
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Schierenbeck M, Alqudah AM, Thabet SG, Avogadro EG, Dietz JI, Simón MR, Börner A. Natural allelic variation confers diversity in the regulation of flag leaf traits in wheat. Sci Rep 2024; 14:13316. [PMID: 38858489 PMCID: PMC11164900 DOI: 10.1038/s41598-024-64161-x] [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: 11/08/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Flag leaf (FL) dimension has been reported as a key ecophysiological aspect for boosting grain yield in wheat. A worldwide winter wheat panel consisting of 261 accessions was tested to examine the phenotypical variation and identify quantitative trait nucleotides (QTNs) with candidate genes influencing FL morphology. To this end, four FL traits were evaluated during the early milk stage under two growing seasons at the Leibniz Institute of Plant Genetics and Crop Plant Research. The results showed that all leaf traits (Flag leaf length, width, area, and length/width ratio) were significantly influenced by the environments, genotypes, and environments × genotypes interactions. Then, a genome-wide association analysis was performed using 17,093 SNPs that showed 10 novel QTNs that potentially play a role in modulating FL morphology in at least two environments. Further analysis revealed 8 high-confidence candidate genes likely involved in these traits and showing high expression values from flag leaf expansion until its senescence and also during grain development. An important QTN (wsnp_RFL_Contig2177_1500201) was associated with FL width and located inside TraesCS3B02G047300 at chromosome 3B. This gene encodes a major facilitator, sugar transporter-like, and showed the highest expression values among the candidate genes reported, suggesting their positive role in controlling flag leaf and potentially being involved in photosynthetic assimilation. Our study suggests that the detection of novel marker-trait associations and the subsequent elucidation of the genetic mechanism influencing FL morphology would be of interest for improving plant architecture, light capture, and photosynthetic efficiency during grain development.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina.
- CONICET CCT La Plata, La Plata, Argentina.
| | - Ahmad Mohammad Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha, Qatar.
| | - Samar Gamal Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Evangelina Gabriela Avogadro
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Juan Ignacio Dietz
- CONICET CCT La Plata, La Plata, Argentina
- EEA INTA Bordenave, Ruta 76 km 36, Bordenave, Argentina
| | - María Rosa Simón
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
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Herol L, Avidar M, Yirmiahu S, Zach YY, Klein T, Shemesh H, Livne-Luzon S. Context-dependent benefits of forest soil addition on Aleppo pine seedling performance under drought and grass competition. MYCORRHIZA 2024; 34:217-227. [PMID: 38762648 PMCID: PMC11166812 DOI: 10.1007/s00572-024-01151-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
Seedling establishment under natural conditions is limited by numerous interacting factors. Here, we tested the combined effects of drought, herbaceous competition, and ectomycorrhizal inoculation on the performance of Aleppo pine seedlings grown in a net-house. The roots of all pine seedlings were strongly dominated by Geopora, a fungal genus known to colonize seedlings in dry habitats. Ectomycorrhizal fungi (EMF) inoculum significantly increased seedling height, biomass, and the number of side branches. However, under either competition or drought, the positive effect of EMF on seedling biomass and height was greatly reduced, while the effect on shoot branching was maintained. Further, under a combination of drought and competition, EMF had no influence on either plant growth or shape. The discrepancy in pine performance across treatments highlights the complexity of benefits provided to seedlings by EMF under ecologically relevant settings.
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Affiliation(s)
- Lior Herol
- Department of Environmental Sciences, Tel-Hai College, Qiryat Shemona, Israel
| | - Mor Avidar
- Department of Environmental Sciences, Tel-Hai College, Qiryat Shemona, Israel
| | - Shahar Yirmiahu
- Department of Environmental Sciences, Tel-Hai College, Qiryat Shemona, Israel
| | - Yair Yehoshua Zach
- Department of Environmental Sciences, Tel-Hai College, Qiryat Shemona, Israel
| | - Tamir Klein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hagai Shemesh
- Department of Environmental Sciences, Tel-Hai College, Qiryat Shemona, Israel
| | - Stav Livne-Luzon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Cao Y, Wang K, Lu F, Li Q, Yang Q, Liu B, Muhammad H, Wang Y, Fu F, Li W, Yu H. Comprehensive identification of maize ZmE2F transcription factors and the positive role of ZmE2F6 in response to drought stress. BMC Genomics 2024; 25:465. [PMID: 38741087 DOI: 10.1186/s12864-024-10369-0] [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: 10/10/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND The early 2 factor (E2F) family is characterized as a kind of transcription factor that plays an important role in cell division, DNA damage repair, and cell size regulation. However, its stress response has not been well revealed. RESULTS In this study, ZmE2F members were comprehensively identified in the maize genome, and 21 ZmE2F genes were identified, including eight E2F subclade members, seven DEL subfamily genes, and six DP genes. All ZmE2F proteins possessed the DNA-binding domain (DBD) characterized by conserved motif 1 with the RRIYD sequence. The ZmE2F genes were unevenly distributed on eight maize chromosomes, showed diversity in gene structure, expanded by gene duplication, and contained abundant stress-responsive elements in their promoter regions. Subsequently, the ZmE2F6 gene was cloned and functionally verified in drought response. The results showed that the ZmE2F6 protein interacted with ZmPP2C26, localized in the nucleus, and responded to drought treatment. The overexpression of ZmE2F6 enhanced drought tolerance in transgenic Arabidopsis with longer root length, higher survival rate, and biomass by upregulating stress-related gene transcription. CONCLUSIONS This study provides novel insights into a greater understanding and functional study of the E2F family in the stress response.
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Affiliation(s)
- Yang Cao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kexin Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fengzhong Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qi Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qingqing Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bingliang Liu
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Hayderbinkhalid Muhammad
- National Research Centre of Intercropping, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Yingge Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haoqiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Dong Q, Zhang Y, Zhong S, Zhang Q, Yang H, Yang H, Yi X, Tan F, Chen C, Luo P. Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China. BMC Ecol Evol 2024; 24:52. [PMID: 38654171 DOI: 10.1186/s12862-024-02243-0] [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: 09/01/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions. RESULTS Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution. CONCLUSIONS Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.
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Affiliation(s)
- Qing Dong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongle Zhang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiuyi Zhang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoxiao Yi
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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Hasnain A, Dadkhah-Aghdash H, Luqman M, Muhammad S, Sardar AA, Ali S, Mehmood F, Khan UA, Mehmood Z, John A, Binyameen, Khan ZI, Yang HH, Farooq Awan MU. Impact of automobile exhaust on biochemical and genomorphic characteristics of Mimusops elengi L. growing along roadsides of Lahore city, Pakistan. Heliyon 2024; 10:e28157. [PMID: 38524624 PMCID: PMC10958417 DOI: 10.1016/j.heliyon.2024.e28157] [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: 10/06/2023] [Revised: 02/27/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024] Open
Abstract
Automobile exhaust releases different types of pollutants that are at great risk to the air quality of the environment and incidental distress to the nature of roadside plants. Mimusops elengi L. is an evergreen medicinal tree cultivated along the roadside of Lahore City. This research aimed to investigate physiological, morphological and genomorphic characteristics of M. elengi under the influence of air pollution from vehicles. Healthy and mature leaves were collected from trees on Canal Bank and Mall roads of Lahore as the experimental sites and control sites were 20 km away from the experimental site. Different physiochemical, morphological, air pollution tolerance index (APTI) and molecular analysis for the detection of DNA damage were performed through comet assay. The results demonstrated the mean accumulated Cd, Pb, Cu and Ni heavy metal contents on the leaves were higher than the control plants (1.27, 3.22, 1.32 and 1.46 μg mg-1). APTI of trees was 9.04. Trees in these roads significantly (p < 0.01) had a lower leaf area, petiole length and leaf dry matter content in comparison to control site. Increased comet tail showed that DNA damage was higher for roadside trees than trees in the control area. For tolerance of air pollution, it necessary to check the APTI value for the M. elengi at the polluted road side of Lahore city. For long-term screening, the source and type of pollutants and consistent monitoring of various responses given by the trees should be known.
