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Wei J, Li H, Huang X, Zhao Y, Ouyang L, Wei M, Wang C, Wang J, Lu G. Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard. PeerJ 2024; 12:e17661. [PMID: 38978758 PMCID: PMC11229683 DOI: 10.7717/peerj.17661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/08/2024] [Indexed: 07/10/2024] Open
Abstract
Leaf mustard (Brassica juncea L. Czern & Coss), an important vegetable crop, experiences pronounced adversity due to seasonal drought stress, particularly at the seed germination stage. Although there is partial comprehension of drought-responsive genes, the role of long non-coding RNAs (lncRNAs) in adjusting mustard's drought stress response is largely unexplored. In this study, we showed that the drought-tolerant cultivar 'Weiliang' manifested a markedly lower base water potential (-1.073 MPa vs -0.437 MPa) and higher germination percentage (41.2% vs 0%) than the drought-susceptible cultivar 'Shuidong' under drought conditions. High throughput RNA sequencing techniques revealed a significant repertoire of lncRNAs from both cultivars during germination under drought stress, resulting in the identification of 2,087 differentially expressed lncRNAs (DELs) and their correspondingly linked 12,433 target genes. It was noted that 84 genes targeted by DEL exhibited enrichment in the photosynthesis pathway. Gene network construction showed that MSTRG.150397, a regulatory lncRNA, was inferred to potentially modulate key photosynthetic genes (Psb27, PetC, PetH, and PsbW), whilst MSTRG.107159 was indicated as an inhibitory regulator of six drought-responsive PIP genes. Further, weighted gene co-expression network analysis (WGCNA) corroborated the involvement of light intensity and stress response genes targeted by the identified DELs. The precision and regulatory impact of lncRNA were verified through qPCR. This study extends our knowledge of the regulatory mechanisms governing drought stress responses in mustard, which will help strategies to augment drought tolerance in this crop.
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Affiliation(s)
- Jinxing Wei
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Haibo Li
- Shaoguan University, Shaoguan, China
| | - Xiaoer Huang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Yongguo Zhao
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Lejun Ouyang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Mingken Wei
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Chun Wang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Junxia Wang
- South China Agricultural University, Guangzhou, China
| | - Guangyuan Lu
- Guangdong University of Petrochemical Technology, Maoming, China
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Moin M, Bommineni PR, Tyagi W. Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits. BMC Genomics 2024; 25:581. [PMID: 38858648 PMCID: PMC11165789 DOI: 10.1186/s12864-024-10504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented. RESULTS In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and non-metal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet. CONCLUSIONS The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.
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Affiliation(s)
- Mazahar Moin
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Pradeep Reddy Bommineni
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Wang W, Liu Y, Kang Y, Liu W, Li S, Wang Z, Xia X, Chen X, Qian L, Xiong X, Liu Z, Guan C, He X. Genome-wide characterization of LEA gene family reveals a positive role of BnaA.LEA6.a in freezing tolerance in rapeseed (Brassica napus L.). BMC PLANT BIOLOGY 2024; 24:433. [PMID: 38773359 PMCID: PMC11106994 DOI: 10.1186/s12870-024-05111-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Freezing stress is one of the major abiotic stresses that causes extensive damage to plants. LEA (Late embryogenesis abundant) proteins play a crucial role in plant growth, development, and abiotic stress. However, there is limited research on the function of LEA genes in low-temperature stress in Brassica napus (rapeseed). RESULTS Total 306 potential LEA genes were identified in B. rapa (79), B. oleracea (79) and B. napus (148) and divided into eight subgroups. LEA genes of the same subgroup had similar gene structures and predicted subcellular locations. Cis-regulatory elements analysis showed that the promoters of BnaLEA genes rich in cis-regulatory elements related to various abiotic stresses. Additionally, RNA-seq and real-time PCR results indicated that the majority of BnaLEA family members were highly expressed in senescent tissues of rapeseed, especially during late stages of seed maturation, and most BnaLEA genes can be induced by salt and osmotic stress. Interestingly, the BnaA.LEA6.a and BnaC.LEA6.a genes were highly expressed across different vegetative and reproductive organs during different development stages, and showed strong responses to salt, osmotic, and cold stress, particularly freezing stress. Further analysis showed that overexpression of BnaA.LEA6.a increased the freezing tolerance in rapeseed, as evidenced by lower relative electrical leakage and higher survival rates compared to the wild-type (WT) under freezing treatment. CONCLUSION This study is of great significance for understanding the functions of BnaLEA genes in freezing tolerance in rapeseed and offers an ideal candidate gene (BnaA.LEA6.a) for molecular breeding of freezing-tolerant rapeseed cultivars.
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Affiliation(s)
- Weiping Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yu Kang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Wei Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shun Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Zhonghua Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiaoyan Xia
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiaoyu Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xinghua Xiong
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xin He
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Zhang Y, Zhang X, Zhu L, Wang L, Zhang H, Zhang X, Xu S, Xue J. Identification of the Maize LEA Gene Family and Its Relationship with Kernel Dehydration. PLANTS (BASEL, SWITZERLAND) 2023; 12:3674. [PMID: 37960031 PMCID: PMC10647770 DOI: 10.3390/plants12213674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/21/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Maize, the most widely planted and highest yielding of the three major crops in the world, requires the development and breeding of new varieties to accommodate the shift towards mechanized harvesting. However, the moisture content of kernels during harvest poses a significant challenge to mechanized harvesting, leading to seed breakage and increased storage costs. Previous studies highlighted the importance of LEA (Late Embryogenesis Abundant) members in regulating kernel dehydration. In this study, we aimed to gain a better understanding of the relationship between the LEA family and grain dehydration in maize. Through expression pattern analysis of maize, we identified 52 LEA genes (ZmLEAs) distributed across 10 chromosomes, organized into seven subgroups based on phylogenetic analysis, gene structure, and conserved motifs. Evolutionary and selective pressure analysis revealed that the amplification of ZmLEA genes primarily resulted from whole-genome or fragment replication events, with strong purifying selection effects during evolution. Furthermore, the transcriptome data of kernels of two maize inbred lines with varying dehydration rates at different developmental stages showed that 14 ZmLEA genes were expressed differentially in the two inbreds. This suggested that the ZmLEA genes might participate in regulating the kernel dehydration rate (KDR) in maize. Overall, this study enhances our understanding of the ZmLEA family and provides a foundation for further research into its role in regulating genes associated with grain dehydration in maize.
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Affiliation(s)
| | | | | | | | | | | | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.Z.); (X.Z.); (L.Z.); (L.W.); (H.Z.); (X.Z.)
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.Z.); (X.Z.); (L.Z.); (L.W.); (H.Z.); (X.Z.)
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Guo B, Zhang J, Yang C, Dong L, Ye H, Valliyodan B, Nguyen HT, Song L. The Late Embryogenesis Abundant Proteins in Soybean: Identification, Expression Analysis, and the Roles of GmLEA4_19 in Drought Stress. Int J Mol Sci 2023; 24:14834. [PMID: 37834282 PMCID: PMC10573439 DOI: 10.3390/ijms241914834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Late embryogenesis abundant (LEA) proteins play important roles in regulating plant growth and responses to various abiotic stresses. In this research, a genome-wide survey was conducted to recognize the LEA genes in Glycine max. A total of 74 GmLEA was identified and classified into nine subfamilies based on their conserved domains and the phylogenetic analysis. Subcellular localization, the duplication of genes, gene structure, the conserved motif, and the prediction of cis-regulatory elements and tissue expression pattern were then conducted to characterize GmLEAs. The expression profile analysis indicated that the expression of several GmLEAs was a response to drought and salt stress. The co-expression-based gene network analysis suggested that soybean LEA proteins may exert regulatory effects through the metabolic pathways. We further explored GnLEA4_19 function in Arabidopsis and the results suggests that overexpressed GmLEA4_19 in Arabidopsis increased plant height under mild or serious drought stress. Moreover, the overexpressed GmLEA4_19 soybean also showed a drought tolerance phenotype. These results indicated that GmLEA4_19 plays an important role in the tolerance to drought and will contribute to the development of the soybean transgenic with enhanced drought tolerance and better yield. Taken together, this study provided insight for better understanding the biological roles of LEA genes in soybean.
