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Muñoz-Jurado A, Escribano BM. Presence of melatonin in foods of daily consumption: The benefit of this hormone for health. Food Chem 2024; 458:140172. [PMID: 38943958 DOI: 10.1016/j.foodchem.2024.140172] [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: 01/19/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
Melatonin (MLT) is a hormone that exists in all living organisms, including bacteria, yeast, fungi, animals, and plants, many of which are ingested daily in the diet. However, the exact concentrations of melatonin in each of the foods and the effect on health of the intake of foods rich in MLT are not known. Therefore, the aim of this review was to gather the available information on the melatonin content of different foods and to evaluate the effect that this hormone has on different pathologies. The amount of MLT may vary depending on the variety, origin, heat treatment, processing, and analysis technique, among other factors. Dietary interventions with foods rich in MLT report health benefits, but there is no evidence that hormone is partially responsible for the clinical improvement. Therefore, it is necessary to evaluate the MLT content in more foods, as well as the effect that cooking/processing has on the amount of MLT, to estimate its total intake in a typical diet and better explore its potential impact on the health.
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Affiliation(s)
- Ana Muñoz-Jurado
- Department of Cell Biology, Physiology and Immunology, Faculty of Veterinary Medicine, University of Cordoba, Spain.; Maimonides Institute for Research in Biomedicine of Cordoba, (IMIBIC), Cordoba, Spain..
| | - Begoña M Escribano
- Department of Cell Biology, Physiology and Immunology, Faculty of Veterinary Medicine, University of Cordoba, Spain.; Maimonides Institute for Research in Biomedicine of Cordoba, (IMIBIC), Cordoba, Spain..
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Chen T, Sheng M, Xiao J, Ai S, Kou J, Yang Q, Ai Y, Ma J, Zhu G, Ai X. Phosphorus pool distributions and adsorption-desorption characteristics of soil aggregates in cut slopes of a permafrost zone in the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176623. [PMID: 39395499 DOI: 10.1016/j.scitotenv.2024.176623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 09/14/2024] [Accepted: 09/28/2024] [Indexed: 10/14/2024]
Abstract
Soil phosphorus (P) has attracted considerable attention from researchers because of its role in the restoration and stabilization processes of cut slopes in permafrost regions. However, the soil P pool distributions and adsorption-desorption characteristics in alpine cut slopes remain unclear. In this context, we examined in this study the P pools in the aggregates of surface cut soil slopes (0-10 cm) in areas with three permafrost types, including perennially frozen soil (PF), seasonally frozen ground (SFG), and non-frozen soil (NFS) in the Qinghai-Tibet Plateau, China. In addition, we assessed the P adsorption-desorption characteristics and their correlations with the P pools. The results showed the significant effects of the permafrost types on the contents of total P (TP), available P (AP), labile P (LP), moderately labile P (MLP) and stable P (SP). The inorganic P (IP) contents were higher than those of organic P (OP) in the cut soil slopes of the three permafrost types. In addition, H2O-Pi and NaHCO3-Pi accounted for small proportions of IP, while NaHCO3-Po accounted for the smallest proportion of OP. On the other hand, the SP contents in the soil aggregates were generally higher than those of MLP and LP. In fact, the LP contents in the PF, SFG, and NFS were 72.55, 44.68, and 49.42 mg/kg, respectively. The AP contents in the cut soil slopes of the three permafrost types were significantly correlated with the MLP and LP contents. Moreover, the P adsorption-desorption characteristics of the SFG and NFS were closely related to AP and MLP. Compared with the PF and NFS, the SFG exhibited low and high P adsorption and desorption capacities, respectively. The findings of this study provided an important theoretical basis for the restoration of cut slopes in alpine permafrost regions.