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Affiliation(s)
- Ali Hasnain
- Department of Botany, Government College University, Lahore, 54000, Pakistan
| | - Hamed Dadkhah-Aghdash
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Muhammad Luqman
- Department of Environmental Sciences, University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
| | - Sohaib Muhammad
- Department of Botany, Government College University, Lahore, 54000, Pakistan
| | | | - Shaukat Ali
- Department of Zoology, Government College University, Lahore, 54000, Pakistan
| | - Farhat Mehmood
- Department of Botany, Government College University, Lahore, 54000, Pakistan
| | - Usman Ahmed Khan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, 54000, Pakistan
| | - Zahid Mehmood
- Department of Botany, Government College University, Lahore, 54000, Pakistan
- Department of Environmental Engineering and Management, Chaoyang University of Technology, Taichung, 413310, Taiwan
| | - Arooba John
- Department of Botany, Government College University, Lahore, 54000, Pakistan
| | - Binyameen
- Department of Botany, Government College University, Lahore, 54000, Pakistan
| | - Zafar Iqbal Khan
- Department of Botany, University of Sargodha, Sargodha, Pakistan
| | - Hsi-Hsien Yang
- Department of Environmental Engineering and Management, Chaoyang University of Technology, Taichung, 413310, Taiwan
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Nikraftar S, Ebrahimzadegan R, Majdi M, Mirzaghaderi G. Genome-wide analysis of the C2H2-ZFP gene family in Stevia rebaudiana reveals involvement in abiotic stress response. Sci Rep 2024; 14:6164. [PMID: 38486071 PMCID: PMC10940304 DOI: 10.1038/s41598-024-56624-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Stevia (Stevia rebaudiana Bertoni) is a natural sweetener plant that accumulates highly sweet steviol glycosides (SGs) especially in leaves. Stevia is native to humid areas and does not have a high tolerance to drought which is the most serious abiotic stress restricting its production worldwide. C2H2 zinc finger proteins (C2H2-ZFPs) are a group of well-known transcription factors that involves in various developmental, physiological and biochemical activities as well as in response to abiotic stresses. Here we analyzed C2H2-ZFP gene family in stevia and identified a total of 185 putative SrC2H2-ZF proteins from the genome sequence of S. rebaudiana. We further characterized the identified C2H2-ZF domains and their organization, additional domains and motifs and analyzed their physicochemical properties, localization and gene expression patterns. The cis-element analysis suggested multiple roles of SrC2H2-ZFPs in response to light, phytohormone, and abiotic stresses. In silico analysis revealed that the stevia C2H2-ZFP genes are interactively expressed in different tissues and developmental stages and some C2H2-ZFP genes are involved in response to drought stress. This study provides a background for future exploration of the functional, and regulatory aspects of the C2H2-ZFP gene family in S. rebaudiana.
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Affiliation(s)
- Shahla Nikraftar
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Rahman Ebrahimzadegan
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Mohammad Majdi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran.
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Fu PC, Guo QQ, Chang D, Gao QB, Sun SS. Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis. PLANT DIVERSITY 2024; 46:194-205. [PMID: 38807911 PMCID: PMC11128845 DOI: 10.1016/j.pld.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 05/30/2024]
Abstract
Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of FST compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qiao-Qiao Guo
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Di Chang
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
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11
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Xiao F, Zhao Y, Wang X, Jian X. Characterization of the chloroplast genome of Gleditsia species and comparative analysis. Sci Rep 2024; 14:4262. [PMID: 38383559 PMCID: PMC10881578 DOI: 10.1038/s41598-024-54608-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8-75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", and "rpl32-trnL" in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- College of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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12
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Chen H, Yuan YW. Genetic basis of nectar guide trichome variation between bumblebee- and self-pollinated monkeyflowers (Mimulus): role of the MIXTA-like gene GUIDELESS. BMC PLANT BIOLOGY 2024; 24:62. [PMID: 38262916 PMCID: PMC10804488 DOI: 10.1186/s12870-024-04736-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
Nectar guide trichomes play crucial ecological roles in bee-pollinated flowers, as they serve as footholds and guides for foraging bees to access the floral rewards. However, the genetic basis of natural variation in nectar guide trichomes among species remains poorly understood. In this study, we performed genetic analysis of nectar guide trichome variation between two closely related monkeyflower (Mimulus) species, the bumblebee-pollinated Mimulus lewisii and self-pollinated M. parishii. We demonstrate that a MIXTA-like R2R3-MYB gene, GUIDELESS, is a major contributor to the nectar guide trichome length variation between the two species. The short-haired M. parishii carries a recessive allele due to non-synonymous substitutions in a highly conserved motif among MIXTA-like MYB proteins. Furthermore, our results suggest that besides GUIDELESS, additional loci encoding repressors of trichome elongation also contribute to the transition from bumblebee-pollination to selfing. Taken together, these results suggest that during a pollination syndrome switch, changes in seemingly complex traits such as nectar guide trichomes could have a relatively simple genetic basis, involving just a few genes of large effects.
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Affiliation(s)
- Hongfei Chen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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13
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Jin G, Zhang X, Yu S, Du Y, Wang M, Zhao C, Zhang M. Screening and validation of optimal miRNA reference genes in different developing stages and tissues of Lilium henryi Baker. Sci Rep 2024; 14:1545. [PMID: 38233457 PMCID: PMC10794412 DOI: 10.1038/s41598-024-51562-1] [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: 08/24/2023] [Accepted: 01/06/2024] [Indexed: 01/19/2024] Open
Abstract
Dynamic miRNA detection using the qRT-PCR technique requires appropriate reference genes to ensure data reliability. Previous studies have screened internal reference genes in plants during embryonic development and various stress treatment, involving relatively few tissues and organs. There is no relevant miRNA study in Lilium henryi Baker and limited research on the optimal miRNA reference genes in lilies, such as 5S, 18S, U6 and Actin. Twelve genes were selected as candidate reference genes whose expression stability was analyzed in petals at different developmental stages and other tissues using various algorithms, such as geNorm, NormFinder, BestKeeper, and Delta CT. The results revealed that the optimal combination of reference genes for Lilium henryi Baker petals at different developmental stages was osa-miR166m and osa-miR166a-3p, while that for different tissues of Lilium henryi Baker was osa-miR166g-3p and osa-miR166a-3p.Four important genes related to growth and development regulation, namely, osa-miR156a, osa-miR395b, osa-miR396a-3p, and osa-miR396a-5p, were selected for validation. The findings of the present study could contribute to future investigations onmiRNA expression and the related functions in Lilium henryi Baker while providing important references for the normalization of the miRNA expression in other varieties of lily.
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Affiliation(s)
- Ge Jin
- Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
- College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, 130118, China
| | - Xiuhai Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
| | - Shiyin Yu
- Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
- College of Landscape Achitecture, Beijing Forestry University, Beijing, 100097, China
| | - Yunpeng Du
- Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100097, China
| | - Meixian Wang
- College of Landscape Achitecture, Beijing Forestry University, Beijing, 100097, China
| | - Chunli Zhao
- College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, 130118, China.
| | - Mingfang Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100097, China.
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14
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Sui C, Cheng S, Wang D, Lv L, Meng H, Du M, Li J, Su P, Guo S. Systematic identification and characterization of the soybean ( Glycine max) B-box transcription factor family. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2155570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Chao Sui
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Shanshan Cheng
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Deying Wang
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Lujia Lv
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Huiran Meng
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Mengxue Du
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Jingyu Li
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Peisen Su
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
| | - Shangjing Guo
- Liaocheng University Crop Germplasm Innovation Research Institute, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, PR China
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15
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Esmail SM, Jarquín D, Börner A, Sallam A. Genome-wide association mapping highlights candidate genes and immune genotypes for net blotch and powdery mildew resistance in barley. Comput Struct Biotechnol J 2023; 21:4923-4932. [PMID: 37867969 PMCID: PMC10585327 DOI: 10.1016/j.csbj.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/08/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
Net blotch (NB) and powdery mildew (PM) are major barley diseases with the potential to cause a dramatic loss in grain yield. Breeding for resistant barley genotypes in combination with identifying candidate resistant genes will accelerate the genetic improvement for resistance to NB and PM. To address this challenge, a set of 122 highly diverse barley genotypes from 34 countries were evaluated for NB and PM resistance under natural infection for in two growing seasons. Moreover, four yield traits; plant height (Ph), spike length (SL), spike weight (SW), and the number of spikelets per spike (NOS) were recorded. High genetic variation was found among genotypes in all traits scored in this study. No significant phenotypic correlation was found in the resistance between PM and NB. Immune genotypes for NB and PM were identified. A total of 21 genotypes were immune to both diseases. Of the 21 genotypes, the German genotype HOR_9570 was selected as the most promising genotype that can be used for future breeding programs. Furthermore, a genome-wide association study (GWAS) was used to identify resistant alleles to PM and NB. The results of GWAS revealed a set of 14 and 25 significant SNPs that were associated with increased resistance to PM and NB, respectively. This study provided very important genetic resources that are highly resistant to the Egyptian PM and NB pathotypes and revealed SNP markers that can be utilized to genetically improve resistance to PM and NB.