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Affiliation(s)
- Binhui Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Jianhua Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
| | - Chunhong Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
| | - Lu Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Babu Valliyodan
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO 65101, USA;
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
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Aziz MA, Sabeem M, Kutty MS, Rahman S, Alneyadi MK, Alkaabi AB, Almeqbali ES, Brini F, Vijayan R, Masmoudi K. Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm. Sci Rep 2023; 13:11878. [PMID: 37482543 PMCID: PMC10363547 DOI: 10.1038/s41598-023-38426-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
In date palm, the LEA2 genes are of abundance with sixty-two members that are nearly all ubiquitous. However, their functions and interactions with potential target molecules are largely unexplored. In this study, five date palm LEA2 genes, PdLEA2.2, PdLEA2.3, PdLEA2.4, PdLEA2.6, and PdLEA2.7 were cloned, sequenced, and three of them, PdLEA2.2, PdLEA2.3, and PdLEA2.4 were functionally characterized for their effects on the thermostability of two distinct enzymes, lactate dehydrogenase (LDH) and β-glucosidase (bglG) in vitro. Overall, PdLEA2.3 and PdLEA2.4 were moderately hydrophilic, PdLEA2.7 was slightly hydrophobic, and PdLEA2.2 and PdLEA2.6 were neither. Sequence and structure prediction indicated the presence of a stretch of hydrophobic residues near the N-terminus that could potentially form a transmembrane helix in PdLEA2.2, PdLEA2.4, PdLEA2.6 and PdLEA2.7. In addition to the transmembrane helix, secondary and tertiary structures prediction showed the presence of a disordered region followed by a stacked β-sheet region in all the PdLEA2 proteins. Moreover, three purified recombinant PdLEA2 proteins were produced in vitro, and their presence in the LDH enzymatic reaction enhanced the activity and reduced the aggregate formation of LDH under the heat stress. In the bglG enzymatic assays, PdLEA2 proteins further displayed their capacity to preserve and stabilize the bglG enzymatic activity.
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Affiliation(s)
- Mughair Abdul Aziz
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - Miloofer Sabeem
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - M Sangeeta Kutty
- Department of Vegetable Science, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, 680656, India
| | - Shafeeq Rahman
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - Maitha Khalfan Alneyadi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - Alia Binghushoom Alkaabi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - Eiman Saeed Almeqbali
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/ University of Sfax, Sfax, Tunisia
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al‑Ain, Abu‑Dhabi, UAE
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab, Emirates University, Al‑Ain, Abu‑Dhabi, UAE.
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Ma J, Zuo D, Ye H, Yan Y, Li M, Zhao P. Genome-wide identification, characterization, and expression pattern of the late embryogenesis abundant (LEA) gene family in Juglans regia and its wild relatives J. mandshurica. BMC PLANT BIOLOGY 2023; 23:80. [PMID: 36740678 PMCID: PMC9901102 DOI: 10.1186/s12870-023-04096-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Late Embryogenesis Abundant (LEA) proteins are a class of proteins associated with plant stress resistance. Two Juglans species, Juglans regia and J. mandshurica, are both diploid (2n = 32), monoecious perennial economic tree species with high edible, pharmaceutical, and timber value. The identification, characterization, and expression patterns of LEA proteins in J. regia and its wild relative, J. mandshurica, would not only provide the genetic basis of this gene family, but it would also supply clues for further studies of the evolution and regulating mechanisms of LEA proteins in other tree species. RESULTS In this study, we identified 25 and 20 members of the LEA gene family in Juglans regia and its wild relative, Juglans mandshurica, respectively. The results of phylogenetic analysis showed that the LEA members were divided into eight main subgroups. Predictions of their physicochemical properties showed the variable characteristics of LEA proteins, and the subcellular localization analysis indicated that most LEA proteins are localized in the nucleus. Chromosomal localization analysis and gene replication pattern prediction indicated that WGD is the predominant duplication mode of LEA genes. The results of the comparative analysis indicated a high level of collinearity between the two Juglans species. Analysis of cis-acting elements indicated that LEA genes had a relatively wide range of responses to abiotic stresses and phytohormonal processes, particularly in two phytohormones, methyl jasmonate and abscisic acid. Transcriptome profiling and qRT-PCR experiments showed that JrLEAs are commonly expressed in leaves, green husks, and male and female flowers, and most JmLEAs are more highly expressed in male flowers. We also hypothesized that JrLEAs are involved in the process of anthracnose resistance. Anthracnose-resistant varieties of JrLEAs presented relatively high expression levels at later stages. CONCLUSION In this study, we provide a theoretical basis for the functional study of LEA genes in J. regia and J. mandshurica. Analysis of cis-acting elements and gene expression indicated that JrLEAs and JmLEAs play important roles in resistance to biotic stresses in these species.
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Affiliation(s)
- Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Dongjun Zuo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
- College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Yujie Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069 Shaanxi China
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Jiang Y, Zhang S, Xu H, Tian H, Zhang M, Zhu S, Wang C, Hou J, Chen G, Tang X, Wang W, Wu J, Huang X, Zhang J, Yuan L. Identification of the BcLEA Gene Family and Functional Analysis of the BcLEA73 Gene in Wucai ( Brassica campestris L.). Genes (Basel) 2023; 14:415. [PMID: 36833342 PMCID: PMC9957401 DOI: 10.3390/genes14020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Late embryogenesis abundant (LEA) proteins are important developmental proteins in the response of plants to abiotic stress. In our previous study, BcLEA73 was differentially expressed under low-temperature stress. Herein, we combined bioinformatics analysis, subcellular localization, expression assays, and stress experiments (including salt, drought, and osmotic stress) to identify and analyze the BcLEA gene family. Gene cloning and functional analysis of BcLEA73 were performed in tobacco and Arabidopsis. Based on the sequence homology and the available conservative motif, 82 BrLEA gene family members were identified and were divided into eight subfamilies in the genome-wide database of Chinese cabbage. The analysis showed that the BrLEA73 gene was located on chromosome A09 and belonged to the LEA_6 subfamily. Quantitative real-time PCR analysis indicated that the BcLEA genes were differentially expressed to varying degrees in the roots, stems, leaves, and petioles of Wucai. The overexpressed BcLEA73 transgenic plants exhibited no significant differences in root length and seed germination rates compared to the wild-type (WT) plants under control conditions. Under salt and osmotic stress treatment, the root length and seed germination rates of the BcLEA73-OE strain were significantly greater than those of WT plants. Under salt stress, the total antioxidant capacity (T-AOC) of the BcLEA73-OE lines increased significantly, and the relative conductivity, (REL), hydrogen peroxide (H2O2) content, and superoxide anion (O2-) production rate decreased significantly. Under drought treatment, the survival rate of the BcLEA73-OE lines was significantly higher than that of WT plants. These results showed that the BcLEA73 gene of Wucai functions in enhancing the tolerance of plants to salt, drought, and osmotic stress. This study provides a theoretical basis to explore the relevant functions of the BcLEA gene family members of Wucai.
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Affiliation(s)
- Yueyue Jiang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Shengnan Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Hongcheng Xu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Hong Tian
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Mengyun Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Shidong Zhu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Wenjie Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Jianqiang Wu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Xingxue Huang
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinlong Zhang
- Vegetable Industry Office, Agricultural and Rural Bureau of He County, Maanshan 238201, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
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Genome-wide study and functional characterization elucidates the potential association of late embryogenesis abundant (LEA) genes with lotus seed development. Int J Biol Macromol 2023; 226:1-13. [PMID: 36481329 DOI: 10.1016/j.ijbiomac.2022.11.301] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins imperatively associated with plant growth and development, as well as cell protection from abiotic stress. However, the genome-wide characterization of LEA gene family remains limited, especially in aquatic species such as lotus (Nelumbo spp.). Here, 57 putative LEA genes, including 28 NnLEAs and 29 NlLEAs were identified in the N.nucifera and N.lutea genomes, respectively. A total of 27 homologous LEA gene pairs were identified, indicating high degree of sequence homologies between the two Nelumbo species. Secondary structure prediction indicated high prevalence of alpha (α) helix structure among LEA proteins in the LEA_1, LEA_4, and SMP groups. Screening of putative promoter cis-elements revealed that NnLEA genes were involved in diverse biological processes. Most NnLEA genes were predominantly expressed in the late cotyledons and plumules development stages, suggesting their potential vital roles in lotus seed maturation. In addition, genes co-expressed with NnLEAs were involved in ABA signaling, seed maturation, and development processes. Overall, this study provides new insights for the in-depth understanding of the functions of NnLEA proteins in lotus seed development, and could act as a useful reference for the molecular breeding of seeds with prolonged lifespan.