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Affiliation(s)
- Tingting Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China
| | - Meihua Sheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China
| | - Jingyao Xiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China
| | - Shenghao Ai
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610213, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianing Kou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China
| | - Qinqing Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China
| | - Yingwei Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China
| | - Jinqiang Ma
- Tibet Huatailong Mining Development Co., Ltd, Lhasa 850200, China
| | - Guoyu Zhu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Sichuan 610065, China
| | - Xiaoyan Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Sichuan 610065, China.
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Lamlom SF, Abdelghany AM, Ren H, Ali HM, Usman M, Shaghaleh H, Alhaj Hamoud Y, El-Sorady GA. Revitalizing maize growth and yield in water-limited environments through silicon and zinc foliar applications. Heliyon 2024; 10:e35118. [PMID: 39157312 PMCID: PMC11328083 DOI: 10.1016/j.heliyon.2024.e35118] [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: 02/24/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
Maize is an economically vital cereal crop. However, water deficiency can severely impact its productivity. Thus, it is necessary to implement an essential approach to increase maize yield while navigating the limitations imposed by scarce water supplies. The present study aimed to investigate whether foliar applications of silicon (Si) and zinc (Zn) could mitigate the adverse effects of water deficiency and improve maize growth and yield. Field experiments were conducted in Egypt during two growing seasons (2021-2022) under three irrigation regimes: full irrigation (ET0), moderate stress (ET1), and severe stress (ET2). The treatments comprised foliar sprays of Si, Zn, Si + Zn, and water control. Phenological, growth, physiological, chemical, and yield-related traits were assessed. Results showed that adequate irrigation (ET0) enhanced most parameters compared to water stress treatments. Under ET0, the combined silicon and zinc treatment resulted in the highest values for plant height, leaf area, chlorophyll content, grains per ear, kernel weight, ear size, and yield compared to other foliar treatments. Under drought stress (ET1, ET2), Si + Zn applications maintained superiority in mitigating yield losses. Proline accumulation was highest under severe stress (ET2) in the absence of foliar sprays, indicating greater drought impacts. Correlation analysis revealed positive associations of grain yield with ear size, leaf area, kernel weight, and biological yield. Cluster analysis separated irrigation regimes and visualized the consistently beneficial effects of Si + Zn across all water levels. Overall, the results demonstrate the synergistic potential of Si and Zn supplementation to sustain maize performance and yields under varying water availability.
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Affiliation(s)
- Sobhi F Lamlom
- Plant Production Department, Faculty of Agriculture Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Ahmed M Abdelghany
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour, 22516, Egypt
| | - Honglei Ren
- Heilongjiang Academy of Agricultural Sciences, Soybean Research Institute, Harbin, 150086, China
| | - Hayssam M Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Muhammad Usman
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, 38000, Punjab, Pakistan
| | - Hiba Shaghaleh
- Key Lab of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yousef Alhaj Hamoud
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Gawhara A El-Sorady
- Plant Production Department, Faculty of Agriculture Saba Basha, Alexandria University, Alexandria, 21531, Egypt
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Guo L, Yang S, Tu Z, Yu F, Qiu C, Huang G, Fang S. An indole-3-acetic acid inhibitor mitigated mild cadmium stress by suppressing peroxide formation in rice seedling roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108823. [PMID: 38905727 DOI: 10.1016/j.plaphy.2024.108823] [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: 02/25/2024] [Revised: 05/28/2024] [Accepted: 06/09/2024] [Indexed: 06/23/2024]
Abstract
Cadmium (Cd) is a widely distributed heavy metal pollutant that is detrimental to growth and development of plants. The secretion of indole-3-acetic acid is one of the defense mechanisms when plants inflict heavy metal stress. This study aimed to explore how 4-phenoxyphenylboronic acid, an effective IAA inhibitor, induces changes in IAA level, Cadmium accumulation, and activation of defense responses in rice seedling roots under different Cadmium concentrations. Our research results show that: 1) root growth was promoted with PPBa addition under mild Cadmium treatment. 2) the root IAA level improved with increasing Cadmium concentration, and PPBa had a significant inhibitory effect on IAA level. 3) PPBa had no effect on the Cadmium accumulation in rice seedling roots. 4) PPBa had a significant inhibitory effect on the generation of H2O2 under mild and moderate Cadmium treatment. 5) PPBa exacerbated the imbalance of osmotic substances in rice seedling roots under severe Cadmium treatment. This study helps us understand the tolerance and endogenous regulation of plants to heavy metal stress.