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Affiliation(s)
- Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Diego Jarquín
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Ahmed Sallam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
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16
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Regmi R, Newman TE, Khentry Y, Kamphuis LG, Derbyshire MC. Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets. BMC Genomics 2023; 24:582. [PMID: 37784009 PMCID: PMC10544508 DOI: 10.1186/s12864-023-09686-7] [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: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Several phytopathogens produce small non-coding RNAs of approximately 18-30 nucleotides (nt) which post-transcriptionally regulate gene expression. Commonly called small RNAs (sRNAs), these small molecules were also reported to be present in the necrotrophic pathogen Sclerotinia sclerotiorum. S. sclerotiorum causes diseases in more than 400 plant species, including the important oilseed crop Brassica napus. sRNAs can further be classified as microRNAs (miRNAs) and short interfering RNAs (siRNAs). Certain miRNAs can activate loci that produce further sRNAs; these secondary sRNA-producing loci are called 'phased siRNA' (PHAS) loci and have only been described in plants. To date, very few studies have characterized sRNAs and their endogenous targets in S. sclerotiorum. RESULTS We used Illumina sequencing to characterize sRNAs from fungal mycelial mats of S. sclerotiorum spread over B. napus leaves. In total, eight sRNA libraries were prepared from in vitro, 12 h post-inoculation (HPI), and 24 HPI mycelial mat samples. Cluster analysis identified 354 abundant sRNA clusters with reads of more than 100 Reads Per Million (RPM). Differential expression analysis revealed upregulation of 34 and 57 loci at 12 and 24 HPI, respectively, in comparison to in vitro samples. Among these, 25 loci were commonly upregulated. Altogether, 343 endogenous targets were identified from the major RNAs of 25 loci. Almost 88% of these targets were annotated as repeat element genes, while the remaining targets were non-repeat element genes. Fungal degradome reads confirmed cleavage of two transposable elements by one upregulated sRNA. Altogether, 24 milRNA loci were predicted with both mature and milRNA* (star) sequences; these are both criteria associated previously with experimentally verified miRNAs. Degradome sequencing data confirmed the cleavage of 14 targets. These targets were related to repeat element genes, phosphate acetyltransferases, RNA-binding factor, and exchange factor. A PHAS gene prediction tool identified 26 possible phased interfering loci with 147 phasiRNAs from the S. sclerotiorum genome, suggesting this pathogen might produce sRNAs that function similarly to miRNAs in higher eukaryotes. CONCLUSIONS Our results provide new insights into sRNA populations and add a new resource for the study of sRNAs in S. sclerotiorum.
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Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
- Present address: Microbiome for One Systems Health, CSIRO, Urrbrae, South Australia, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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Tian Y, Liu X, Xu Y, Yu B, Wang L, Qu X. Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots. Sci Rep 2023; 13:15622. [PMID: 37730791 PMCID: PMC10511529 DOI: 10.1038/s41598-023-42945-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people's republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.
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Affiliation(s)
- Yulu Tian
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, No. 1166 Liutai Avenue, Wenjiang District, Chengdu, 611137, China
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Xue Liu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
| | - Yuanjiang Xu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Le Wang
- College of Life Science and Food Engineering, Chongqing Three Gorges University, 666 Tianxing Road, Wanzhou District, Chongqing, 404100, China
| | - Xianyou Qu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
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Rehman OU, Uzair M, Farooq MS, Saleem B, Attacha S, Attia KA, Farooq U, Fiaz S, El-Kallawy WH, Kimiko I, Khan MR. Comprehensive insights into the regulatory mechanisms of lncRNA in alkaline-salt stress tolerance in rice. Mol Biol Rep 2023; 50:7381-7392. [PMID: 37450076 DOI: 10.1007/s11033-023-08648-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Alkaline-salt is one of the abiotic stresses that slows plant growth and developmental processes and threatens crop yield. Long non-coding RNAs (lncRNAs) are endogenous RNA found in plants that engage in a variety of cellular functions and stress responses. METHOD lncRNAs act as competing endogenous RNAs (ceRNA) and constitute a new set of gene control. The precise regulatory mechanism by which lncRNAs function as ceRNAs in response to alkaline-salt stress remains unclear. We identified alkaline-salt responsive lncRNAs using transcriptome-wide analysis of two varieties including alkaline-salt tolerant [WD20342 (WD)] and alkaline-salt sensitive [Caidao (CD)] rice cultivar under control and alkaline-salt stress treated [WD20342 (WDT, and Caidao (CDT)] conditions. RESULTS Investigating the competitive relationships between mRNAs and lncRNAs, we next built a ceRNA network involving lncRNAs based on the ceRNA hypothesis. Expression profiles revealed that a total of 65, 34, and 1549 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs were identified in alkaline-salt tolerant WD (Control) vs. WDT (Treated). Similarly, 75 DE-lncRNAs, 34 DE-miRNAs, and 1725 DE-mRNAs (including up-regulated and down-regulated) were identified in alkaline-salt sensitive CD (Control) vs. CDT (Treated), respectively. An alkaline-salt stress ceRNA network discovered 321 lncRNA-miRNA-mRNA triplets in CD and CDT, with 32 lncRNAs, 121 miRNAs, and 111 mRNAs. Likewise, 217 lncRNA-miRNA-mRNA triplets in WD and WDT revealed the NONOSAT000455-osa_miR5809b-LOC_Os11g01210 triplet with the highest degree as a hub node with the most significant positive correlation in alkaline-salt stress response. CONCLUSION The results of our investigation indicate that osa-miR5809b is dysregulated and plays a part in regulating the defense response of rice against alkaline-salt stress. Our study highlights the regulatory functions of lncRNAs acting as ceRNAs in the mechanisms underlying alkaline-salt resistance in rice.
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Affiliation(s)
- Obaid Ur Rehman
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
| | - Muhammad Shahbaz Farooq
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Safira Attacha
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, Science College, King Saud University, POX, Riyadh, 2455-11451, Saudi Arabia.
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Wael H El-Kallawy
- Agriculture Research Center, (ARC), Rice Research and Training Center, (RRTC) Sakha, Field Crop Research Institute, Sakha, Egypt
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
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Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Meghana R, Anand PP, Vardhanan YS. Molecular and morphometric analyses reveal host-specific cryptic speciation in a mite species, Tetranychus neocaledonicus (Andre, 1933) (Acari: Tetranychidae). Zootaxa 2023; 5306:61-96. [PMID: 37518535 DOI: 10.11646/zootaxa.5306.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 08/01/2023]
Abstract
Host- and habitat-induced morphological shape and size variations are common in phytophagous and parasitic taxa. Several integrated morphological and molecular techniques have been commonly used to understand host-induced morpho-cryptic species forms. Compared to other arthropods, cryptic speciation was more common in Acari. This study focused on the host-specific morphological cryptic shape and size variations of Tetranychus neocaledonicus, collected from moringa and cassava hosts. We used geometric morphometric analysis to uncover the shape and size of inter-and intra-spider mite populations, and discovered that host-specific shape and size variations existed in spider mites regardless of sex. Interestingly, there was no phylogenetic signal in spider mites, implying that the morpho-cryptic speciation of T. neocaledonicus is solely based on the host-induced selection. The molecular clock hypothesis was accepted in our CO1 and 18s rRNA phylogeny analyses, and spider mites collected from both hosts were genetically less diverse. We conclude that T. neocaledonicus exhibited morphologically detectable cryptic population diversity in each host but that these populations are evolutionarily young form. Apart from these host-induced variations, we also monitored the impact of the clearing agent (lactic acid) on the shape and size of T. neocaledonicus; from this study, we proved that the clearing agent significantly alters the taxonomically important morphological traits of spider mites irrespective of the mites' sex, as confirmed by multivariate statistical analysis. This is the first study report to investigated the host-induced morphological variations of spider mites and the impact of a clearing agent.
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Affiliation(s)
- R Meghana
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
| | - P P Anand
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
| | - Y Shibu Vardhanan
- Biochemistry & Toxicology Division; Department of Zoology; University of Calicut; Kerala; India.
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21
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Umer MJ, Zheng J, Yang M, Batool R, Abro AA, Hou Y, Xu Y, Gebremeskel H, Wang Y, Zhou Z, Cai X, Liu F, Zhang B. Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer. Funct Integr Genomics 2023; 23:142. [PMID: 37121989 DOI: 10.1007/s10142-023-01065-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
The soil-borne pathogen Verticillium dahliae, also referred as "The Cotton Cancer," is responsible for causing Verticillium wilt in cotton crops, a destructive disease with a global impact. To infect cotton plants, the pathogen employs multiple virulence mechanisms such as releasing enzymes that degrade cell walls, activating genes that contribute to virulence, and using protein effectors. Conversely, cotton plants have developed numerous defense mechanisms to combat the impact of V. dahliae. These include strengthening the cell wall by producing lignin and depositing callose, discharging reactive oxygen species, and amassing hormones related to defense. Despite the efforts to develop resistant cultivars, there is still no permanent solution to Verticillium wilt due to a limited understanding of the underlying molecular mechanisms that drive both resistance and pathogenesis is currently prevalent. To address this challenge, cutting-edge technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), host-induced gene silencing (HIGS), and gene delivery via nano-carriers could be employed as effective alternatives to control the disease. This article intends to present an overview of V. dahliae virulence mechanisms and discuss the different cotton defense mechanisms against Verticillium wilt, including morphophysiological and biochemical responses and signaling pathways including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and strigolactones (SLs). Additionally, the article highlights the significance of microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) in gene expression regulation, as well as the different methods employed to identify and functionally validate genes to achieve resistance against this disease. Gaining a more profound understanding of these mechanisms could potentially result in the creation of more efficient strategies for combating Verticillium wilt in cotton crops.