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10
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Jia C, Guo B, Wang B, Li X, Yang T, Li N, Wang J, Yu Q. The LEA gene family in tomato and its wild relatives: genome-wide identification, structural characterization, expression profiling, and role of SlLEA6 in drought stress. BMC PLANT BIOLOGY 2022; 22:596. [PMID: 36536303 PMCID: PMC9762057 DOI: 10.1186/s12870-022-03953-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins are widely distributed in higher plants and play crucial roles in regulating plant growth and development processes and resisting abiotic stress. Cultivated tomato (Solanum lycopersicum) is an important vegetable crop worldwide; however, its growth, development, yield, and quality are currently severely constrained by abiotic stressors. In contrast, wild tomato species are more tolerant to abiotic stress and can grow normally in extreme environments. The main objective of this study was to identify, characterize, and perform gene expression analysis of LEA protein families from cultivated and wild tomato species to mine candidate genes and determine their potential role in abiotic stress tolerance in tomatoes. RESULTS Total 60, 69, 65, and 60 LEA genes were identified in S. lycopersicum, Solanum pimpinellifolium, Solanum pennellii, and Solanum lycopersicoides, respectively. Characterization results showed that these genes could be divided into eight clusters, with the LEA_2 cluster having the most members. Most LEA genes had few introns and were non-randomly distributed on chromosomes; the promoter regions contained numerous cis-acting regulatory elements related to abiotic stress tolerance and phytohormone responses. Evolutionary analysis showed that LEA genes were highly conserved and that the segmental duplication event played an important role in evolution of the LEA gene family. Transcription and expression pattern analyses revealed different regulatory patterns of LEA genes between cultivated and wild tomato species under normal conditions. Certain S. lycopersicum LEA (SlLEA) genes showed similar expression patterns and played specific roles under different abiotic stress and phytohormone treatments. Gene ontology and protein interaction analyses showed that most LEA genes acted in response to abiotic stimuli and water deficit. Five SlLEA proteins were found to interact with 11 S. lycopersicum WRKY proteins involved in development or resistance to stress. Virus-induced gene silencing of SlLEA6 affected the antioxidant and reactive oxygen species defense systems, increased the degree of cellular damage, and reduced drought resistance in S. lycopersicum. CONCLUSION These findings provide comprehensive information on LEA proteins in cultivated and wild tomato species and their possible functions under different abiotic and phytohormone stresses. The study systematically broadens our current understanding of LEA proteins and candidate genes and provides a theoretical basis for future functional studies aimed at improving stress resistance in tomato.
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Affiliation(s)
- Chunping Jia
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Bin Guo
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Xin Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
- College of Life Science and Technology, Xinjiang University, Urumqi, China.
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11
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Xiao Z, Zhang C, Qu C, Wei L, Zhang L, Yang B, Lu K, Li J. Identification of candidate genes regulating seed oil content by QTL mapping and transcriptome sequencing in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:1067121. [PMID: 36570918 PMCID: PMC9779944 DOI: 10.3389/fpls.2022.1067121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/24/2022] [Indexed: 06/12/2023]
Abstract
Increasing oil production is a major goal in rapeseed (Brassica napus) molecular breeding programs. Identifying seed oil content (SOC)-related candidate genes is an important step towards achieving this goal. We performed quantitative trait locus (QTL) mapping of SOC in B. napus using a high-density SNP genetic map constructed from recombinant inbred lines and the Illumina InfiniumTM 60K SNP array. A total of 26 QTLs were detected in three years on A01, A03, A05, A06, A09, C01, C03 and C05, which accounted for 3.69%~18.47% of the phenotypic variation in SOC. Of these, 13 QTLs are reported here for the first time. 1713 candidate genes in the 26 QTLs confidence interval were obtained. We then identified differentially expressed genes (DEGs) between the high- and low-SOC accessions, to narrow down our focus to 21 candidate genes (Y1-Y21) related to SOC, and we will focus on 11 (Y1-Y11) candidate genes that contribute to the formation of high-SOC. In addition to providing insight into the genetic basis of SOC in B. napus, the loci identified and candidate genes in this study can be used in molecular breeding strategies to increase SOC in this important seed crop.
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Affiliation(s)
- Zhongchun Xiao
- Key Laboratory of Biological Genetic Resources Mining and Molecular Breeding of Qianxinan Prefecture, College of Biology and Chemistry, Minzu Normal University of Xingyi, Xingyi, China
| | - Chao Zhang
- Guizhou Oil Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Cunmin Qu
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Lijuan Wei
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Liyuan Zhang
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bo Yang
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Kun Lu
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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12
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Lu M, Meng XX, Zhang YM, Zhu XW, Li J, Chen WQ, Wan HH, Wang SF, Cao X, Sun W, Mi YL, Zhai JW. Genome-Wide Identification and Expression Profiles of bZIP Genes in Cannabis sativa L. Cannabis Cannabinoid Res 2022; 7:882-895. [PMID: 35020417 DOI: 10.1089/can.2021.0153] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background: The bZIP gene family plays roles in biotic and abiotic stress, secondary metabolism, and other aspects in plants. They have been reported in Arabidopsis thaliana, Oryza sativa, Artemisia annua, and other plants, but their roles in Cannabis sativa have not been determined. Materials and Methods: In this study, we analyzed the genome-wide identification and expression profile of the bZIP gene family in C. sativa. Results: A total of 51 members of the bZIP gene family were identified based on the C. sativa genome and numbered in order from CsbZIP1 to CsbZIP51. Their phylogenetic relationships, cis-elements in promoter region, gene structures and motif compositions, physicochemical properties, chromosome locations, and expression profiles, were analyzed. The results showed that the 51 CsbZIPs were unevenly distributed on 10 chromosomes and could be clustered into 11 subfamilies. Furthermore, CsbZIPs located in the same subfamilies presented similar intron/exon organization and motif composition. The expression levels of CsbZIPs in various tissues (flowers, bracts, vegetative leaves, stems, and seeds) were determined using reverse transcription quantitative polymerase chain reaction. The expression levels of CsbZIPs were higher in flowers and bracts. The 51 CsbZIPs were explored, and their structure, evolution, and expression pattern in different tissues of C. sativa were characterized synthetically. The findings indicated that CsbZIPs are essential for the growth and development of C. sativa. Conclusions: These results provide a theoretical basis for subsequent research on hemp bZIP transcription factors and the cultivation of high-cannabidiol and low-tetrahydrocannabinol high-quality cannabis varieties.
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Affiliation(s)
- Meng Lu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fuzhou, China
| | - Xiang-Xiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yi-Ming Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fuzhou, China
| | - Xue-Wen Zhu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei-Qiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hui-Hua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Si-Fan Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xue Cao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yao-Lei Mi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun-Wen Zhai
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fuzhou, China
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13
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Megha S, Wang Z, Kav NNV, Rahman H. Genome-wide identification of biotin carboxyl carrier subunits of acetyl-CoA carboxylase in Brassica and their role in stress tolerance in oilseed Brassica napus. BMC Genomics 2022; 23:707. [PMID: 36253756 PMCID: PMC9578262 DOI: 10.1186/s12864-022-08920-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
Background Biotin carboxyl carrier protein (BCCP) is a subunit of Acetyl CoA-carboxylase (ACCase) which catalyzes the conversion of acetyl-CoA to malonyl-CoA in a committed step during the de novo biosynthesis of fatty acids. Lipids, lipid metabolites, lipid-metabolizing and -modifying enzymes are known to play a role in biotic and abiotic stress tolerance in plants. In this regard, an understanding of the Brassica napus BCCP genes will aid in the improvement of biotic and abiotic stress tolerance in canola. Results In this study, we identified 43 BCCP genes in five Brassica species based on published genome data. Among them, Brassica rapa, Brassica oleracea, Brassica nigra, Brassica napus and Brassica juncea had six, seven, seven, 10 and 13 BCCP homologs, respectively. Phylogenetic analysis categorized them into five classes, each with unique conserved domains. The promoter regions of all BCCP genes contained stress-related cis-acting elements as determined by cis-element analysis. We identified four and three duplicated gene pairs (segmental) in B. napus and B. juncea respectively, indicating the role of segmental duplication in the expansion of this gene family. The Ka/Ks ratios of orthologous gene pairs between Arabidopsis thaliana and five Brassica species were mostly less than 1.0, implying that purifying selection, i.e., selective removal of deleterious alleles, played a role during the evolution of Brassica genomes. Analysis of 10 BnaBCCP genes using qRT-PCR showed a different pattern of expression because of exposure of the plants to biotic stresses, such as clubroot and sclerotinia diseases, and abiotic stresses such as drought, low temperature and salinity stresses. Conclusions The identification and functional analysis of the Brassica BCCPs demonstrated that some of these genes might play important roles in biotic and abiotic stress responses. Results from this study could lay the foundation for a better understanding of these genes for the improvement of Brassica crops for stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08920-y.