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Affiliation(s)
- Lin Guo
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Siying Yang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zihao Tu
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fengyue Yu
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chaoqian Qiu
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guanjun Huang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sheng Fang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University/College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
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Chen W, Li X, Zhang X, Chachar Z, Lu C, Qi Y, Chang H, Wang Q. Genome-wide association study of trace elements in maize kernels. BMC PLANT BIOLOGY 2024; 24:724. [PMID: 39080529 PMCID: PMC11287846 DOI: 10.1186/s12870-024-05419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/15/2024] [Indexed: 08/03/2024]
Abstract
Maize (Zea mays L.), a staple food and significant economic crop, is enriched with riboflavin, micronutrients and other compounds that are beneficial for human health. As emphasis on the nutritional quality of crops increases maize research has expanded to focus on both yield and quality. This study exploreed the genetic factors influencing micronutrient levels in maize kernels through a comprehensive genome-wide association study (GWAS). We utilized a diverse panel of 244 inbred maize lines and approximately 3 million single nucleotide polymorphisms (SNPs) to investigate the accumulation of essential and trace elements including cadmium (Cd), cobalt (Co), copper (Cu), nickel (Ni), selenium (Se) and zinc (Zn). Our analysis identified 842 quantitative trait loci (QTLs), with 12 QTLs shared across multiple elements and pinpointed 524 potential genes within a 100 kb radius of these QTLs. Notably ZmHMA3 has emerged as a key candidate gene previously reported to influence the Cd accumulation. We highlighted ten pivotal genes associated with trace element transport including those encoding heavy metal ATPases, MYB transcription factors, ABC transporters and other crucial proteins involved in metal handling. Additionally, haplotype analysis revealed that eight inbred linesaccumulated relatively high levels of beneficial elements while harmful elements were minimized. These findings elucidate the genetic mechanisms underlying trace element accumulation in maize kernels and provide a foundation for the breeding of nutritionally enhanced maize varieties.
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Affiliation(s)
- Weiwei Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Xuhui Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Xiangbo Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Zaid Chachar
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Chuanli Lu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China
| | - Yongwen Qi
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510325, China
| | - Hailong Chang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China.
| | - Qinnan Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, 510316, China.
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Li B, Huang K, Chen X, Qin C, Zhang X. Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis. BMC Genom Data 2024; 25:57. [PMID: 38858616 PMCID: PMC11165809 DOI: 10.1186/s12863-024-01232-y] [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: 06/29/2023] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
The Quercus L. species is widely recognized as a significant group in the broad-leaved evergreen forests of tropical and subtropical East Asia. These plants hold immense economic value for their use as firewood, furniture, and street trees. However, the identification of Quercus species is considered challenging, and the relationships between these species remain unclear. In this study, we sequenced and assembled the chloroplast (cp.) genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui). Additionally, we retrieved six published cp. genome sequences of Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia). Our aim was to perform comparative genomics and phylogenetic analyses of the cp. whole genome sequences of ten Quercus section Cyclobalanopsis species. The results revealed that: (1) Quercus species exhibit a typical tetrad structure, with the cp. genome lengths of the newly sequenced species (Q. disciformis, Q. dinghuensis, Q. blakei, and Q. hui) being 160,805 bp, 160,801 bp, 160,787 bp, and 160,806 bp, respectively; (2) 469 SSRs were detected, among which A/T base repeats were the most common; (3) no rearrangements or inversions were detected within the chloroplast genomes. Genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2, provided potential reference loci for molecular identification within the Cyclobalanopsis section; (4) phylogenetic analysis showed that the four sections of Cyclobalanopsis were grouped into sister taxa, with Q. hui being the first to diverge from the evolutionary branch and Q. disciformis being the most closely related to Q. blackei. The results of this study form the basis for future studies on taxonomy and phylogenetics.