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Affiliation(s)
- Muhammad Jawad Umer
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Zheng
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China
| | - Mengying Yang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Raufa Batool
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aamir Ali Abro
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Haileslassie Gebremeskel
- Mehoni Agricultural Research Center, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Yuhong Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - ZhongLi Zhou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.
| | - Baohong Zhang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Luo S, Zhang G, Zhang Z, Wan Z, Liu Z, Lv J, Yu J. Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.). BMC PLANT BIOLOGY 2023; 23:214. [PMID: 37095428 PMCID: PMC10123990 DOI: 10.1186/s12870-023-04216-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND BRASSINAZOLE-RESISTANT (BZR) is a class of specific transcription factor (TFs) involved in brassinosteroid (BR) signal transduction. The regulatory mechanism of target genes mediated by BZR has become one of the key research areas in plant BR signaling networks. However, the functions of the BZR gene family in cucumber have not been well characterized. RESULTS In this study, six CsBZR gene family members were identified by analyzing the conserved domain of BES1 N in the cucumber genome. The size of CsBZR proteins ranges from 311 to 698 amino acids and are mostly located in the nucleus. Phylogenetic analysis divided CsBZR genes into three subgroups. The gene structure and conserved domain showed that the BZR genes domain in the same group was conserved. Cis-acting element analysis showed that cucumber BZR genes were mainly involved in hormone response, stress response and growth regulation. The qRT-PCR results also confirmed CsBZR response to hormones and abiotic stress. CONCLUSION Collectively, the CsBZR gene is involved in regulating cucumber growth and development, particularly in hormone response and response to abiotic stress. These findings provide valuable information for understanding the structure and expression patterns of BZR genes.
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Affiliation(s)
- Shilei Luo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Guobin Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zeyu Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zilong Wan
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zeci Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jian Lv
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jihua Yu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China.
- College of Horticulture, Gansu Agricultural University, Lanzhou, China.
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Ramazan S, Jan N, John R. Comparative protein analysis of two maize genotypes with contrasting tolerance to low temperature. BMC PLANT BIOLOGY 2023; 23:183. [PMID: 37020183 PMCID: PMC10074880 DOI: 10.1186/s12870-023-04198-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Low temperature (LT) stress is one of the major environmental stress factors affecting the growth and yield of maize (Zea mays L.). Hence, it is important to unravel the molecular mechanisms behind LT stress tolerance to improve molecular breeding in LT tolerant genotypes. In the present study, two maize genotypes viz. Gurez local from Kashmir Himalaya and tropical grown GM6, were dissected for their LT stress response in terms of accumulation of differentially regulated proteins (DRPs). Leaf proteome analysis at three-leaf stage of maize seedlings subjected to LT stress of 6 °C for a total of 12 h duration was performed using two dimensional gel electrophoresis (2D-PAGE) followed by subsequent identification of the proteins involved. RESULTS After MALDI-TOF (Matrix-assisted laser desorption/ionization-time of flight) and bioinformatics analysis, 19 proteins were successfully identified in Gurez local, while as 10 proteins were found to get successful identification in GM6. The interesting observations from the present investigation is the identification of three novel proteins viz. threonine dehydratase biosynthetic chloroplastic, thylakoidal processing peptidase 1 chloroplastic, and nodulin-like protein, whose role in abiotic stress tolerance, in general, and LT stress, in particular, has not been reported so far. It is important to highlight here that most of LT responsive proteins including the three novel proteins were identified from Gurez local only, owing to its exceptional LT tolerance. From the protein profiles, obtained in both genotypes immediately after LT stress perception, it was inferred that stress responsive protein accumulation and their expression fashion help the Gurez local in seedling establishment and withstand unfavorable conditions as compared to GM6. This was inferred from the findings of pathway enrichment analysis like regulation of seed growth, timing of floral transition, lipid glycosylation, and aspartate family amino acid catabolic processes, besides other key stress defense mechanisms. However, in GM6, metabolic pathways enriched were found to be involved in more general processes including cell cycle DNA replication and regulation of phenylpropanoid metabolism. Furthermore, majority of the qRT-PCR results of the selected proteins demonstrated positive correlation between protein levels and transcript abundance, thereby strengthening our findings. CONCLUSIONS In conclusion, our findings reported majority of the identified proteins in Gurez local exhibiting up-regulated pattern under LT stress as compared to GM6. Furthermore, three novel proteins induced by LT stress were found in Gurez local, requiring further functional validation. Therefore, our results offer more insights for elucidating the molecular networks mediating LT stress tolerance in maize.
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Affiliation(s)
- Salika Ramazan
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India
| | - Nelofer Jan
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India
| | - Riffat John
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India.
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24
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Borah P, Rene ER, Rangan L, Mitra S. Phytoremediation of nickel and zinc using Jatropha curcas and Pongamia pinnata from the soils contaminated by municipal solid wastes and paper mill wastes. ENVIRONMENTAL RESEARCH 2023; 219:115055. [PMID: 36574797 DOI: 10.1016/j.envres.2022.115055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/14/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The primary source of soil pollution is a complex mixture of numerous inorganic and organic compounds (including chlorinated compounds, nutrients, and heavy metals, etc.). The presence of all of these compounds makes remediation and cleanup difficult. In this study, the phytoremediation ability of Jatropha curcas and Pongamia pinnata was tested to remove nickel (Ni) and Zinc (Zn) from paper mill and municipal landfill contaminated soils, to understand the uptake potential and to estimate the accumulation pattern of Ni and Zn in the vegetative parts of the plant. The experiments were carried out in pots (3 kg capacity) and the different combinations of soil were made by mixing the contaminated soil with a reference soil (forest soil) as T0, T25, T50, T75 and T100. The plant biomass, chlorophyll content, proline, nitrate reductase activity and metal removal efficiency (%)were determined after 120 DAS (i.e., the days after sowing). The results of the study showed that with increasing metal stress, there is a reduction in the above-ground biomass content in both the plant species with a slightly less impact on the root biomass. Over a period of 4 months, J. curcas and P. pinnata removed 82-86% and 93-90% Ni, respectively. The removal of Zn was significantly less as compared to Ni as most of the Zn remained in the belowground part (roots) and in the soil. Besides, the phytostabilization capacities of the plants were calculated on the basis of their tolerance index (TI), bioaccumulation factor (BAF) and translocation factor (TF). The low BAF and TF values with increasing heavy metals (HMs) content indicates its higher phytostabilization capacity in the root and rhizospheric region as compared to phytoaccumulation.
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Affiliation(s)
- Pallabi Borah
- Department of Environmental Science, Royal Global University, Guwahati, Assam, 781035, India
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands
| | - Latha Rangan
- Applied Biodiversity Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Assam, 781039, India
| | - Sudip Mitra
- Agro-ecotechnology Laboratory, School of Agro & Rural Technology, Indian Institute of Technology Guwahati (IITG), Assam, 781039, India; Centre for Disaster Management and Research, Indian Institute of Technology Guwahati (IITG), Assam, 781039, India.
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25
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Haghighi TM, Saharkhiz MJ, Kavoosi G, Zarei M. Adaptation of Glycyrrhiza glabra L. to water deficiency based on carbohydrate and fatty acid quantity and quality. Sci Rep 2023; 13:1766. [PMID: 36721012 PMCID: PMC9889331 DOI: 10.1038/s41598-023-28807-6] [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: 09/28/2022] [Accepted: 01/24/2023] [Indexed: 02/02/2023] Open
Abstract
Water deficit affects agricultural systems negatively globally. This research objective was to mitigate drought's detrimental effects on plants metabolite profiling by utilizing biofertilizers and mineral nutrition. The carbohydrate content and fatty acid profile of Licorice (Glycyrrhiza glabra) were assessed under Silicon (Si) nutrition, Claroiedoglomus etunicatum inoculation (F), and drought stress (100, 80, 60, 40, and 20% of field capacity (FC)). Results showed that Si application increased total sugar content under severe drought levels (20 and 40% FC) and made it reach 12.41 and 12.63 g/100 g DW, respectively. Sucrose, as the predominant sugar of licorice, was at its highest level (13.1 g/100 g DW) in response to integrated values of F and Si (60% FC). Gas chromatography-mass spectrometry showed that the majority of fatty acid components in plants were 9-Octadecenoic acid (8.72-71.27%), 9,12-Octadecadienoic acid (0.1-56.43%), Hexadecanoic acid (12.84-30.59%), Octadecanoic acid (6.9-15.3%), Docosanoic acid (0.57-2.77%), Eicosanoic acid (1.07-2.64%), and 7-Hexadecenoic acid (0.26-2.62%). Since a lower omega6/omega3 ratio represents a healthier product, the lowest ratio (0.25%) was observed in well-watered inoculated plants. Also, severe drought-treated plants under integrated Si and F applications showed a low omega6/omega3 ratio (1.88%). In conclusion, Si and F improved synergistically the carbohydrate content and fatty acid profile in plants, despite the drought stress.
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Affiliation(s)
- Tahereh Movahhed Haghighi
- Department of Horticultural Science, Faculty of Agriculture, Shiraz University, Shiraz, 71441-13131, Iran
| | - Mohammad Jamal Saharkhiz
- Department of Horticultural Science, Faculty of Agriculture, Shiraz University, Shiraz, 71441-13131, Iran. .,Medicinal Plants Processing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Gholamreza Kavoosi
- Institute of Biotechnology, Shiraz University, Shiraz, 71441-65186, Iran
| | - Mehdi Zarei
- Department of Soil Science, College of Agriculture, University of Shiraz, Shiraz, Iran.,Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, 73819-43885, Iran
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26
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Jiang D, Cai X, Gong M, Xia M, Xing H, Dong S, Tian S, Li J, Lin J, Liu Y, Li HL. Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae). BMC Genomics 2023; 24:30. [PMID: 36653780 PMCID: PMC9848714 DOI: 10.1186/s12864-023-09115-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. RESULTS We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. CONCLUSIONS This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.