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Affiliation(s)
- Swati Megha
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Zhengping Wang
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nat N V Kav
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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14
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Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum. PLANTS 2022; 11:plants11192511. [PMID: 36235376 PMCID: PMC9572532 DOI: 10.3390/plants11192511] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022]
Abstract
The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.
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15
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Lv P, Zhang C, Xie P, Yang X, El-Sheikh MA, Hefft DI, Ahmad P, Zhao T, Bhat JA. Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max). Life (Basel) 2022; 12:life12091340. [PMID: 36143377 PMCID: PMC9504482 DOI: 10.3390/life12091340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I–V. From a broader view, the I–V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.
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Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Xie
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Yang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Daniel Ingo Hefft
- School of Chemical Engineering, Edgbaston Campus, University of Birmingham, Birmingham B15 2TT, UK
| | - Parvaiz Ahmad
- Department of Botany, GDC, Pulwama 192301, Jammu and Kashmir, India
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
| | - Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
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16
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Wang G, Xu X, Gao Z, Liu T, Li Y, Hou X. Genome-wide identification of LEA gene family and cold response mechanism of BcLEA4-7 and BcLEA4-18 in non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111291. [PMID: 35696933 DOI: 10.1016/j.plantsci.2022.111291] [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: 01/26/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Cold stress is a key factor limiting the yield and quality of non-heading Chinese cabbage. The hydrophilic protective protein LEA plays an important role in plant abiotic stress. In this study, 72 BcLEAs were identified from non-heading Chinese cabbage and divided into 9 subfamilies by phylogenetic analysis. Gene structure analysis showed that BcLEAs were unevenly distributed on 10 chromosomes, with few introns. Through analyzing the expression of these genes under cold stress by RNA-seq and qRT-PCR, two genes (BcLEA4-7 and BcLEA4-18) highly sensitive to cold stress were identified, whose roles in cold tolerance of non-heading Chinese cabbage were demonstrated by virus-induced gene silencing. The BcLEA promoters were analyzed to study the cold response mechanism of BcLEA4-7 and BcLEA4-18, revealing that both BcLEA4-7 and BcLEA4-18 promoters contained two CRT/DRE elements. Subsequently, it was found that the promoters isolated from non-heading Chinese cabbage could be activated at low temperatures. Further analysis showed BcCBF2 in non-heading Chinese cabbage interacted with two CRT/DRE elements in BcLEA4-7 and BcLEA4-18 promoters to stimulate their activity, indicating that BcCBF2 is an upstream regulator. Meanwhile, the CRT/DRE element located in BcLEA4-7 promoter (-219 bp to -171 bp) and BcLEA4-18 promoter (-234 bp to -186 bp) was more likely to be activated by BcCBF2, which may be attributed to its flanking sequence. These data laid a foundation for further understanding the functional role and regulatory mechanism of BcLEAs in cold stress tolerance.
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Affiliation(s)
- Guangpeng Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs, PR China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, PR China; Nanjing Suman Plasma Engineering Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinfeng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs, PR China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, PR China
| | - Zhanyuan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs, PR China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, PR China; Nanjing Suman Plasma Engineering Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs, PR China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, PR China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs, PR China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, PR China; Nanjing Suman Plasma Engineering Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs, PR China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, PR China; Nanjing Suman Plasma Engineering Research Institute, Nanjing Agricultural University, Nanjing 210095, China.
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17
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Zhou Z, Lin B, Tan J, Hao P, Hua S, Deng Z. Tandem Mass Tag-Based Quantitative Proteomics Reveals Implication of a Late Embryogenesis Abundant Protein (BnLEA57) in Seed Oil Accumulation in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:907244. [PMID: 35720596 PMCID: PMC9201403 DOI: 10.3389/fpls.2022.907244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Enhancing oil content is one of the major goals in Brassica napus breeding; however, genetic regulation of seed oil content in plants is complex and not fully elucidated. In this study, we report proteins that were differentially accumulated in immature seeds of 35 days after anthesis between two recombinant inbred lines with contrasting seed oil content, high oil content line (HOCL) and low oil content line (LOCL) using a multiplex isobaric tandem mass tags (TMT)-based quantitative proteomic approach. Over 4,600 proteins were quantified in seeds of the two lines, and 342 proteins showed differential accumulation between seeds of HOCL and LOCL. Gene Ontology enrichment analysis revealed that the differentially accumulated proteins were enriched in proteins involved in lipid biosynthesis and metabolism, photosynthesis, and nutrient reservoir activity. Western blot confirmed the increased abundance of a late embryogenesis abundant protein (BnLEA57) in HOCL seeds compared with LOCL seeds, and overexpression of either BnLEA57 gene or its homology BnLEA55 in transgenic Arabidopsis thaliana enhanced oil content in Arabidopsis seeds. Our work provides new insights into the molecular regulatory mechanism of seed oil content in B. napus.
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Affiliation(s)
- Zhongjing Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogang Lin
- Zhejiang Key Laboratory of Digital Dry Land Crops, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinjuan Tan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pengfei Hao
- Zhejiang Key Laboratory of Digital Dry Land Crops, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shuijin Hua
- Zhejiang Key Laboratory of Digital Dry Land Crops, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Huang R, Xiao D, Wang X, Zhan J, Wang A, He L. Genome-wide identification, evolutionary and expression analyses of LEA gene family in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2022; 22:155. [PMID: 35354373 PMCID: PMC8966313 DOI: 10.1186/s12870-022-03462-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins are a group of highly hydrophilic glycine-rich proteins, which accumulate in the late stage of seed maturation and are associated with many abiotic stresses. However, few peanut LEA genes had been reported, and the research on the number, location, structure, molecular phylogeny and expression of AhLEAs was very limited. RESULTS In this study, 126 LEA genes were identified in the peanut genome through genome-wide analysis and were further divided into eight groups. Sequence analysis showed that most of the AhLEAs (85.7%) had no or only one intron. LEA genes were randomly distributed on 20 chromosomes. Compared with tandem duplication, segmental duplication played a more critical role in AhLEAs amplication, and 93 segmental duplication AhLEAs and 5 pairs of tandem duplication genes were identified. Synteny analysis showed that some AhLEAs genes come from a common ancestor, and genome rearrangement and translocation occurred among these genomes. Almost all promoters of LEAs contain ABRE, MYB recognition sites, MYC recognition sites, and ERE cis-acting elements, suggesting that the LEA genes were involved in stress response. Gene transcription analyses revealed that most of the LEAs were expressed in the late stages of peanut embryonic development. LEA3 (AH16G06810.1, AH06G03960.1), and Dehydrin (AH07G18700.1, AH17G19710.1) were highly expressed in roots, stems, leaves and flowers. Moreover, 100 AhLEAs were involved in response to drought, low-temperature, or Al stresses. Some LEAs that were regulated by different abiotic stresses were also regulated by hormones including ABA, brassinolide, ethylene and salicylic acid. Interestingly, AhLEAs that were up-regulated by ethylene and salicylic acid showed obvious subfamily preferences. Furthermore, three AhLEA genes, AhLEA1, AhLEA3-1, and AhLEA3-3, which were up-regulated by drought, low-temperature, or Al stresses was proved to enhance cold and Al tolerance in yeast, and AhLEA3-1 enhanced the drought tolerance in yeast. CONCLUSIONS AhLEAs are involved in abiotic stress response, and segmental duplication plays an important role in the evolution and amplification of AhLEAs. The genome-wide identification, classification, evolutionary and transcription analyses of the AhLEA gene family provide a foundation for further exploring the LEA genes' function in response to abiotic stress in peanuts.
