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Ceasar SA, Prabhu S, Ebeed HT. Protein research in millets: current status and way forward. PLANTA 2024; 260:43. [PMID: 38958760 DOI: 10.1007/s00425-024-04478-z] [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: 05/10/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
MAIN CONCLUSION Millets' protein studies are lagging behind those of major cereals. Current status and future insights into the investigation of millet proteins are discussed. Millets are important small-seeded cereals majorly grown and consumed by people in Asia and Africa and are considered crops of future food security. Although millets possess excellent climate resilience and nutrient supplementation properties, their research advancements have been lagging behind major cereals. Although considerable genomic resources have been developed in recent years, research on millet proteins and proteomes is currently limited, highlighting a need for further investigation in this area. This review provides the current status of protein research in millets and provides insights to understand protein responses for climate resilience and nutrient supplementation in millets. The reference proteome data is available for sorghum, foxtail millet, and proso millet to date; other millets, such as pearl millet, finger millet, barnyard millet, kodo millet, tef, and browntop millet, do not have any reference proteome data. Many studies were reported on stress-responsive protein identification in foxtail millet, with most studies on the identification of proteins under drought-stress conditions. Pearl millet has a few reports on protein identification under drought and saline stress. Finger millet is the only other millet to have a report on stress-responsive (drought) protein identification in the leaf. For protein localization studies, foxtail millet has a few reports. Sorghum has the highest number of 40 experimentally proven crystal structures, and other millets have fewer or no experimentally proven structures. Further proteomics studies will help dissect the specific proteins involved in climate resilience and nutrient supplementation and aid in breeding better crops to conserve food security.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India.
| | - Srinivasan Prabhu
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India
| | - Heba T Ebeed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
- National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
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Chen C, Yang Y, Pan L, Xia W, Xu L, Hua B, Zhang Z, Miao M. Genome-Wide Identification of WD40 Proteins in Cucurbita maxima Reveals Its Potential Functions in Fruit Development. Genes (Basel) 2023; 14:genes14010220. [PMID: 36672961 PMCID: PMC9859561 DOI: 10.3390/genes14010220] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
WD40 proteins, a super gene family in eukaryotes, are involved in multiple biological processes. Members of this family have been identified in several plants and shown to play key roles in various development processes, including acting as scaffolding molecules with other proteins. However, WD40 proteins have not yet been systematically analyzed and identified in Cucurbita maxima. In this study, 231 WD40 proteins (CmWD40s) were identified in C. maxima and classified into five clusters. Eleven subfamilies were identified based on different conserved motifs and gene structures. The CmWD40 genes were distributed in 20 chromosomes; 5 and 33 pairs of CmWD40s were distinguished as tandem and segmental duplications, respectively. Overall, 58 pairs of orthologous WD40 genes in C. maxima and Arabidopsis thaliana, and 56 pairs of orthologous WD40 genes in C. maxima and Cucumis sativus were matched. Numerous CmWD40s had diverse expression patterns in fruits, leaf, stem, and root. Several genes were involved in responses to NaCl. The expression pattern of CmWD40s suggested their key role in fruit development and abiotic stress response. Finally, we identified 14 genes which might be involved in fruit development. Our results provide valuable basis for further functional verification of CmWD40s in C. maxima.