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Affiliation(s)
- Dongzhu Jiang
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.410654.20000 0000 8880 6009College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200 China
| | - Xiaodong Cai
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Min Gong
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.411581.80000 0004 1790 0881College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, 404100 China
| | - Maoqin Xia
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Haitao Xing
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Shanshan Dong
- grid.9227.e0000000119573309Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Shuming Tian
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.411581.80000 0004 1790 0881College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, 404100 China
| | - Jialin Li
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Junyao Lin
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Yiqing Liu
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.410654.20000 0000 8880 6009College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200 China
| | - Hong-Lei Li
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
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Wang W, Wang X, Shi Y, Yin Q, Gao R, Wang M, Xiang L, Wu L. Identification of Laportea bulbifera using the complete chloroplast genome as a potentially effective super-barcode. J Appl Genet 2023; 64:231-245. [PMID: 36633756 DOI: 10.1007/s13353-022-00746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/12/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Laportea bulbifera, a Miao medicine grown in karst areas, has exerted a unique curative effect on skin itching in the elderly, with an annual sales of > 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation high-throughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence is used as a potentially effective super-barcode and the highly variable regions (ycf1, matK, and ndhD) can be used as potentially specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species.
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Affiliation(s)
- Wenting Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xingwen Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qinggang Yin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ranran Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengyue Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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28
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Zhao ZN, Yu X. The complete chloroplast genome of Cynoglossum amabile Stapf & J. R. Drumm., 1906 (Boraginaceae), a traditional Chinese herbal medicine. Mitochondrial DNA B Resour 2023; 8:52-56. [PMID: 36620318 PMCID: PMC9815245 DOI: 10.1080/23802359.2022.2160219] [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] [Indexed: 01/04/2023] Open
Abstract
Cynoglossum amabile Stapf & J. R. Drumm., 1906 is a traditional Chinese herbal medicine from southwest China. To better determine its phylogenetic relatedness to other Boraginaceae species, the chloroplast (cp) genome of C. amabile was sequenced. The complete cp genome of C. amabile is 151,532 bp in length, containing a small single-copy (SSC) region with a length of 17,366 bp, a large single-copy (LSC) region with a length of 82,902 bp, and a pair of inverted repeats (IRs) regions each with a length of 25,632 bp. The overall GC content of the cp genome is 37.4%. The maximum-likelihood phylogenetic tree showed that Bothriospermum zeylanicum (J. Jacq.) Druce, 1917 was closely related to C. amabile.
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Affiliation(s)
- Zhen-Ning Zhao
- School of Forestry, Southwest Forestry University, Kunming, China
| | - Xiao Yu
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China,CONTACT Xiao Yu School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China
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29
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Motafeghi F, Gerami M, Mortazavi P, Khayambashi B, Ghassemi-Barghi N, Shokrzadeh M. Green synthesis of silver nanoparticles, graphene, and silver-graphene nanocomposite using Melissa officinalis ethanolic extract: Anticancer effect on MCF-7 cell line. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2023; 26:57-68. [PMID: 36594058 PMCID: PMC9790052 DOI: 10.22038/ijbms.2022.65503.14410] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/12/2022] [Indexed: 01/04/2023]
Abstract
Objectives Nanotechnology has helped a lot in diagnosing and treating multiple illnesses, specifically cancer, and increasing the development of targeted drug delivery methods. Nanocomposites are materials with at least one component smaller than 100 nm. Therefore, this study aims to assess the anticancer effects of silver-graphene nanocomposite on MCF-7. Materials and Methods In this study, the rate of inhibition of cancer cell growth and production of reactive oxygen radicals, malondialdehyde, and glutathione stores in MCF7 cells were investigated. Cancer cells were exposed to nano particles for 48 hr. Silver nanoparticles and graphene both reduced the growth rate of MCF-7. Results Subsequently, by treating the cells with silver-graphene nanocomposite, the rate of inhibition of cell growth at the highest concentration was 84.60%. Nanoparticles also inhibited the growth of cancer cells through the oxidative stress pathway by increasing the amount of intracellular ROS, followed by increasing malondialdehyde and decreasing glutathione stores, so that at the highest combined concentration of nanoparticles, the amounts of LPO and ROS increased up to 70% and 74 %, and glutathione reserves decreased by 16%. Conclusion Treatment of MCF-7 cells with silver or graphene nanoparticles and combination treatment with these two substances against cisplatin have sound effects, and by affecting oxidative stress factors, such as increased ROS and subsequent increase in lipid membrane damage, inhibit cell growth and proliferation. According to the mathematical model, silver graphene nanocomposite> silver nanoparticles> graphene has the best effect in inhibiting the growth of cancer cells, respectively.
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Affiliation(s)
- Farzaneh Motafeghi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran ,Corresponding authors: Farzaneh Motafeghi. Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran. ; Mohammad Shokrzadeh. Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mahyar Gerami
- Ministry of Science, Research and Technology, Department of Plant Physiology Biology, Sana Higher Education Institute, Mazandaran, Sari, Iran
| | - Parham Mortazavi
- Student Research Committee, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Babak Khayambashi
- Soil and Water Research Department, Isfahan Agricultural and Natural Resources Research and Education Center, AREEO, Isfahan, Iran
| | - Nasrin Ghassemi-Barghi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Shokrzadeh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran ,Corresponding authors: Farzaneh Motafeghi. Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran. ; Mohammad Shokrzadeh. Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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Karam A, El-Assal SEDS, Hussein BA, Atia MAM. Transcriptome data mining towards characterization of single nucleotide polymorphisms (SNPs) controlling salinity tolerance in bread wheat. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2081516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Ahmed Karam
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | | | - Mohamed Atia Mohamed Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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Dong R, Luo B, Tang L, Wang QX, Lu ZJ, Chen C, Yang F, Wang S, He J. A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.). BMC Genomics 2022; 23:814. [PMID: 36482290 PMCID: PMC9733113 DOI: 10.1186/s12864-022-09039-w] [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: 07/06/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown. RESULTS We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance. CONCLUSION This study identifies specific genes involved in Ca2+ signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.
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Affiliation(s)
- Rui Dong
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Ben Luo
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Li Tang
- grid.428986.90000 0001 0373 6302School of Tropical Crops, Hainan University, Haikou, China
| | - Qiu-xia Wang
- grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-ecosystems, China, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhong-Jie Lu
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Chao Chen
- grid.443382.a0000 0004 1804 268XDepartment of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China ,grid.443382.a0000 0004 1804 268XKey Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Feng Yang
- Grassland Technology Experiment and Extension Station, Guiyang, China
| | - Song Wang
- Grassland Technology Experiment and Extension Station, Guiyang, China
| | - Jin He
- grid.443382.a0000 0004 1804 268XCollege of Agriculture, Guizhou University, Guiyang, China
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He K, Yang J, Shi Q, Guan L, Sun L, Chen Z, Feng J, Dong S. Fluorescent aptamer-modified mesoporous silica nanoparticles for quantitative acetamiprid detection. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:88182-88192. [PMID: 35831655 DOI: 10.1007/s11356-022-21970-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Acetamiprid (ACE) is widely used to control aphids, brown planthoppers, and other pests in agricultural production. However, ACE is difficult to degrade in the environment, resulting in excessive residue, which causes acute and chronic toxicity to human beings and non-target organisms. Therefore, the development of a rapid, convenient, and highly sensitive method to quantify ACE is essential. In this study, aminated mesoporous silica nanoparticles (MSNs-NH2) were synthesized by one-pot method, and 6-carboxyl fluorescein modified aptamers (FAM-Apt) of ACE were adsorbed on the surface of MSNs-NH2 by electrostatic interaction. Finally, a simple and sensitive fluorescence analysis method for the rapid detection of ACE was established. In the absence of ACE, the negatively charged FAM-Apt was electrostatically bound to the positively charged MSNs-NH2, followed by centrifugation to precipitate MSNs-NH2@FAM-Apt, and no fluorescent signal was detected in the supernatant. In the presence of ACE, the specific combination of FAM-Apt with ACE was greater than its electrostatic interaction with MSNs-NH2, so that FAM-Apt was separated from MSNs-NH2, and the supernatant had strong fluorescence signal after centrifugation. For ACE detection, the linear concentration range was 50-1100 ng/mL, and the detection limit (LOD) was 30.26 ng/mL. The method exhibited high sensitivity, selectivity and reproducibility, which is suitable for practical sample analysis and provides guidance for rapid detection of pesticide residues.