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Affiliation(s)
- RuoLan Huang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Dong Xiao
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, China.
- Key Laboratory of Crop Cultivation and Tillage, Guangxi Colleges and Universities, Nanning, 530004, China.
| | - Xin Wang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Jie Zhan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, Guangxi Colleges and Universities, Nanning, 530004, China
| | - AiQing Wang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, Guangxi Colleges and Universities, Nanning, 530004, China
| | - LongFei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, Guangxi Colleges and Universities, Nanning, 530004, China
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Singh CM, Kumar M, Pratap A, Tripathi A, Singh S, Mishra A, Kumar H, Nair RM, Singh NP. Genome-Wide Analysis of Late Embryogenesis Abundant Protein Gene Family in Vigna Species and Expression of VrLEA Encoding Genes in Vigna glabrescens Reveal Its Role in Heat Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:843107. [PMID: 35392521 PMCID: PMC8981728 DOI: 10.3389/fpls.2022.843107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/02/2022] [Indexed: 06/12/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are identified in many crops for their response and role in adaptation to various abiotic stresses, such as drought, salinity, and temperature. The LEA genes have been studied systematically in several crops but not in Vigna crops. In this study, we reported the first comprehensive analysis of the LEA gene family in three legume species, namely, mung bean (Vigna radiata), adzuki bean (Vigna angularis), and cowpea (Vigna unguiculata), and the cross-species expression of VrLEA genes in a wild tetraploid species, Vigna glabrescens. A total of 201 LEA genes from three Vigna crops were identified harboring the LEA conserved motif. Among these 55, 64, and 82 LEA genes were identified in mung bean, adzuki bean, and cowpea genomes, respectively. These LEA genes were grouped into eight different classes. Our analysis revealed that the cowpea genome comprised all eight classes of LEA genes, whereas the LEA-6 class was absent in the mung bean genome. Similarly, LEA-5 and LEA-6 were absent in the adzuki bean genome. The analysis of LEA genes provides an insight into their structural and functional diversity in the Vigna genome. The genes, such as VrLEA-2, VrLEA-40, VrLEA-47, and VrLEA-55, were significantly upregulated in the heat-tolerant genotype under stress conditions indicating the basis of heat tolerance. The successful amplification and expression of VrLEA genes in V. glabrescens indicated the utility of the developed markers in mung bean improvement. The results of this study increase our understanding of LEA genes and provide robust candidate genes for future functional investigations and a basis for improving heat stress tolerance in Vigna crops.
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Affiliation(s)
- Chandra Mohan Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Mukul Kumar
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Anupam Tripathi
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Smita Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Anuj Mishra
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | - Hitesh Kumar
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
| | | | - Narendra Pratap Singh
- Department of Genetics and Plant Breeding, Banda University of Agriculture and Technology, Banda, India
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20
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Baloch AA, Raza AM, Rana SSA, Ullah S, Khan S, Zaib-un-Nisa, Zahid H, Malghani GK, Kakar KU. BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. Sci Rep 2021; 11:24203. [PMID: 34921218 PMCID: PMC8683401 DOI: 10.1038/s41598-021-03712-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022] Open
Abstract
CNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.
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Affiliation(s)
- Akram Ali Baloch
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Agha Muhammad Raza
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Shahjahan Shabbir Ahmed Rana
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Saad Ullah
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Samiullah Khan
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Zaib-un-Nisa
- grid.411555.10000 0001 2233 7083Department of Botany, GC University Lahore, Lahore, Pakistan
| | - Humera Zahid
- grid.413062.2Department of Zoology, University of Balochistan, Quetta, Pakistan
| | - Gohram Khan Malghani
- grid.440526.10000 0004 0609 3164Department of Environmental Sciences, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Kaleem U. Kakar
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
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21
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Li C, Qi Y, Zhao C, Wang X, Zhang Q. Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum. Front Genet 2021; 12:770742. [PMID: 34868259 PMCID: PMC8637539 DOI: 10.3389/fgene.2021.770742] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Eutrema salsugineum can grow in natural harsh environments; however, the underlying mechanisms for salt tolerance of Eutrema need to be further understood. Herein, the transcriptome profiling of Eutrema leaves and roots exposed to 300 mM NaCl is investigated, and the result emphasized the role of genes involved in lignin biosynthesis, autophagy, peroxisome, and sugar metabolism upon salt stress. Furthermore, the expression of the lignin biosynthesis and autophagy-related genes, as well as 16 random selected genes, was validated by qRT-PCR. Notably, the transcript abundance of a large number of lignin biosynthesis genes such as CCoAOMT, C4H, CCR, CAD, POD, and C3′H in leaves was markedly elevated by salt shock. And the examined lignin content in leaves and roots demonstrated salt stress led to lignin accumulation, which indicated the enhanced lignin level could be an important mechanism for Eutrema responding to salt stress. Additionally, the differentially expressed genes (DEGs) assigned in the autophagy pathway including Vac8, Atg8, and Atg4, as well as DEGs enriched in the peroxisome pathway such as EsPEX7, EsCAT, and EsSOD2, were markedly induced in leaves and/or roots. In sugar metabolism pathways, the transcript levels of most DEGs associated with the synthesis of sucrose, trehalose, raffinose, and xylose were significantly enhanced. Furthermore, the expression of various stress-related transcription factor genes including WRKY, AP2/ERF-ERF, NAC, bZIP, MYB, C2H2, and HSF was strikingly improved. Collectively, the increased expression of biosynthesis genes of lignin and soluble sugars, as well as the genes in the autophagy and peroxisome pathways, suggested that Eutrema encountering salt shock possibly possess a higher capacity to adjust osmotically and facilitate water transport and scavenge reactive oxidative species and oxidative proteins to cope with the salt environment. Thus, this study provides a new insight for exploring the salt tolerance mechanism of halophytic Eutrema and discovering new gene targets for the genetic improvement of crops.
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Affiliation(s)
- Chuanshun Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yuting Qi
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Chuanzhi Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China.,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xingjun Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China.,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Quan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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22
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Divya K, Palakolanu SR, Kavi Kishor P, Rajesh AS, Vadez V, Sharma KK, Mathur PB. Functional characterization of late embryogenesis abundant genes and promoters in pearl millet (Pennisetum glaucum L.) for abiotic stress tolerance. PHYSIOLOGIA PLANTARUM 2021; 173:1616-1628. [PMID: 34455597 DOI: 10.1111/ppl.13544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Late embryogenesis abundant (LEA) genes display distinct functions in response to abiotic stresses in plants. In pearl millet (Pennisetum glaucum L.), a total of 21 PgLEA genes were identified and classified into six groups including LEA1, LEA2, LEA3, LEA5, LEA7, and dehydrins (DHN). Open reading frames (ORFs) of PgLEAs range from 291 bp (PgLEA1-1) to 945 bp (PgLEA2-11) and distributed randomly among the seven chromosomes. Phylogenetic analysis revealed that all PgLEA proteins are closely related to sorghum LEA proteins. The PgLEAs were found to be expressed differentially under high progressive vapor pressure deficit (VPD), PgLEA7 was significantly expressed under high VPD and was selected for functional validation. In silico analysis of the PgLEA promoter regions revealed abiotic stress-specific cis-acting elements such as ABRE, CCAAT, MYBS, and LTRE. Based on the type of motifs, PgLEAPC promoter (758 bp), its deletion 1 (PgLpd1, 349 bp) and deletion 2 (PgLpd2, 125 bp) were cloned into the plant expression vector pMDC164 having the promoter-less uidA gene. All the three plant expression vectors were introduced into tobacco through Agrobacterium tumefaciens-mediated transformation to obtain T1 and T2 generations of transgenic plants. Based on expression of the uidA gene, tissue-specific expression was observed in mature stems, roots and seedlings of PgLEAPC and PgLpd1 carrying transgenics only. While the transgenic PgLEAPC plants displayed significantly higher uidA expression in the stem and root tissues under salt, drought, heat, and cold stresses, very low or no expression was observed in PgLpd1 and PgLpd2 transgenics under the tested stress conditions. The results of this study indicate that the complete promoter of PgLEAPC plays a role in developing abiotic stress tolerance in plants.