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Affiliation(s)
- Chen Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Yating Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Liu Pan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Wenhao Xia
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Lanruoyan Xu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Bing Hua
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhiping Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Minmin Miao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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De Y, Shi F, Gao F, Mu H, Yan W. Siberian Wildrye ( Elymus sibiricus L.) Abscisic Acid-Insensitive 5 Gene Is Involved in Abscisic Acid-Dependent Salt Response. PLANTS 2021; 10:plants10071351. [PMID: 34371554 PMCID: PMC8309358 DOI: 10.3390/plants10071351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/22/2023]
Abstract
Siberian wildrye (Elymus sibiricus L.) is a salt-tolerant, high-quality forage grass that plays an important role in forage production and ecological restoration. Abscisic acid (ABA)-insensitive 5 (ABI5) is essential for the normal functioning of the ABA signal pathway. However, the role of ABI5 from Siberian wildrye under salt stress remains unclear. Here, we evaluated the role of Elymus sibiricus L. abscisic acid-insensitive 5 (EsABI5) in the ABA-dependent regulation of the response of Siberian wildrye to salt stress. The open reading frame length of EsABI5 isolated from Siberian wildrye was 1170 bp, and it encoded a 389 amino acid protein, which was localized to the nucleus, with obvious coiled coil areas. EsABI5 had high homology, with ABI5 proteins from Hordeum vulgare, Triticum monococcum, Triticum aestivum, and Aegilops tauschii. The conserved domains of EsABI5 belonged to the basic leucine zipper domain superfamily. EsABI5 had 10 functional interaction proteins with credibility greater than 0.7. EsABI5 expression was upregulated in roots and leaves under NaCl stress and was upregulated in leaves and downregulated in roots under ABA treatment. Notably, tobacco plants overexpressing the EsABI5 were more sensitive to salt stress, as confirmed by the determining of related physiological indicators. EsABI5 expression affected the ABA and mitogen-activated protein kinase pathways. Therefore, EsABI5 is involved in antisalt responses in these pathways and plays a negative regulatory role during salt stress.
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Affiliation(s)
- Ying De
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China;
- Chinese Academy of Agricultural Sciences, Grassland Research Institute, Hohhot 010010, China; (F.G.); (H.M.); (W.Y.)
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China;
- Correspondence: ; Tel.: +86-04714308458
| | - Fengqin Gao
- Chinese Academy of Agricultural Sciences, Grassland Research Institute, Hohhot 010010, China; (F.G.); (H.M.); (W.Y.)
| | - Huaibin Mu
- Chinese Academy of Agricultural Sciences, Grassland Research Institute, Hohhot 010010, China; (F.G.); (H.M.); (W.Y.)
| | - Weihong Yan
- Chinese Academy of Agricultural Sciences, Grassland Research Institute, Hohhot 010010, China; (F.G.); (H.M.); (W.Y.)
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Shi H, Guan W, Shi Y, Wang S, Fan H, Yang J, Chen W, Zhang W, Sun D, Jing R. QTL mapping and candidate gene analysis of seed vigor-related traits during artificial aging in wheat (Triticum aestivum). Sci Rep 2020; 10:22060. [PMID: 33328518 PMCID: PMC7745025 DOI: 10.1038/s41598-020-75778-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022] Open
Abstract
High vigor seeds have greater yield potential than those with low vigor; however, long-term storage leads to a decline in this trait. The objective of this study was to identify quantitative trait loci (QTLs) for seed vigor-related traits under artificial aging conditions using a high-density genetic linkage map of wheat (Triticum aestivum) and mine the related candidate genes. A doubled haploid population, derived from a cross between Hanxuan 10 × Lumai 14, was used as the experimental material. Six controlled-environment treatments were set up, i.e. the seeds were aged for 0, 24, 36, 48, 60, and 72 h at a high temperature (48 °C) and under high humidity (relative humidity 100%). Eight traits including seed germination percentage, germination energy, germination index, seedling length, root length, seedling weight, vigor index, and simple vigor index were measured. With the prolongation of artificial aging treatment, these traits showed a continuous downward trend and significant correlations were observed between most of them. A total of 49 additive QTLs for seed vigor-related traits were mapped onto 12 chromosomes (1B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5B, 5D, 6D, and 7A); and each one accounted for 6.01–17.18% of the phenotypic variations. Twenty-five pairs of epistatic QTLs were detected on all chromosomes, except for 5D, 6A, and 7D, and each epistasis accounted for 7.35–26.06% of the phenotypic variations. Three additive QTL hot spots were found on chromosomes 5A, 5B, and 5D, respectively. 13 QTLs, QGEe5B, QGIe5B, QSLc5B, QSLd5B, QSLf5B, QRLd5B, QRLe5B, QRLf5B, QVId5B, QVIe5B, QVIf5B, QSVId5B, and QSVIe5B, were located in the marker interval AX-94643729 ~ AX-110529646 on 5B and the physical interval 707,412,449–710,959,479 bp. Genes including TRAESCS5B01G564900, TRAESCS5B01G564200, TRAESCS5B01G562600, TraesCS5B02G562700, TRAESCS5B01G561300, TRAESCS5B01G561400, and TRAESCS5B01G562100, located in this marker interval, were found to be involved in regulating the processes of carbohydrate and lipid metabolism, transcription, and cell division during the germination of aging seeds, thus they were viewed as candidate genes for seed viability-related traits. These findings provide the basis for the seed-based cloning and functional identification of related candidate genes for seed vigor.