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Affiliation(s)
- Kangli He
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Jinghan Yang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Qiuyun Shi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Lingjun Guan
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Li Sun
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyang Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Jianguo Feng
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Sa Dong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
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Ren W, Chen L, Xie ZM, Peng X. Combined transcriptome and metabolome analysis revealed pathways involved in improved salt tolerance of Gossypium hirsutum L. seedlings in response to exogenous melatonin application. BMC PLANT BIOLOGY 2022; 22:552. [PMID: 36451095 PMCID: PMC9710056 DOI: 10.1186/s12870-022-03930-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Salinization is major abiotic stress limiting cotton production. Melatonin (MT) has been implicated in salt stress tolerance in multiple crops including upland cotton. Here, we explored the transcriptomic and metabolomic response of a salt-tolerant self-bred high-yielding cotton line SDS-01, which was exogenously sprayed with four MT concentrations (50, 100, 200, and 500 μM). RESULTS Here we found that MT improves plant biomass and growth under salt stress. The combined transcriptome sequencing and metabolome profiling approach revealed that photosynthetic efficiency is improved by increasing the expressions of chlorophyll metabolism and antenna proteins in MT-treated seedlings. Additionally, linoleic acid and flavonoid biosynthesis were improved after MT treatment. The Na+/K+ homeostasis-related genes were increasingly expressed in salt-stressed seedlings treated with MT as compared to the ones experiencing only salt stress. Melatonin treatment activated a cascade of plant-hormone signal transduction and reactive oxygen scavenging genes to alleviate the detrimental effects of salt stress. The global metabolome profile revealed an increased accumulation of flavonoids, organic acids, amino acids and derivatives, saccharides, and phenolic acids in MT-treated seedlings. Interestingly, N, N'-Diferuloylputrescine a known antioxidative compound was highly accumulated after MT treatment. CONCLUSION Collectively, our study concludes that MT is a salt stress regulator in upland cotton and alleviates salt-stress effects by modulating the expressions of photosynthesis (and related pathways), flavonoid, ROS scavenging, hormone signaling, linoleic acid metabolism, and ion homeostasis-related genes.
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Affiliation(s)
- Wei Ren
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
- China Fukang Station of Desert Ecology, Chinese Academy of Sciences, Fukang, 831505 Xinjiang China
| | - Li Chen
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
- China Fukang Station of Desert Ecology, Chinese Academy of Sciences, Fukang, 831505 Xinjiang China
| | - Zong ming Xie
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, Xinjiang China
| | - Xiaofeng Peng
- Agricultural Science Research Institute of the third division of Xinjiang production and Construction Corps, Tumushuke, 843800 Xinjiang China
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Kumari B, Bharti VK. Recent advancements in toxicology, modern technology for detection, and remedial measures for arsenic exposure: review. Biotechnol Genet Eng Rev 2022:1-43. [PMID: 36411979 DOI: 10.1080/02648725.2022.2147664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/15/2022] [Indexed: 11/23/2022]
Abstract
Arsenic toxicity has become a major global health concern for humans and animals due to extensive environmental and occupational exposure to arsenic-contaminated water, air, soil, and plant and animal origin food. It has a wide range of detrimental effects on animals, humans, and the environment. As a result, various experimental and clinical studies were undertaken and are undergoing to understand its source of exposures, pathogenesis, identify key biomarkers, the medical and economic impact on affected populations and ecosystems, and their timely detection and control measures. Despite these extensive studies, no conclusive information for the prevention and control of arsenic toxicity is available, owing to complex epidemiology and pathogenesis, including an imprecise approach and repetitive work. As a result, there is a need for literature that focuses on recent studies on the epidemiology, pathogenesis, detection, and ameliorative measures of arsenic toxicity to assist researchers and policymakers in the practical future planning of research and community control programs. According to the preceding viewpoint, this review article provides an extensive analysis of the recent progress on arsenic exposure to humans through the environment, livestock, and fish, arsenic toxicopathology, nano-biotechnology-based detection, and current remedial measures for the benefit of researchers, academicians, and policymakers in controlling arsenic eco-toxicology and directing future research. Arsenic epidemiology should therefore place the greatest emphasis on the prevalence of different direct and indirect sources in the afflicted areas, followed by control strategies.
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Affiliation(s)
- Bibha Kumari
- Department of Zoology, Magadh Mahila College, Patna University, Patna, India
| | - Vijay K Bharti
- DRDO-Defence Institute of High-Altitude Research (DIHAR), Leh, UT Ladakh, India
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Sun D, Zhang J, He J, Geng Z, Li S, Zhang J, Li P, Zhang L, Wang Z, Wang L, Chen F, Song A. Whole-transcriptome profiles of Chrysanthemum seticuspe improve genome annotation and shed new light on mRNA-miRNA-lncRNA networks in ray florets and disc florets. BMC PLANT BIOLOGY 2022; 22:515. [PMID: 36333790 PMCID: PMC9636758 DOI: 10.1186/s12870-022-03889-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Chrysanthemum seticuspe has emerged as a model plant species of cultivated chrysanthemums, especially for studies involving diploid and self-compatible pure lines (Gojo-0). Its genome was sequenced and assembled into chromosomes. However, the genome annotation of C. seticuspe still needs to be improved to elucidate the complex regulatory networks in this species. RESULTS In addition to the 74,259 mRNAs annotated in the C. seticuspe genome, we identified 18,265 novel mRNAs, 51,425 novel lncRNAs, 501 novel miRNAs and 22,065 novel siRNAs. Two C-class genes and YABBY family genes were highly expressed in disc florets, while B-class genes were highly expressed in ray florets. A WGCNA was performed to identify the hub lncRNAs and mRNAs in ray floret- and disc floret-specific modules, and CDM19, BBX22, HTH, HSP70 and several lncRNAs were identified. ceRNA and lncNAT networks related to flower development were also constructed, and we found a latent functional lncNAT-mRNA combination, LXLOC_026470 and MIF2. CONCLUSIONS The annotations of mRNAs, lncRNAs and small RNAs in the C. seticuspe genome have been improved. The expression profiles of flower development-related genes, ceRNA networks and lncNAT networks were identified, laying a foundation for elucidating the regulatory mechanisms underlying disc floret and ray floret formation.
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Affiliation(s)
- Daojin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiqiang Geng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Song Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiali Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peiling Li
- Henan Key Laboratory of Tea Comprehensive utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Lingling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenxing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Xu YL, Shen HH, Du XY, Lu L. Plastome characteristics and species identification of Chinese medicinal wintergreens ( Gaultheria, Ericaceae). PLANT DIVERSITY 2022; 44:519-529. [PMID: 36540705 PMCID: PMC9751084 DOI: 10.1016/j.pld.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 06/17/2023]
Abstract
Wintergreen oil is a folk medicine widely used in foods, pesticides, cosmetics and drugs. In China, nine out of 47 species within Gaultheria (Ericaceae) are traditionally used as Chinese medicinal wintergreens; however, phylogenetic approaches currently used to discriminating these species remain unsatisfactory. In this study, we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria. Each Gaultheria plastome contained 110 unique genes (76 protein-coding, 30 tRNA, and four rRNA genes). Duplication of trnfM, rps14, and rpl23 genes were detected, while all plastomes lacked ycf1 and ycf2 genes. Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene. Moreover, plastomes of Gaultheria leucocarpa var. yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene. Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales. Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species. Additionally, seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens. Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria. In addition, our findings provide important resources for identification of Chinese medicinal wintergreens.
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Affiliation(s)
- Yan-Ling Xu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, China
| | - Hao-Hua Shen
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, China
| | - Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lu Lu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, China
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The heat stress transcription factor family in Aegilops tauschii: genome-wide identification and expression analysis under various abiotic stresses and light conditions. Mol Genet Genomics 2022; 297:1689-1709. [DOI: 10.1007/s00438-022-01952-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/03/2022] [Indexed: 10/14/2022]
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Shah SMR, Hameed M, Ahmad MSA, Wahid MA. Invasive success of Ipomoea carnea Jacq. through plasticity in physio-anatomical and phytochemical traits across diversified habitats. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02909-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Anilkumar C, Sah RP, Muhammed Azharudheen TP, Behera S, Singh N, Prakash NR, Sunitha NC, Devanna BN, Marndi BC, Patra BC, Nair SK. Understanding complex genetic architecture of rice grain weight through QTL-meta analysis and candidate gene identification. Sci Rep 2022; 12:13832. [PMID: 35974066 PMCID: PMC9381546 DOI: 10.1038/s41598-022-17402-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Quantitative trait loci (QTL) for rice grain weight identified using bi-parental populations in various environments were found inconsistent and have a modest role in marker assisted breeding and map-based cloning programs. Thus, the identification of a consistent consensus QTL region across populations is critical to deploy in marker aided breeding programs. Using the QTL meta-analysis technique, we collated rice grain weight QTL information from numerous studies done across populations and in diverse environments to find constitutive QTL for grain weight. Using information from 114 original QTL in meta-analysis, we discovered three significant Meta-QTL (MQTL) for grain weight on chromosome 3. According to gene ontology, these three MQTL have 179 genes, 25 of which have roles in developmental functions. Amino acid sequence BLAST of these genes indicated their orthologue conservation among core cereals with similar functions. MQTL3.1 includes the OsAPX1, PDIL, SAUR, and OsASN1 genes, which are involved in grain development and have been discovered to play a key role in asparagine biosynthesis and metabolism, which is crucial for source-sink regulation. Five potential candidate genes were identified and their expression analysis indicated a significant role in early grain development. The gene sequence information retrieved from the 3 K rice genome project revealed the deletion of six bases coding for serine and alanine in the last exon of OsASN1 led to an interruption in the synthesis of α-helix of the protein, which negatively affected the asparagine biosynthesis pathway in the low grain weight genotypes. Further, the MQTL3.1 was validated using linked marker RM7197 on a set of genotypes with extreme phenotypes. MQTL that have been identified and validated in our study have significant scope in MAS breeding and map-based cloning programs for improving rice grain weight.