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Affiliation(s)
- Kummari Divya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Polavarapu Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Aishwarya Shankhapal Rajesh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Kiran K Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Pooja Bhatnagar Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
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Abdul Aziz M, Sabeem M, Mullath SK, Brini F, Masmoudi K. Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses. Biomolecules 2021; 11:1662. [PMID: 34827660 PMCID: PMC8615533 DOI: 10.3390/biom11111662] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
In response to various environmental stresses, plants have evolved a wide range of defense mechanisms, resulting in the overexpression of a series of stress-responsive genes. Among them, there is certain set of genes that encode for intrinsically disordered proteins (IDPs) that repair and protect the plants from damage caused by environmental stresses. Group II LEA (late embryogenesis abundant) proteins compose the most abundant and characterized group of IDPs; they accumulate in the late stages of seed development and are expressed in response to dehydration, salinity, low temperature, or abscisic acid (ABA) treatment. The physiological and biochemical characterization of group II LEA proteins has been carried out in a number of investigations because of their vital roles in protecting the integrity of biomolecules by preventing the crystallization of cellular components prior to multiple stresses. This review describes the distribution, structural architecture, and genomic diversification of group II LEA proteins, with some recent investigations on their regulation and molecular expression under various abiotic stresses. Novel aspects of group II LEA proteins in Phoenix dactylifera and in orthodox seeds are also presented. Genome-wide association studies (GWAS) indicated a ubiquitous distribution and expression of group II LEA genes in different plant cells. In vitro experimental evidence from biochemical assays has suggested that group II LEA proteins perform heterogenous functions in response to extreme stresses. Various investigations have indicated the participation of group II LEA proteins in the plant stress tolerance mechanism, spotlighting the molecular aspects of group II LEA genes and their potential role in biotechnological strategies to increase plants' survival in adverse environments.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (M.A.A.); (M.S.)
| | - Miloofer Sabeem
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (M.A.A.); (M.S.)
| | - Sangeeta Kutty Mullath
- Department of Vegetable Science, College of Agriculture, Kerala Agricultural University, Thrissur 680656, India;
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, B.P 1177, Sfax 3018, Tunisia;
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (M.A.A.); (M.S.)
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24
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Wu C, Dai J, Chen Z, Tie W, Yan Y, Yang H, Zeng J, Hu W. Comprehensive analysis and expression profiles of cassava UDP-glycosyltransferases (UGT) family reveal their involvement in development and stress responses in cassava. Genomics 2021; 113:3415-3429. [PMID: 34371100 DOI: 10.1016/j.ygeno.2021.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 07/12/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022]
Abstract
UDP-glycosyltransferases (UGTs) are widely involved in plant growth and stress responses. However, UGT family are not well understood in cassava. Here, we identified 121 MeUGT genes and classified them into 14 subfamilies by phylogenetic analysis. All MeUGT proteins have typical feature of the UGTs family. Tandem duplications are the crucial driving force for the expansion of MeUGT family. Cis-Acting elements analysis uncovered those 14 kinds of cis-elements associated with biotic and abiotic stress responses. Transcriptomic and qRT-PCR analyses indicated that MeUGT genes participate in postharvest physiological deterioration of storage root and the responses of biotic and abiotic stresses. Of which, MeUGT-14/41 were significantly induced after Xam treatment. Silencing of MeUGT-14 or MeUGT-41 reduced cassava resistance to Xam, verifying the accuracy of transcriptomic data for function prediction. Together, this study characterized the MeUGTs family and revealed their potential functions, which build a solid foundation for MeUGTs associated genetic improvement of cassava.
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Affiliation(s)
- Chunlai Wu
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jing Dai
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhisheng Chen
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China,.
| | - Yan Yan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Hai Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Jian Zeng
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China.
| | - Wei Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China,.
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25
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Bano N, Patel P, Chakrabarty D, Bag SK. Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco ( Nicotiana tabacum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1747-1764. [PMID: 34539114 PMCID: PMC8405835 DOI: 10.1007/s12298-021-01042-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED The basic helix-loop-helix (bHLH) is the second-largest TF family in plants that play important roles in plant growth, development, and stress responses. In this study, a total of 100 bHLHs were identified using Hidden Markov Model profiles in the Nicotiana tabacum genome, clustered into 15 major groups (I-XV) based on their conserved domains and phylogenetic relationships. Group VIII genes were found to be the most abundant, with 27 NtbHLH members. The expansion of NtbHLHs in the genome was due to segmental and tandem duplication. The purifying selection was found to have an important role in the evolution of NtHLHs. Subsequent qRT-PCR validation of five selected genes from transcriptome data revealed that NtbHLH3.1, NtbHLH3.2, NtbHLH24, NtbHLH50, and NtbHLH59.2 have higher expressions at 12 and 24 h in comparison to 0 h (control) of chilling stress. The validated results demonstrated that NtbHLH3.2 and NtbHLH24 genes have 3 and fivefold higher expression at 12 h and 2 and threefold higher expression at 24 h than control plant, shows high sensitivity towards chilling stress. Moreover, the co-expression of positively correlated genes of NtbHLH3.2 and NtbHLH24 confirmed their functional significance in chilling stress response. Therefore, suggesting the importance of NtbHLH3.2 and NtbHLH24 genes in exerting control over the chilling stress responses in tobacco. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01042-x.
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Affiliation(s)
- Nasreen Bano
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Preeti Patel
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Debasis Chakrabarty
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sumit Kumar Bag
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Chen K, Huang Y, Liu C, Liang Y, Li M. Transcriptome Profile Analysis of Arabidopsis Reveals the Drought Stress-Induced Long Non-coding RNAs Associated With Photosynthesis, Chlorophyll Synthesis, Fatty Acid Synthesis and Degradation. FRONTIERS IN PLANT SCIENCE 2021; 12:643182. [PMID: 34113361 PMCID: PMC8185149 DOI: 10.3389/fpls.2021.643182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/12/2021] [Indexed: 06/02/2023]
Abstract
Long non-coding RNAs (lncRNAs) play an important role in the response of plants to drought stress. The previous studies have reported that overexpression of LEA3 and VOC could enhance drought tolerance and improve the oil content in Brassica napus and Arabidopsis thaliana, and most of the efforts have been invested in the gene function analysis, there is little understanding of how genes that involved in these important pathways are regulated. In the present study, the transcriptomic results of LEA3 and VOC over-expressed (OE) lines were compared with the RNAi lines, mutant lines and control lines under long-term and short-term drought treatment, a series of differentially expressed lncRNAs were identified, and their regulation patterns in mRNA were also investigated in above mentioned materials. The regulation of the target genes of differentially expressed lncRNAs on plant biological functions was studied. It was revealed that the mutant lines had less drought-response related lncRNAs than that of the OE lines. Functional analysis demonstrated that multiple genes were involved in the carbon-fixing and chlorophyll metabolism, such as CDR1, CHLM, and CH1, were regulated by the upregulated lncRNA in OE lines. In LEA-OE, AT4G13180 that promotes the fatty acid synthesis was regulated by five lncRNAs that were upregulated under both long-term and short-term drought treatments. The key genes, including of SHM1, GOX2, and GS2, in the methylglyoxal synthesis pathway were all regulated by a number of down-regulated lncRNAs in OE lines, thereby reducing the content of such harmful compounds produced under stress in plants. This study identified a series of lncRNAs related to the pathways that affect photosynthesis, chlorophyll synthesis, fatty acid synthesis, degradation, and other important effects on drought resistance and oil content. The present study provided a series of lncRNAs for further improvement of crop varieties, especially drought resistant and oil content traits.