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Affiliation(s)
- Huawei Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Wanghui Guan
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Yugang Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Shuguang Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Hua Fan
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Jinwen Yang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Weiguo Chen
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Wenjun Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China.
| | - Ruilian Jing
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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Liu YC, Ma W, Niu JF, Li B, Zhou W, Liu S, Yan YP, Ma J, Wang ZZ. Systematic analysis of SmWD40s, and responding of SmWD40-170 to drought stress by regulation of ABA- and H 2O 2-induced stomal movement in Salvia miltiorrhiza bunge. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 153:131-140. [PMID: 32502715 DOI: 10.1016/j.plaphy.2020.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/28/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
WD40 proteins play crucial roles in response to abiotic stress. By screening the genome sequences of Salvia miltiorrhiza Bunge, 225 SmWD40 genes were identified and divided into 9 subfamilies (I-IX). Physiological, biochemical, gene structure, conserved protein motif and GO annotation analyses were performed on SmWD40 family members. The SmWD40-170 was found in 110 SmWD40 genes that contain drought response elements, SmWD40-170 was one of these genes whose response in terms of expression under drought was significant. The expression of SmWD40-170 was also up-regulated by ABA and H2O2. Through observed the stomatal phenotype of SmWD40-170 transgenic lines, the stomatal closure was abolished under dehydration, ABA and H2O2 treatment in SmWD40-170 knockdown lines. Abscisic acid (ABA), as the key phytohormone, elevates reactive oxygen species (ROS) levels under drought stress. The ABA-ROS interaction mediated the generation of H2O2 and the activation of anion channel in guard cells. The osmolality alteration of guard cells further accelerated the stomatal closure. As a second messenger, nitric oxide (NO) regulated ABA signaling, the NO stimulated protein kinase activity inhibited the K+ influx which result in stomatal closure. These NO-relevant events were essential for ABA-induced stomatal closure. The reduction of NO production was also observed in the guard cells of SmWD40-170 knockdown lines. The abolished of stomatal closure attributed to the SmWD40-170 deficiency induced the reduction of NO content. In general, the SmWD40-170 is a critical drought response gene in SmWD40 gene family and regulates ABA- and H2O2-induced stomatal movement by affecting the synthesis of NO.
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Affiliation(s)
- Yuan-Chu Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Wen Ma
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Jun-Feng Niu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Bin Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Wen Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Shuai Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Ya-Ping Yan
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Ji Ma
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Zhe-Zhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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Renganathan VG, Vanniarajan C, Karthikeyan A, Ramalingam J. Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction. Front Genet 2020; 11:500. [PMID: 32655612 PMCID: PMC7325689 DOI: 10.3389/fgene.2020.00500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023] Open
Abstract
Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Jegadeesan Ramalingam
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
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Nadeem F, Ahmad Z, Ul Hassan M, Wang R, Diao X, Li X. Adaptation of Foxtail Millet ( Setaria italica L.) to Abiotic Stresses: A Special Perspective of Responses to Nitrogen and Phosphate Limitations. FRONTIERS IN PLANT SCIENCE 2020; 11:187. [PMID: 32184798 PMCID: PMC7058660 DOI: 10.3389/fpls.2020.00187] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/07/2020] [Indexed: 05/12/2023]
Abstract
Amongst various environmental constraints, abiotic stresses are increasing the risk of food insecurity worldwide by limiting crop production and disturbing the geographical distribution of food crops. Millets are known to possess unique features of resilience to adverse environments, especially infertile soil conditions, although the underlying mechanisms are yet to be determined. The small diploid genome, short stature, excellent seed production, C4 photosynthesis, and short life cycle of foxtail millet make it a very promising model crop for studying nutrient stress responses. Known to be a drought-tolerant crop, it responds to low nitrogen and low phosphate by respective reduction and enhancement of its root system. This special response is quite different from that shown by maize and some other cereals. In contrast to having a smaller root system under low nitrogen, foxtail millet enhances biomass accumulation, facilitating root thickening, presumably for nutrient translocation. The low phosphate response of foxtail millet links to the internal nitrogen status, which tends to act as a signal regulating the expression of nitrogen transporters and hence indicates its inherent connection with nitrogen nutrition. Altogether, the low nitrogen and low phosphate responses of foxtail millet can act as a basis to further determine the underlying molecular mechanisms. Here, we will highlight the abiotic stress responses of foxtail millet with a key note on its low nitrogen and low phosphate adaptive responses in comparison to other crops.