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Affiliation(s)
- Buyu Li
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Ke Huang
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Xiaoli Chen
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Chun Qin
- College of Life Science, China West Normal University, Nanchong, 637000, China
| | - Xuemei Zhang
- College of Life Science, China West Normal University, Nanchong, 637000, China.
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Li J, Wen X, Zhang Q, Tian Y, Pu Y, Wang J, Liu B, Du Y, Dai S. cla-miR164- NO APICAL MERISTEM ( ClNAM) regulates the inflorescence architecture development of Chrysanthemum lavandulifolium. HORTICULTURE RESEARCH 2024; 11:uhae039. [PMID: 38623074 PMCID: PMC11017518 DOI: 10.1093/hr/uhae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/28/2024] [Indexed: 04/17/2024]
Abstract
Chrysanthemum × morifolium has great ornamental and economic value on account of its exquisite capitulum. However, previous studies have mainly focused on the corolla morphology of the capitulum. Such an approach cannot explain the variable inflorescence architecture of the chrysanthemum. Previous research from our group has shown that NO APICAL MERISTEM (ClNAM) is likely to function as a hub gene in capitulum architecture in the early development stage. In the present study, ClNAM was used to investigate the function of these boundary genes in the capitulum architecture of Chrysanthemum lavandulifolium, a closely related species of C. × morifolium in the genus. Modification of ClNAM in C. lavandulifolium resulted in an advanced initiation of the floral primordium at the capitulum. As a result, the receptacle morphology was altered and the number of florets decreased. The ray floret corolla was shortened, but the disc floret was elongated. The number of capitula increased significantly, arranged in more densely compounded corymbose synflorescences. The yeast and luciferase reporter system revealed that ClAP1, ClRCD2, and ClLBD18 target and activate ClNAM. Subsequently, ClNAM targets and activates ClCUC2a/c, which regulates the initiation of floral and inflorescence in C. lavandulifolium. ClNAM was also targeted and cleaved by cla-miR164 in this process. In conclusion, this study established a boundary gene regulatory network with cla-miR164-ClNAM as the hub. This network not only influences the architecture of capitulum, but also affects compound corymbose synflorescences of the C. lavandulifolium. These results provide new insights into the mechanisms regulating inflorescence architecture in chrysanthemum.
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Affiliation(s)
- Junzhuo Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Xiaohui Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
- Flower Research and Development Center, Zhejiang Academy of Agricultural Sciences, Hangzhou 311202, China
| | - Qiuling Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Yuankai Tian
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Ya Pu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Jiaying Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Bo Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Yihan Du
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083, China
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Zhang L, Meng Y, Wang D, He GH, Zhang JM, Wen J, Nie ZL. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae). BMC Genomics 2024; 25:247. [PMID: 38443830 PMCID: PMC10916268 DOI: 10.1186/s12864-024-10149-w] [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: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights. RESULTS We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa. CONCLUSIONS Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.
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Affiliation(s)
- Lei Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Ying Meng
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Da Wang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Guan-Hao He
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun-Ming Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ze-Long Nie
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.