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Affiliation(s)
- C Anilkumar
- ICAR-National Rice Research Institute, Cuttack, India.
| | | | | | | | - Namita Singh
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Nitish Ranjan Prakash
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Canning Town, India
| | - N C Sunitha
- University of Agricultural Sciences, Bangalore, India
| | - B N Devanna
- ICAR-National Rice Research Institute, Cuttack, India
| | - B C Marndi
- ICAR-National Rice Research Institute, Cuttack, India
| | - B C Patra
- ICAR-National Rice Research Institute, Cuttack, India
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Mamedi A, Salehi P, Divargar F. Response of F. arundinacea seed germination to temperatures, water potentials, and priming treatments using hydro- and thermal-time models. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1545-1558. [PMID: 36389090 PMCID: PMC9530090 DOI: 10.1007/s12298-022-01229-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED The germination process and seedling development are the determining steps in the plant lifecycle that are the most sensitive to adverse environmental conditions. Therefore, this study was conducted to explore the effects of temperature and osmotic potential on germination responses using threshold models and to establish an optimal priming protocol for improving tolerance responses against osmotic stress in early growth stages. The results demonstrated that osmotic stress of - 0.8 MPa significantly influenced the extent, timing, and speed of seed germination. In addition, priming treatments led to an enhanced performance of early growth stages in response to osmotic stress. Based on thermal-time and hydro-time models, the predicted physiological parameters of the median thermal-time at sub-optimal temperature ( θ T 50 = 909.09 ∘ C h), the median ceiling temperature for 50% germination (Tc(50) = 39.29 °C), the common base temperature (Tb = 7.88 °C), the constant thermal-time at supra-optimal temperature ( θ T = 805.96 °C h), the threshold water potential (Ψb(50) = - 1.13 MPa), and the hydro-time constant ( θ H = 56.09 MPa h) quantitatively describe the tolerance threshold of the germination process under different osmotic and temperature conditions. The results also showed that the efficiency of seed treatments depended on the priming conditions, including temperature, duration, and also concentration of the priming agent. However, the treatments of gibberellic acid (5 days, 10 °C, 100 ppm), salicylic acid (5 days, 10 °C, 50 ppm), calcium chloride (3 days, 10 °C, 10 mM), potassium nitrate (3 days, 10 °C, 100 mM), and hydro-priming (3 days, 10 °C) were optimal protocols of each priming method, resulting in an increased seed vigor under osmotic stress. Hence, the predicted biological parameters could easily be applied to determine the physiological changes of germination under environmental factors over time. Also, results suggest that recommended osmo-, hydro-, and hormonal-priming treatments could be efficient methods for ameliorating the osmotic tolerance in the post-priming stages of this plant, especially in arid lands. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01229-w.
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Affiliation(s)
- Arash Mamedi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Parvin Salehi
- Research Institute of Forests and Rangelands, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
| | - Fatemeh Divargar
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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Ge H, Xu J, Hua M, An W, Wu J, Wang B, Li P, Fang H. Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench. BMC Genomics 2022; 23:538. [PMID: 35879672 PMCID: PMC9310384 DOI: 10.1186/s12864-022-08776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum. RESULTS Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum. CONCLUSIONS In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.
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Affiliation(s)
- Hanqiu Ge
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Jingjing Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Mingzhu Hua
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Wenwen An
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, 226368, Jiangsu, People's Republic of China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
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Duan Y, Ma S, Chen X, Shen X, Yin C, Mao Z. Transcriptome changes associated with apple (Malus domestica) root defense response after Fusarium proliferatum f. sp. malus domestica infection. BMC Genomics 2022; 23:484. [PMID: 35780085 PMCID: PMC9250749 DOI: 10.1186/s12864-022-08721-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Apple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves in apple seedlings, leading to plant death. A comparative transcriptome analysis was conducted using the Illumina Novaseq platform to identify the molecular defense mechanisms of the susceptible M.26 and the resistant M9T337 apple rootstocks to Fpmd MR5 infection. RESULTS Approximately 518.1 million high-quality reads were generated using RNA sequencing (RNA-seq). Comparative analysis between the mock-inoculated and Fpmd MR5 infected apple rootstocks revealed 28,196 significantly differentially expressed genes (DEGs), including 14,572 up-regulated and 13,624 down-regulated genes. Among them, the transcriptomes in the roots of the susceptible genotype M.26 were reflected by overrepresented DEGs. MapMan analysis indicated that a large number of DEGs were involved in the response of apple plants to Fpmd MR5 stress. The important functional groups identified via gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were responsible for fundamental biological regulation, secondary metabolism, plant-pathogen recognition, and plant hormone signal transduction (ethylene and jasmonate). Furthermore, the expression of 33 up-regulated candidate genes (12 related to WRKY DNA-binding proteins, one encoding endochitinase, two encoding beta-glucosidases, ten related to pathogenesis-related proteins, and eight encoding ethylene-responsive transcription factors) were validated by quantitative real-time PCR. CONCLUSION RNA-seq profiling was performed for the first time to analyze response of apple root to Fpmd MR5 infection. We found that the production of antimicrobial compounds and antioxidants enhanced plant resistance to pathogens, and pathogenesis-related protein (PR10 homologs, chitinase, and beta-glucosidase) may play unique roles in the defense response. These results provide new insights into the mechanisms of the apple root response to Fpmd MR5 infection.
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Affiliation(s)
- Yanan Duan
- College of Horticulture Science and Engineering, National Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shangdong, China
| | - Shurui Ma
- College of Horticulture Science and Engineering, National Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shangdong, China
| | - Xuesen Chen
- College of Horticulture Science and Engineering, National Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shangdong, China
| | - Xiang Shen
- College of Horticulture Science and Engineering, National Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shangdong, China
| | - Chengmiao Yin
- College of Horticulture Science and Engineering, National Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shangdong, China.
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, National Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shangdong, China.
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Jiao Y, Gong X, Qi K, Xie Z, Wang Y, Yuan K, Pan Q, Zhang S, Shiratake K, Khanizadeh S, Tao S. Transcriptome analysis provides new ideas for studying the regulation of glucose-induced lignin biosynthesis in pear calli. BMC PLANT BIOLOGY 2022; 22:310. [PMID: 35754039 PMCID: PMC9235211 DOI: 10.1186/s12870-022-03658-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Glucose can be involved in metabolic activities as a structural substance or signaling molecule and plays an important regulatory role in fruit development. Glucose metabolism is closely related to the phenylpropanoid pathway, but the specific role of glucose in regulating lignin biosynthesis in pear fruit is still unclear. The transcriptome of pear calli generated from fruit and treated with glucose was analyzed to investigate the role of glucose in lignin biosynthesis. RESULTS The treatment of exogenous glucose significantly enhanced the accumulation of lignin in pear calli. A total of 6566 differentially expressed genes were obtained by transcriptome sequencing. Glycolysis was found to be the pathway with significant changes. Many differentially expressed genes were enriched in secondary metabolic pathways, especially the phenylpropanoid pathway. Expression of structural genes (PbPAL, PbHCT, PbCOMT, PbPRX) in lignin biosynthesis was up-regulated after glucose treatment. In addition, glucose might regulate lignin biosynthesis through interactions with ABA, GA, and SA signaling. Several candidate MYB transcription factors involved in glucose-induced lignin biosynthesis have also been revealed. The qRT-PCR analyses showed that the expression pattern of PbPFP at early developmental stage in 'Dangshansuli' fruits was consistent with the trend of lignin content. Transient expression of PbPFP resulted in a significant increase of lignin content in 'Dangshansuli' fruits at 35 days after full bloom (DAB) and tobacco leaves, indicating that PbPFP (Pbr015118.1) might be associated with the enhancement of lignin biosynthesis in response to glucose treatment. CONCLUSIONS PbPFP plays a positive role in regulating lignin biosynthesis in response to glucose treatment. This study may reveal the regulatory pathway related to lignin accumulation in pear calli induced by glucose.