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Affiliation(s)
- Faisal Nadeem
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Zeeshan Ahmad
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Mahmood Ul Hassan
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Ruifeng Wang
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuexian Li
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
- *Correspondence: Xuexian Li,
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Zhu CY, Liu W, Kang LF, Xu Q, Xing SL, Fan YY, Song ZH, Yan J, Li JQ, Sang T. Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments. THE PLANT GENOME 2017; 10. [PMID: 28724071 DOI: 10.3835/plantgenome2016.11.0119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Adaptation is a characteristic that enhances the survival or reproduction of organisms; selection is the critical process leading to adaptive evolution. Therefore, detecting selection is important in studying evolutionary biology. Changes in allele frequency are fundamental to adaptive evolution. The allele frequency of entire genes at the genomic scale is more intensive and precise for analyzing selection effects, compared with simple sequence repeat and single nucleotide polymorphism (SNP) alleles from nuclear gene fragments. Here, we analyzed 29,094 SNPs derived from 80 individuals of 14 L. Liou ex S.L. Chen & Renvoize populations planted near their native habitat (Jiangxia, Hubei Province, JH) and a stressful environment (Qingyang, Gansu Province, QG) to detect selection during initial adaptation. The nucleotide diversity of over 60% of genes was decreased in QG compared with JH, suggesting that most genes were undergoing selection in the stressful environment. We explored a new approach based on haplotype data inferred from RNA-seq data to analyze the change in frequency between two sites and to detect selection signals. In total, 402 and 51 genes were found to be targets of positive and negative selection, respectively. Among these candidate genes, the enrichment of abiotic stress-response genes and photosynthesis-related genes might have been responsible for establishment in the stressful environment. This is the first study assessing the change in allele frequency at the genomic level during adaptation. The method in which allele frequency detects selection during initial adaptation using population RNA-seq data would be useful for developing evolutionary biology.
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Shafique S, Rashid S. Antiviral drug acyclovir exhibits antitumor activity via targeting βTrCP1: Molecular docking and dynamics simulation study. J Mol Graph Model 2017; 72:96-105. [DOI: 10.1016/j.jmgm.2016.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/15/2016] [Accepted: 12/29/2016] [Indexed: 10/20/2022]
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Bandyopadhyay T, Muthamilarasan M, Prasad M. Millets for Next Generation Climate-Smart Agriculture. FRONTIERS IN PLANT SCIENCE 2017; 8:1266. [PMID: 28769966 PMCID: PMC5513978 DOI: 10.3389/fpls.2017.01266] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/05/2017] [Indexed: 05/04/2023]
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Goyal E, Amit SK, Singh RS, Mahato AK, Chand S, Kanika K. Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local. Sci Rep 2016; 6:27752. [PMID: 27293111 PMCID: PMC4904219 DOI: 10.1038/srep27752] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/24/2016] [Indexed: 11/23/2022] Open
Abstract
Kharchia Local wheat variety is an Indian salt tolerant land race known for its tolerance to salinity. However, there is a lack of detailed information regarding molecular mechanism imparting tolerance to high salinity in this bread wheat. In the present study, differential root transcriptome analysis identifying salt stress responsive gene networks and functional annotation under salt stress in Kharchia Local was performed. A total of 453,882 reads were obtained after quality filtering, using Roche 454-GS FLX Titanium sequencing technology. From these reads 22,241 ESTs were generated out of which, 17,911 unigenes were obtained. A total of 14,898 unigenes were annotated against nr protein database. Seventy seven transcription factors families in 826 unigenes and 11,002 SSRs in 6,939 unigenes were identified. Kyoto Encyclopedia of Genes and Genomes database identified 310 metabolic pathways. The expression pattern of few selected genes was compared during the time course of salt stress treatment between salt-tolerant (Kharchia Local) and susceptible (HD2687). The transcriptome data is the first report, which offers an insight into the mechanisms and genes involved in salt tolerance. This information can be used to improve salt tolerance in elite wheat cultivars and to develop tolerant germplasm for other cereal crops.