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Affiliation(s)
- Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Guangxi Normal University, Guilin, China
| | - Yang Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Guangxi Normal University, Guilin, China
- School of Mechanical and Electrical Engineering, Guilin University of Electronic Technology, Guilin, China
| | - Chunni Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Guangxi Normal University, Guilin, China
| | - Yu Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Guangxi Normal University, Guilin, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Chen J, Li N, Wang X, Meng X, Cui X, Chen Z, Ren H, Ma J, Liu H. Late embryogenesis abundant (LEA) gene family in Salvia miltiorrhiza: identification, expression analysis, and response to drought stress. PLANT SIGNALING & BEHAVIOR 2021; 16:1891769. [PMID: 33818288 PMCID: PMC8078505 DOI: 10.1080/15592324.2021.1891769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 05/19/2023]
Abstract
Late embryogenesis abundant (LEA) proteins play important roles in plant defense response to drought stress. However, genome-wide identification of the LEA gene family was not revealed in Salvia miltiorrhiza. In this study, 61 SmLEA genes were identified from S. miltiorrhiza and divided into 7 subfamilies according to their conserved domains and phylogenetic relationships. SmLEA genes contained the LEA conserved motifs and few introns. SmLEA genes of the same subfamilies had similar gene structures and predicted subcellular locations. Our results indicated that the promoters of SmLEA genes contained various cis-acting elements associated with abiotic stress response. In addition, RNA-seq and real-time PCR results suggested that SmLEA genes are specifically expressed in different tissue, and most SmLEA genes can be induced by drought stress. These results provide a valuable foundation for future functional investigations of SmLEA genes and drought stress-resistant breeding of S. miltiorrhiza.
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Affiliation(s)
- Juan Chen
- Shaanxi Academy of Traditional Chinese Medicine, Xi’an Shaanxi, China
| | - Na Li
- College of Agriculture, Henan University of Science and Technology, Luoyang Henan, China
| | - Xiaoyu Wang
- College of Life Science, Northwest A&F University, Yangling Shaanxi, China
| | - Xue Meng
- Shaanxi Academy of Traditional Chinese Medicine, Xi’an Shaanxi, China
| | - Xiaomin Cui
- Shaanxi Academy of Traditional Chinese Medicine, Xi’an Shaanxi, China
| | - Zhiyong Chen
- Shaanxi Academy of Traditional Chinese Medicine, Xi’an Shaanxi, China
| | - Hui Ren
- Shaanxi Academy of Traditional Chinese Medicine, Xi’an Shaanxi, China
| | - Jing Ma
- Inspection and Testing Center for Quality and Safety of Agricultural Products, Ningxia Institute of Agricultural Survey and Design, Yinchuan Ningxia, China
| | - Hao Liu
- College of Life Science, Northwest A&F University, Yangling Shaanxi, China
- College of Agriculture, Ludong University, Yantai Shandong, China
- CONTACT Hao Liu College of Life Science, Northwest A&F University, Yangling Shaanxi 712100, China; College of Agriculture, Ludong University, Yantai Shandong264001, China
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Li Z, Chi H, Liu C, Zhang T, Han L, Li L, Pei X, Long Y. Genome-wide identification and functional characterization of LEA genes during seed development process in linseed flax (Linum usitatissimum L.). BMC PLANT BIOLOGY 2021; 21:193. [PMID: 33882851 PMCID: PMC8059249 DOI: 10.1186/s12870-021-02972-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/06/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND LEA proteins are widely distributed in the plant and animal kingdoms, as well as in micro-organisms. LEA genes make up a large family and function in plant protection against a variety of adverse conditions. RESULTS Bioinformatics approaches were adopted to identify LEA genes in the flax genome. In total, we found 50 LEA genes in the genome. We also conducted analyses of the physicochemical parameters and subcellular location of the genes and generated a phylogenetic tree. LuLEA genes were unevenly mapped among 15 flax chromosomes and 90% of the genes had less than two introns. Expression profiles of LuLEA showed that most LuLEA genes were expressed at a late stage of seed development. Functionally, the LuLEA1 gene reduced seed size and fatty acid contents in LuLEA1-overexpressed transgenic Arabidopsis lines. CONCLUSION Our study adds valuable knowledge about LEA genes in flax which can be used to improve related genes of seed development.
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Affiliation(s)
- Zhen Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hui Chi
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianbao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yan Long
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Ding M, Wang L, Zhan W, Sun G, Jia X, Chen S, Ding W, Yang J. Genome-wide identification and expression analysis of late embryogenesis abundant protein-encoding genes in rye (Secale cereale L.). PLoS One 2021; 16:e0249757. [PMID: 33831102 PMCID: PMC8031920 DOI: 10.1371/journal.pone.0249757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/24/2021] [Indexed: 11/18/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are members of a large and highly diverse family that play critical roles in protecting cells from abiotic stresses and maintaining plant growth and development. However, the identification and biological function of genes of Secale cereale LEA (ScLEA) have been rarely reported. In this study, we identified 112 ScLEA genes, which can be divided into eight groups and are evenly distributed on all rye chromosomes. Structure analysis revealed that members of the same group tend to be highly conserved. We identified 12 pairs of tandem duplication genes and 19 pairs of segmental duplication genes, which may be an expansion way of LEA gene family. Expression profiling analysis revealed obvious temporal and spatial specificity of ScLEA gene expression, with the highest expression levels observed in grains. According to the qRT-PCR analysis, selected ScLEA genes were regulated by various abiotic stresses, especially PEG treatment, decreased temperature, and blue light. Taken together, our results provide a reference for further functional analysis and potential utilization of the ScLEA genes in improving stress tolerance of crops.
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Affiliation(s)
- Mengyue Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Lijian Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Department of Criminal Science and Technology, Henan Police College, Zhengzhou, China
- * E-mail: (JY); (LW)
| | - Weimin Zhan
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Guanghua Sun
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaolin Jia
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shizhan Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wusi Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianping Yang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- * E-mail: (JY); (LW)
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He C, Liu X, Teixeira da Silva JA, Wang H, Peng T, Zhang M, Si C, Yu Z, Tan J, Zhang J, Luo J, Duan J. Characterization of LEA genes in Dendrobium officinale and one Gene in induction of callus. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153356. [PMID: 33423816 DOI: 10.1016/j.jplph.2020.153356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are widely involved in plant stress responsive, while their involvement in callus formation is largest unknown. In this study, we identified and conducted expression analysis of the LEA genes from Phalaenopsis equestris and Dendrobium officinale, and characterized a LEA gene from D. officinale. A total 57 and 59 LEA genes were identified in P. equestris and D. officinale, respectively. A phylogenetic analysis showed that AtM, LEA_5 and Dehydrin groups were absent in both orchids. LEA_1 group genes were strongly expressed in seeds, significantly down-regulated in flowers, and absent in vegetative organs (leaves, stems and roots) in both orchids. Moreover, LEA_1 and LEA_4 group genes from D. officinale were abundant in the protocorm-like body stage and were dramatically up-regulated in response to abscisic acid and salinity stress. A LEA_1 gene (DoLEA43) was selected for further functional analysis. DoLEA43 protein was localized in the cytoplasm and nucleus, and its promoter contained a WUN-motif that was modulated by wounding. Overexpression of DoLEA43 in Arabidopsis enhanced callus induction, causing changes to callus formation-related genes such as WIND1. Our results indicate the involvement of LEA genes in the induction of callus, which provide insights into plant regeneration.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jaime A Teixeira da Silva
- Independent researcher, P. O. Box 7, Miki-cho post office, Ikenobe 3011-2, Kagawa-ken, 761-0799, Japan
| | - Haobin Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Peng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jianwen Tan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianxia Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianping Luo
- School of Food Engineering and Biotechnology, Hefei University of Technology, Hefei, 230009, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Ma L, Zhu T, Wang H, Zhou H, Shao L, Ding Q, Zhang D, Ma L. Genome-wide identification, phylogenetic analysis and expression profiling of the late embryogenesis-abundant (LEA) gene family in Brachypodium distachyon. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:386-401. [PMID: 33278911 DOI: 10.1071/fp20143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/29/2020] [Indexed: 05/14/2023]
Abstract
Late embryogenesis-abundant (LEA) proteins are the products of an important gene family in plants that play vital roles in regulating growth and development as well as a variety of stress responses. In our study, 67 members of LEA (BdLEA) were identified in the genome of Brachypodium distachyon L. Analyses of gene structure, evolutionary relationships and protein motifs showed that the BdLEAs belonged to six subfamilies. Analyses of chromosomal locations and duplication events revealed that the 67 BdLEAs were distributed over all five chromosomes and 26 BdLEAs were identified as products of duplication events. Gene Ontology (GO) annotation results suggested that nearly 60% of BdLEAs could be involved in stress response. Furthermore, transcriptomic analysis showed that the BdLEAs were differentially expressed in nine organs and responded to low stringency of exogenous phytohormones. Subsequently, 18 BdLEAs from six subfamilies were randomly selected for quantitative real-time PCR (qRT-PCR) analysis, which showed that they were mainly expressed in the spikelets and they may preferentially respond to salt, drought and abscisic acid (ABA) stress. This study is the first to report the characteristics of the BdLEA family, providing valuable information for understanding the evolution of LEAs in the model plant B. distachyon and supporting future functional research on these proteins.