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Affiliation(s)
- Yuru Jiao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xin Gong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihua Xie
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yanling Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kaili Yuan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Qi Pan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | | | | | - Shutian Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Ma Y, Han Y, Feng X, Gao H, Cao B, Song L. Genome-wide identification of BAM (β-amylase) gene family in jujube (Ziziphus jujuba Mill.) and expression in response to abiotic stress. BMC Genomics 2022; 23:438. [PMID: 35698031 PMCID: PMC9195466 DOI: 10.1186/s12864-022-08630-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Elevated temperature and drought stress have substantial impacts on fruit quality, especially in terms of sugar metabolism and content. β-Amylase (BAM) plays a critical role in regulating jujube fruit sugar levels and abiotic stress response. Nevertheless, little is known about the regulatory functions of the BAM genes in jujube fruit. Results Nine jujube BAM genes were identified, clustered into four groups, and characterized to elucidate their structure, function, and distribution. Multiple sequence alignment and gene structure analysis showed that all ZjBAM genes contain Glu-186 and Glu-380 residues and are highly conserved. Phylogenetic and synteny analysis further indicated that the ZjBAM gene family is evolutionarily conserved and formed collinear pairs with the BAM genes of peach, apple, poplar, Arabidopsis thaliana, and cucumber. A single tandem gene pair was found within the ZjBAM gene family and is indicative of putative gene duplication events. We also explored the physicochemical properties, conserved motifs, and chromosomal and subcellular localization of ZjBAM genes as well as the interaction networks and 3D structures of ZjBAM proteins. A promoter cis-acting element analysis suggested that ZjBAM promoters comprise elements related to growth, development, phytohormones, and stress response. Furthermore, a metabolic pathways annotation analysis showed that ZjBAMs are significantly upregulated in the starch and sucrose metabolism, thereby controlling starch-maltose interconversion and hydrolyzing starch to maltose. Transcriptome and qRT-PCR analyses revealed that ZjBAMs respond positively to elevated temperature and drought stress. Specifically, ZjBAM1, ZjBAM2, ZjBAM5, and ZjBAM6 are significantly upregulated in response to severe drought. Bimolecular fluorescence complementation analysis demonstrated ZjBAM1-ZjAMY3, ZjBAM8-ZjDPE1, and ZjBAM7-ZjDPE1 protein interactions that were mainly present in the plasma membrane and nucleus. Conclusion The jujube BAM gene family exhibits high evolutionary conservation. The various expression patterns of ZjBAM gene family members indicate that they play key roles in jujube growth, development, and abiotic stress response. Additionally, ZjBAMs interact with α-amylase and glucanotransferase. Collectively, the present study provides novel insights into the structure, evolution, and functions of the jujube BAM gene family, thus laying a foundation for further exploration of ZjBAM functional mechanisms in response to elevated temperature and drought stress, while opening up avenues for the development of economic forests in arid areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08630-5.
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Affiliation(s)
- Yaping Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.,College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yaru Han
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xuerui Feng
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Handong Gao
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China. .,Southern Tree Seed Inspection Center, Nanjing, 210037, China.
| | - Bing Cao
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Lihua Song
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
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Guo H, Pu X, Jia H, Zhou Y, Ye G, Yang Y, Na T, Wang J. Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.). BMC PLANT BIOLOGY 2022; 22:282. [PMID: 35676629 PMCID: PMC9178895 DOI: 10.1186/s12870-022-03652-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Nitrogen (N) is a major element and fundamental constituent of grain yield. N fertilizer plays an essential role in the roots, shoots, and leaves of crop plants. Here, we obtained two N-sensitive potato cultivars. RESULTS The plants were cultivated in the pots using N-deficient and N-sufficient conditions. Crop height, leaf chlorophyll content, dry matter, and N-accumulation significantly decreased under N-deficient conditions. Furthermore, we performed a comprehensive analysis of the phenotype and transcriptome, GO terms, and KEGG pathways. We used WGCNA of co-expressed genes, and 116 differentially expressed hub genes involved in photosynthesis, nitrogen metabolism, and secondary metabolites to generate 23 modules. Among those modules, six NRT gene families, four pigment genes, two auxin-related genes, and two energy-related genes were selected for qRT-PCR validation. CONCLUSIONS Overall, our study demonstrates the co-expressed genes and potential pathways associated with N transport and accumulation in potato cultivars' roots, shoots, and leaves under N-deficient conditions. Therefore, this study provides new ideas to conduct further research on improving nitrogen use efficiency in potatoes.
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Affiliation(s)
- Heng Guo
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Xiuqin Pu
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Hao Jia
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Yun Zhou
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Guangji Ye
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Yongzhi Yang
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Tiancang Na
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Jian Wang
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
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Sheikh-Assadi M, Naderi R, Kafi M, Fatahi R, Salami SA, Shariati V. Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution. Sci Rep 2022; 12:9375. [PMID: 35672390 PMCID: PMC9174193 DOI: 10.1038/s41598-022-13449-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/24/2022] [Indexed: 01/02/2023] Open
Abstract
Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.
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Affiliation(s)
- Morteza Sheikh-Assadi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
| | - Mohsen Kafi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Reza Fatahi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Vahid Shariati
- NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Lai D, Fan Y, Xue G, He A, Yang H, He C, Li Y, Ruan J, Yan J, Cheng J. Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica). BMC Genomics 2022; 23:389. [PMID: 35596144 PMCID: PMC9122484 DOI: 10.1186/s12864-022-08633-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. Results In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. Conclusions In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08633-2.
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Affiliation(s)
- Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.,School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin He
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524000, People's Republic of China
| | - Yijing Li
- Henan Cancer Hospital, Zhengzhou, 450001, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Jun Yan
- School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.
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Öztürk Gökçe ZN, Gökçe AF, Junaid MD, Chaudhry UK. Comparative transcriptomics of drought stress response of taproot meristem region of contrasting purple carrot breeding lines supported by physio-biochemical parameters. Funct Integr Genomics 2022; 22:697-710. [PMID: 35590117 DOI: 10.1007/s10142-022-00868-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022]
Abstract
Carrot is one of the nutritious vegetable crops sensitive to drought stress resulting in loss of quality and yield. There are a lot of studies on detailed molecular mechanisms of drought stress response of main crops; however, very little information available on vegetables, including carrots. Hence, in this study, we investigated root transcriptome profiles from the meristematic region of two contrasting purple carrot (B7262A, drought tolerant; P1129, drought sensitive) lines under varying stress levels (85% and 70%) by using RNA-Seq technique. The morpho-physiological and biochemical response of B7262A line exhibited tolerance behavior to both DS (85% and 70%). RNA-Seq analysis revealed that 15,839 genes were expressed commonly in both carrot lines. The carrot line B7262A showed regulation of 514 genes in response to 85% DS, whereas P1129 showed differential regulation of 622 genes under 70% DS. The B7262A carrot line showed higher upregulation of transcripts that suggested its resilient behavior contrary to P1129 line. Furthermore, validation of transcript gene by qRT-PCR also confirmed the RNA-Seq analysis resulting in elevated expression levels of MYB48 transcription factor, MAPK mitogen-activated protein kinase ANP1, GER geraniol 8-hydroxylase, ABA ABA-induced in somatic embryo 3, FBOX putative F-box protein, FRO ferric reduction oxidase, and PDR probable disease resistance protein. Current study provided unprecedented insights of purple carrot lines that can be potentially exploited for the screening and development of resilient carrot.
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Affiliation(s)
- Zahide Neslihan Öztürk Gökçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey.
| | - Ali Fuat Gökçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Muhammad Daniyal Junaid
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
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Hinge VR, Shaikh IM, Chavhan RL, Deshmukh AS, Shelake RM, Ghuge SA, Dethe AM, Suprasanna P, Kadam US. Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars. Sci Rep 2022; 12:7979. [PMID: 35562398 PMCID: PMC9106755 DOI: 10.1038/s41598-022-11992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Banana is an important fruit crop in the tropics and subtropics; however, limited information on biomarkers and signature volatiles is available for selecting commercial cultivars. Clonal fidelity is a major contributor to banana yield and aroma; however, there are no useful biomarkers available to validate clonal fidelity. In this study, we performed the molecular profiling of 20 banana cultivars consisting of diploid (AA or AB) and triploid (AAA or AAB or ABB) genomic groups. We screened 200 molecular markers, of which 34 markers (11 RAPD, 11 ISSR, and 12 SSR) yielded unequivocally scorable biomarker profiles. About 75, 69, and 24 allelic loci per marker were detected for RAPD, ISSR, and SSR markers, respectively. The statistical analysis of molecular variance (AMOVA) exhibited a high genetic difference of 77% with a significant FST value of 0.23 (p < 0.001). Interestingly, the UBC-858 and SSR CNMPF-13 markers were unique to Grand Nain and Ardhapuri cultivars, respectively, which could be used for clonal fidelity analysis. Furthermore, the analysis of banana fruit volatilome using headspace solid-phase microextraction-gas chromatography-tandem mass spectrometry (HS-SPME-GCMS) revealed a total of fifty-four volatile compounds in nine banana cultivars with 56% of the total volatile compounds belonging to the ester group as the significant contributor of aroma. The study assumes significance with informative biomarkers and signature volatiles which could be helpful in breeding and for the authentic identification of commercial banana cultivars.
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Affiliation(s)
- Vidya R Hinge
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Irfan M Shaikh
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Rahul L Chavhan
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Abhijit S Deshmukh
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Sandip A Ghuge
- Agricultural Research Organization (ARO), The Volcani Institute, P. O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Amol M Dethe
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Penna Suprasanna
- Homi Bhabha National Institute (HBNI) and Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Mumbai, India
| | - Ulhas Sopanrao Kadam
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India. .,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
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Liu K, Kabir N, Wei Z, Sun Z, Wang J, Qi J, Liu M, Liu J, Zhou K. Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.. PeerJ 2022; 10:e13372. [PMID: 35586135 PMCID: PMC9109687 DOI: 10.7717/peerj.13372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/12/2022] [Indexed: 01/13/2023] Open
Abstract
Background Cotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development. Methods Using genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum. Results Chromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton.
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Affiliation(s)
- Kun Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhenzhen Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jian Wang
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jing Qi
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Miaoyang Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Kehai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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