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Affiliation(s)
- Etika Goyal
- Banasthali University, Banasthali, Rajasthan, India.,Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Singh K Amit
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Ravi S Singh
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Ajay K Mahato
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Suresh Chand
- Banasthali University, Banasthali, Rajasthan, India.,Devi Ahilya University, Indore, India
| | - Kumar Kanika
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
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12
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Zhou XX, Yang LT, Qi YP, Guo P, Chen LS. Mechanisms on boron-induced alleviation of aluminum-toxicity in Citrus grandis seedlings at a transcriptional level revealed by cDNA-AFLP analysis. PLoS One 2015; 10:e0115485. [PMID: 25747450 PMCID: PMC4352013 DOI: 10.1371/journal.pone.0115485] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/24/2014] [Indexed: 11/18/2022] Open
Abstract
The physiological and biochemical mechanisms on boron (B)-induced alleviation of aluminum (B)-toxicity in plants have been examined in some details, but our understanding of the molecular mechanisms underlying these processes is very limited. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in Citrus grandis roots responsive to B and Al interactions, and isolated 100 differentially expressed genes. Results showed that genes related to detoxification of reactive oxygen species (ROS) and aldehydes (i.e., glutathione S-transferase zeta class-like isoform X1, thioredoxin M-type 4, and 2-alkenal reductase (NADP+-dependent)-like), metabolism (i.e., carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like, nicotianamine aminotransferase A-like isoform X3, thiosulfate sulfurtransferase 18-like isoform X1, and FNR, root isozyme 2), cell transport (i.e., non-specific lipid-transfer protein-like protein At2g13820-like and major facilitator superfamily protein), Ca signal and hormone (i.e., calcium-binding protein CML19-like and IAA-amino acid hydrolase ILR1-like 4-like), gene regulation (i.e., Gag-pol polyprotein) and cell wall modification (i.e., glycosyl hydrolase family 10 protein) might play a role in B-induced alleviation of Al-toxicity. Our results are useful not only for our understanding of molecular processes associated with B-induced alleviation of Al-toxicity, but also for obtaining key molecular genes to enhance Al-tolerance of plants in the future.
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Affiliation(s)
- Xin-Xing Zhou
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Peng Guo
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- * E-mail:
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Kong D, Li M, Dong Z, Ji H, Li X. Identification of TaWD40D, a wheat WD40 repeat-containing protein that is associated with plant tolerance to abiotic stresses. PLANT CELL REPORTS 2015; 34:395-410. [PMID: 25447637 DOI: 10.1007/s00299-014-1717-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE TaWD40D that encodes a member of WD40 family proteins is a novel gene involved in the wheat response to abiotic stress. TaWD40D functions as a positive regulator of plant responses to salt stress and osmotic stress in plant. Abiotic stresses can severely affect plant growth and crop productivity. WD40 repeat-containing proteins play a key role in protein-protein or protein-DNA interactions by acting as scaffolding molecules and promoting protein activity. In this study, a stress-inducible gene, TaWD40D, was identified from Chinese spring wheat (Triticum aestivum L.). TaWD40D encodes a protein containing seven WD40 domains. Subcellular localization in Nicotiana benthamiana mesophyll cells and Arabidopsis root cells showed the presence of TaWD40D in the cytoplasm and nucleus. Heterologous overexpression of TaWD40D in Arabidopsis greatly increased plant tolerance to abscisic acid (ABA), salt stress, and osmotic stress during seed germination and seedling development. The expression patterns of two genes from the SOS pathway (SOS2 and SOS3) and three ABA genes (ABI2, RAB18 and DREB2A) functioning in ABA-dependent and ABA-independent pathways were altered in the transgenic lines overexpressing TaWD40D under the treatments. Notably, the basal level of the ABI2 expression was substantially increased in the TaWD40D overexpression lines. The down-regulation of TaWD40D in wheat by virus-induced gene silencing resulted in a decreased relative water content and less vigorous growth compared to non-silenced lines. Our results suggest that TaWD40D functions as a positive regulator of plant responses to salt stress and osmotic stress that could be utilized for the genetic improvement of stress tolerance in crop plants.