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Byregowda R, Nagarajappa N, Rajendra Prasad S, Kumar MP. Comparative regulatory network of transcripts behind radicle emergence and seedling stage of maize ( Zea mays L.). Heliyon 2024; 10:e25683. [PMID: 38370253 PMCID: PMC10869873 DOI: 10.1016/j.heliyon.2024.e25683] [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: 08/28/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
The transition from radicle emergence to seedling growth in maize is a crucial phase in the plant's life cycle, where rapid physiological and biochemical changes occur to facilitate successful development. In this study, we conducted a comparative transcriptomic analysis to gain a deeper understanding of the molecular processes driving this critical transition. The early divergence in gene expression patterns highlighted the upregulation of a substantial number of genes during radicle emergence. During radicle emergence, gene ontology (GO) term enrichment analysis unveiled active participation in biological processes such as chromatin assembly, cellular response to abiotic stress, and hormone signaling. This indicates that the initial stages of growth are marked by cellular expansion and adaptation to environmental stimuli. Conversely, in the seedling growth stage, GO analysis demonstrated a shift toward processes such as photosynthesis, nitrogen metabolism, and secondary metabolite biosynthesis, reflecting a transition to energy production and enhanced growth. In contrast, seedling growth was characterized by pathways related to photosynthesis and the production of gibberellins, crucial for robust seedling development. Hormonal regulation and starch metabolism were also prominent during radicle emergence, with various hormones, including auxins, diterpenoids, and brassinosteroids, driving processes like cell enlargement and stem growth. Moreover, starch and sucrose metabolism genes were expressed to mobilize stored reserves for energy during this stage. These findings offer valuable insights into the dynamic regulation of genes and pathways during this critical phase of maize development.
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Affiliation(s)
- Roopashree Byregowda
- Department of Seed Science and Technology, University of Agricultural Sciences, Bangalore 560065, India
| | - Nethra Nagarajappa
- Seed Technology Research Center, All India Co-ordinated Research Project on Seed (Crops), Gandhi Krishi Vignana Kendra, University of Agricultural Sciences, Bangalore 560065, India
| | | | - M.K. Prasanna Kumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study. BMC PLANT BIOLOGY 2024; 24:124. [PMID: 38373874 PMCID: PMC10877931 DOI: 10.1186/s12870-024-04810-5] [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: 12/15/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. RESULTS Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. CONCLUSIONS Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
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Grants
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
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Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India.
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
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11
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Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [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: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
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Ma J, Jia B, Bian Y, Pei W, Song J, Wu M, Wang W, Kashif, Shahzad, Wang L, Zhang B, Feng P, Yang L, Zhang J, Yu J. Genomic and co-expression network analyses reveal candidate genes for oil accumulation based on an introgression population in Upland cotton (Gossypium hirsutum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:23. [PMID: 38231256 DOI: 10.1007/s00122-023-04527-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
KEY MESSAGE Integrated QTL mapping and WGCNA condense the potential gene regulatory network involved in oil accumulation. A glycosyl hydrolases gene (GhHSD1) for oil biosynthesis was confirmed in Arabidopsis, which will provide useful knowledge to understand the functional mechanism of oil biosynthesis in cotton. Cotton is an economical source of edible oil for the food industry. The genetic mechanism that regulates oil biosynthesis in cottonseeds is essential for the genetic enhancement of oil content (OC). To explore the functional genomics of OC, this study utilized an interspecific backcross inbred line population to dissect the quantitative trait locus (QTL) interlinked with OC. In total, nine OC QTLs were identified, four of which were novel, and each QTL explained 3.62-34.73% of the phenotypic variation of OC. The comprehensive transcript profiling of developing cottonseeds revealed 3,646 core genes differentially expressed in both inbred parents. Functional enrichment analysis determined 43 genes were annotated with oil biosynthesis processes. Implementation of weighted gene co-expression network analysis showed that 803 differential genes had a significant correlation with the OC phenotype. Further integrated analysis identified seven important genes located in OC QTLs. Of which, the GhHSD1 gene located in stable QTL qOC-Dt3-1 exhibited the highest functional linkages with the other network genes. Phylogenetic analysis showed significant evolutionary differences in the HSD1 sequences between oilseed- and starch- crops. Furthermore, the overexpression of GhHSD1 in Arabidopsis yielded almost 6.78% higher seed oil. This study not only uncovers important genetic loci for oil accumulation in cottonseed, but also provides a set of new candidate genes that potentially influence the oil biosynthesis pathway in cottonseed.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Yingying Bian
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Wenkui Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | | | - Shahzad
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Pan Feng
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Liupeng Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, USA.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China.
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China.
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