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Affiliation(s)
- Dejing Kong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, Hebei, China
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Zhang C, Zhang F. The Multifunctions of WD40 Proteins in Genome Integrity and Cell Cycle Progression. J Genomics 2015; 3:40-50. [PMID: 25653723 PMCID: PMC4316180 DOI: 10.7150/jgen.11015] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome encodes numerous WD40 repeat proteins, which generally function as platforms of protein-protein interactions and are involved in numerous biological process, such as signal transduction, gene transcriptional regulation, protein modifications, cytoskeleton assembly, vesicular trafficking, DNA damage and repair, cell death and cell cycle progression. Among these diverse functions, genome integrity maintenance and cell cycle progression are extremely important as deregulation of them is clinically linked to uncontrolled proliferative diseases such as cancer. Thus, we mainly summarize and discuss the recent understanding of WD40 proteins and their molecular mechanisms linked to genome stability and cell cycle progression in this review, thereby demonstrating their pervasiveness and importance in cellular networks.
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Affiliation(s)
- Caiguo Zhang
- 1. Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Fan Zhang
- 2. Orthopedics Department, Changhai Hospital Affiliated to Second Military Medical University, Shanghai, 200433, China
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Lu YB, Qi YP, Yang LT, Lee J, Guo P, Ye X, Jia MY, Li ML, Chen LS. Long-term boron-deficiency-responsive genes revealed by cDNA-AFLP differ between Citrus sinensis roots and leaves. FRONTIERS IN PLANT SCIENCE 2015; 6:585. [PMID: 26284101 PMCID: PMC4517394 DOI: 10.3389/fpls.2015.00585] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/13/2015] [Indexed: 05/20/2023]
Abstract
Seedlings of Citrus sinensis (L.) Osbeck were supplied with boron (B)-deficient (without H3BO3) or -sufficient (10 μM H3BO3) nutrient solution for 15 weeks. We identified 54 (38) and 38 (45) up (down)-regulated cDNA-AFLP bands (transcript-derived fragments, TDFs) from B-deficient leaves and roots, respectively. These TDFs were mainly involved in protein and amino acid metabolism, carbohydrate and energy metabolism, nucleic acid metabolism, cell transport, signal transduction, and stress response and defense. The majority of the differentially expressed TDFs were isolated only from B-deficient roots or leaves, only seven TDFs with the same GenBank ID were isolated from the both. In addition, ATP biosynthesis-related TDFs were induced in B-deficient roots, but unaffected in B-deficient leaves. Most of the differentially expressed TDFs associated with signal transduction and stress defense were down-regulated in roots, but up-regulated in leaves. TDFs related to protein ubiquitination and proteolysis were induced in B-deficient leaves except for one TDF, while only two down-regulated TDFs associated with ubiquitination were detected in B-deficient roots. Thus, many differences existed in long-term B-deficiency-responsive genes between roots and leaves. In conclusion, our findings provided a global picture of the differential responses occurring in B-deficient roots and leaves and revealed new insight into the different adaptive mechanisms of C. sinensis roots and leaves to B-deficiency at the transcriptional level.
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Affiliation(s)
- Yi-Bin Lu
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical SciencesFuzhou, China
| | - Lin-Tong Yang
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jinwook Lee
- Department of Horticultural Science, Kyungpook National UniversityDaegu, South Korea
| | - Peng Guo
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xin Ye
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Meng-Yang Jia
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Mei-Li Li
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Li-Song Chen
- Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Plant Physiology, Biochemistry, and Molecular Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Li-Song Chen, Department of Resource and Environment, College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Boxue Building, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
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Muthamilarasan M, Prasad M. Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1-14. [PMID: 25239219 DOI: 10.1007/s00122-014-2399-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 05/18/2023]
Abstract
Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.
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Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
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Sharma M, Pandey GK. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1218. [PMID: 26793205 PMCID: PMC4707873 DOI: 10.3389/fpls.2015.01218] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants.
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Sun ZM, Zhou ML, Xiao XG, Tang YX, Wu YM. Genome-wide analysis of AP2/ERF family genes from Lotus corniculatus shows LcERF054 enhances salt tolerance. Funct Integr Genomics 2014; 14:453-66. [PMID: 24777608 DOI: 10.1007/s10142-014-0372-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/30/2014] [Accepted: 04/03/2014] [Indexed: 11/29/2022]
Abstract
Lotus corniculatus is used in agriculture as a main forage plant. Members of the Apetala2/ethylene response factor (AP2/ERF) family play important roles in regulating gene expression in response to many forms of stress, including drought and salt. Here, starting from database of the L. corniculatus var. japonicus genome, we identified 127 AP2/ERF genes by insilico cloning method. The phylogeny, gene structures, and putative conserved motifs in L. corniculatus var. japonicus ERF proteins were analyzed. Based on the number of AP2/ERF domains and the function of the genes, 127 AP2/ERF genes from L. corniculatus var. japonicus were classified into five subfamilies named the AP2, dehydration-responsive element binding factor (DREB), ERF, RAV, and a soloist. Outside the AP2/ERF domain, many L. corniculatus var. japonicus-specific conserved motifs were detected. Expression profile analysis of AP2/ERF genes by quantitative real-time PCR revealed that 19 LcERF genes, including LcERF054 (KJ004728), were significantly induced by salt stress. The results showed that the LcERF054 gene encodes a nuclear transcription activator. Overexpression of LcERF054 in Arabidopsis enhanced the tolerances to salt stress, showed higher germination ratio of seeds, and had elevated levels of relative moisture contents, soluble sugars, proline, and lower levels of malondialdehyde under stress conditions compared to wild-type plants. The expression of hyperosmotic salinity response genes COR15A, LEA4-5, P5CS1, and RD29A was found to be elevated in the LcERF054-overexpressing Arabidopsis plants compared to wild type. These results revealed that the LcERF genes play important roles in L. corniculatus cv Leo under salt stress and that LcERFs are attractive engineering targets in applied efforts to improve abiotic stress tolerances in L. corniculatus cv Leo or other crops.
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Affiliation(s)
- Zhan-Min Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Room 211, Zhongguancun South Street No. 12, Haidian District, 100081, Beijing, China
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Mishra AK, Muthamilarasan M, Khan Y, Parida SK, Prasad M. Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.). PLoS One 2014; 9:e86852. [PMID: 24466268 PMCID: PMC3900672 DOI: 10.1371/journal.pone.0086852] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/19/2013] [Indexed: 12/16/2022] Open
Abstract
WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these WD40 genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential WD40 genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I–V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of SiWD40 genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses.
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Affiliation(s)
| | | | - Yusuf Khan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi
- * E-mail:
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20
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Zhou CP, Qi YP, You X, Yang LT, Guo P, Ye X, Zhou XX, Ke FJ, Chen LS. Leaf cDNA-AFLP analysis of two citrus species differing in manganese tolerance in response to long-term manganese-toxicity. BMC Genomics 2013; 14:621. [PMID: 24034812 PMCID: PMC3847489 DOI: 10.1186/1471-2164-14-621] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/11/2013] [Indexed: 01/17/2023] Open
Abstract
Background Very little is known about manganese (Mn)-toxicity-responsive genes in citrus plants. Seedlings of ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) were irrigated for 17 weeks with nutrient solution containing 2 μM (control) or 600 μM (Mn-toxicity) MnSO4. The objectives of this study were to understand the mechanisms of citrus Mn-tolerance and to identify differentially expressed genes, which might be involved in Mn-tolerance. Results Under Mn-toxicity, the majority of Mn in seedlings was retained in the roots; C. sinensis seedlings accumulated more Mn in roots and less Mn in shoots (leaves) than C. grandis ones and Mn concentration was lower in Mn-toxicity C. sinensis leaves compared to Mn-toxicity C. grandis ones. Mn-toxicity affected C. grandis seedling growth, leaf CO2 assimilation, total soluble concentration, phosphorus (P) and magenisum (Mg) more than C. sinensis. Using cDNA-AFLP, we isolated 42 up-regulated and 80 down-regulated genes in Mn-toxicity C. grandis leaves. They were grouped into the following functional categories: biological regulation and signal transduction, carbohydrate and energy metabolism, nucleic acid metabolism, protein metabolism, lipid metabolism, cell wall metabolism, stress responses and cell transport. However, only 7 up-regulated and 8 down-regulated genes were identified in Mn-toxicity C. sinensis ones. The responses of C. grandis leaves to Mn-toxicity might include following several aspects: (1) accelerating leaf senescence; (2) activating the metabolic pathway related to ATPase synthesis and reducing power production; (3) decreasing cell transport; (4) inhibiting protein and nucleic acid metabolisms; (5) impairing the formation of cell wall; and (6) triggering multiple signal transduction pathways. We also identified many new Mn-toxicity-responsive genes involved in biological and signal transduction, carbohydrate and protein metabolisms, stress responses and cell transport. Conclusions Our results demonstrated that C. sinensis was more tolerant to Mn-toxicity than C. grandis, and that Mn-toxicity affected gene expression far less in C. sinensis leaves. This might be associated with more Mn accumulation in roots and less Mn accumulation in leaves of Mn-toxicity C. sinensis seedlings than those of C. grandis seedlings. Our findings increase our understanding of the molecular mechanisms involved in the responses of plants to Mn-toxicity.
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Affiliation(s)
- Chen-Ping Zhou
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.
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B VS, Muthamilarasan M, Misra G, Prasad M. FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS One 2013; 8:e71418. [PMID: 23951158 PMCID: PMC3741111 DOI: 10.1371/journal.pone.0071418] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/01/2013] [Indexed: 11/18/2022] Open
Abstract
The prominent attributes of foxtail millet (Setaria italica L.) including its small genome size, short life cycle, inbreeding nature, and phylogenetic proximity to various biofuel crops have made this crop an excellent model system to investigate various aspects of architectural, evolutionary and physiological significances in Panicoid bioenergy grasses. After release of its whole genome sequence, large-scale genomic resources in terms of molecular markers were generated for the improvement of both foxtail millet and its related species. Hence it is now essential to congregate, curate and make available these genomic resources for the benefit of researchers and breeders working towards crop improvement. In view of this, we have constructed the Foxtail millet Marker Database (FmMDb; http://www.nipgr.res.in/foxtail.html), a comprehensive online database for information retrieval, visualization and management of large-scale marker datasets with unrestricted public access. FmMDb is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity.
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Affiliation(s)
| | | | - Gopal Misra
- National Institute of Plant Genome Research, New Delhi, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
- * E-mail:
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Kumar S, Jordan MC, Datla R, Cloutier S. The LuWD40-1 gene encoding WD repeat protein regulates growth and pollen viability in flax (Linum Usitatissimum L.). PLoS One 2013; 8:e69124. [PMID: 23935935 PMCID: PMC3728291 DOI: 10.1371/journal.pone.0069124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/11/2013] [Indexed: 01/22/2023] Open
Abstract
As a crop, flax holds significant commercial value for its omega-3 rich oilseeds and stem fibres. Canada is the largest producer of linseed but there exists scope for significant yield improvements. Implementation of mechanisms such as male sterility can permit the development of hybrids to assist in achieving this goal. Temperature sensitive male sterility has been reported in flax but the leakiness of this system in field conditions limits the production of quality hybrid seeds. Here, we characterized a 2,588 bp transcript differentially expressed in male sterile lines of flax. The twelve intron gene predicted to encode a 368 amino acid protein has five WD40 repeats which, in silico, form a propeller structure with putative nucleic acid and histone binding capabilities. The LuWD40-1 protein localized to the nucleus and its expression increased during the transition and continued through the vegetative stages (seed, etiolated seedling, stem) while the transcript levels declined during reproductive development (ovary, anthers) and embryonic morphogenesis of male fertile plants. Knockout lines for LuWD40-1 in flax failed to develop shoots while overexpression lines showed delayed growth phenotype and were male sterile. The non-viable flowers failed to open and the pollen grains from these flowers were empty. Three independent transgenic lines overexpressing the LuWD40-1 gene had ∼80% non-viable pollen, reduced branching, delayed flowering and maturity compared to male fertile genotypes. The present study provides new insights into a male sterility mechanism present in flax.
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Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Mark C. Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Raju Datla
- National Research Council, Saskatoon, Saskatchewan, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
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