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Affiliation(s)
- LiTing Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ting Zhu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - HaiRong Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - LeiLei Shao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; and Corresponding author. ; ;
| | - DaZhong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China; and Corresponding author. ; ;
| | - LingJian Ma
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China; and Corresponding author. ; ;
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Wei J, Zhao H, Liu X, Liu S, Li L, Ma H. Physiological and Biochemical Characteristics of Two Soybean Cultivars with Different Seed Vigor During Seed Physiological Maturity. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666200127142051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background:
The soybean seed’s physiological maturity (R7) period is an extraordinary period
for the formation of seed vigor. However, how proteins and their related metabolic pathways in
seed and leaf change during seed physiological maturity is still not fully understood.
Methods:
In the present study, using a pair of pre-harvest seed deterioration-sensitive and -resistant
soybean cultivars Ningzhen No. 1 and Xiangdou No. 3, the changes were investigated through analyzing
leaf, cotyledon and embryo at the levels of protein, ultrastructure, and physiology and biochemistry.
Results:
Soybean cultivars with stronger photosynthetic capacity in leaf, higher nutrients accumulation
and protein biosynthesis in cotyledon, as well as stronger resistant-pathogen ability and cell stability in
embryo during seed physiological maturity, would produce higher vitality seeds.
Conclusion:
Such a study allows us to further understand the changes at protein, ultrastructure, and
physiology and biochemistry levels in developing seeds during the physiological maturity and provide
a theoretical basis for cultivating soybean cultivars with higher seed vigor.
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Affiliation(s)
- Jiaping Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Haihong Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaolin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Sushuang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Linzhi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Das Laha S, Dutta S, Schäffner AR, Das M. Gene duplication and stress genomics in Brassicas: Current understanding and future prospects. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153293. [PMID: 33181457 DOI: 10.1016/j.jplph.2020.153293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.
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Affiliation(s)
- Shayani Das Laha
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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Ning L, Wang H, Li D, Li Y, Chen K, Chao H, Li H, He J, Li M. Genome-wide identification of the restorer-of-fertility-like (RFL) gene family in Brassica napus and expression analysis in Shaan2A cytoplasmic male sterility. BMC Genomics 2020; 21:765. [PMID: 33148177 PMCID: PMC7641866 DOI: 10.1186/s12864-020-07163-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
Background Cytoplasmic male sterility (CMS) is very important in hybrid breeding. The restorer-of-fertility (Rf) nuclear genes rescue the sterile phenotype. Most of the Rf genes encode pentatricopeptide repeat (PPR) proteins. Results We investigated the restorer-of-fertility-like (RFL) gene family in Brassica napus. A total of 53 BnRFL genes were identified. While most of the BnRFL genes were distributed on 10 of the 19 chromosomes, gene clusters were identified on chromosomes A9 and C8. The number of PPR motifs in the BnRFL proteins varied from 2 to 19, and the majority of BnRFL proteins harbored more than 10 PPR motifs. An interaction network analysis was performed to predict the interacting partners of RFL proteins. Tissue-specific expression and RNA-seq analyses between the restorer line KC01 and the sterile line Shaan2A indicated that BnRFL1, BnRFL5, BnRFL6, BnRFL8, BnRFL11, BnRFL13 and BnRFL42 located in gene clusters on chromosomes A9 and C8 were highly expressed in KC01. Conclusions In the present study, identification and gene expression analysis of RFL gene family in the CMS system were conducted, and seven BnRFL genes were identified as candidates for the restorer genes in Shaan2A CMS. Taken together, this method might provide new insight into the study of Rf genes in other CMS systems. Supplementary Information Supplementary information accompanies this paper at 10.1186/s12864-020-07163-z.
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Affiliation(s)
- Luyun Ning
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China. .,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
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Singh KK, Graether SP. Conserved sequence motifs in the abiotic stress response protein late embryogenesis abundant 3. PLoS One 2020; 15:e0237177. [PMID: 32760115 PMCID: PMC7410210 DOI: 10.1371/journal.pone.0237177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/21/2020] [Indexed: 01/02/2023] Open
Abstract
LEA3 proteins, a family of abiotic stress proteins, are defined by the presence of a tryptophan-containing motif, which we name the W-motif. We use Pfam LEA3 sequences to search the Phytozome database to create a W-motif definition and a LEA3 sequence dataset. A comprehensive analysis of these sequences revealed four N-terminal motifs, as well as two previously undiscovered C-terminal motifs that contain conserved acidic and hydrophobic residues. The general architecture of the LEA3 sequences consisted of an N-terminal motif with a potential mitochondrial transport signal and the twin-arginine motif cut-site, followed by a W-motif and often a C-terminal motif. Analysis of species distribution of the motifs showed that one architecture was found exclusively in Commelinids, while two were distributed fairly evenly over all species. The physiochemical properties of the different architectures showed clustering in a relatively narrow range compared to the previously studied dehydrins. The evolutionary analysis revealed that the different sequences grouped into clades based on architecture, and that there appear to be at least two distinct groups of LEA3 proteins based on their architectures and physiochemical properties. The presence of LEA3 proteins in non-vascular plants but their absence in algae suggests that LEA3 may have arisen in the evolution of land plants.
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Affiliation(s)
- Karamjeet K. Singh
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steffen P. Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- Graduate Program in Bioinformatics, University of Guelph, Guelph, Ontario, Canada
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Genes, proteins and other networks regulating somatic embryogenesis in plants. J Genet Eng Biotechnol 2020; 18:31. [PMID: 32661633 PMCID: PMC7359197 DOI: 10.1186/s43141-020-00047-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/01/2020] [Indexed: 11/21/2022]
Abstract
Background Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUS-LIKE 15 (AGL15) are very important and are part of molecular network. Main text (observation) This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation. Conclusions The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.
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Han S, Khan MHU, Yang Y, Zhu K, Li H, Zhu M, Amoo O, Khan SU, Fan C, Zhou Y. Identification and comprehensive analysis of the CLV3/ESR-related (CLE) gene family in Brassica napus L. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:709-721. [PMID: 32223006 DOI: 10.1111/plb.13117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 03/05/2020] [Indexed: 05/14/2023]
Abstract
The CLE (CLAVATA3/ESR) gene family, encoding a group of small secretory peptides, plays important roles in cell-to-cell communication, thereby controlling a broad spectrum of development processes. The CLE family has been systematically characterized in some plants, but not in Brassica napus. In the present study, 116 BnCLE genes were identified in the B. napus genome, including seven unannotated, six incorrectly predicted and five multi-CLE domain-encoding genes. These BnCLE members were separated into seven distinct groups based on phylogenetic analysis, which might facilitate the functional characterization of the peptides. Further characterization of CLE pre-propeptides revealed 31 unique CLE peptides from 45 BnCLE genes, which may give rise to distinct roles of BnCLE and expansion of the gene family. The biological activity of these unique CLE dodecamer peptides was tested further through in vitro peptide assays. Variations in several important residues were identified as key contributors to the functional differentiation of BnCLE and expansion of the gene family in B. napus. Expression profile analysis helped to characterize possible functional redundancy and sub-functionalization among the BnCLE members. This study presents a comprehensive overview of the CLE gene family in B. napus and provides a foundation for future evolutionary and functional studies.
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Affiliation(s)
- S Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - M H U Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Y Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - K Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - H Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - M Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - O Amoo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - S U Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - C Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Y Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Wang Z, Ma LY, Li X, Zhao FY, Sarwar R, Cao J, Li YL, Ding LN, Zhu KM, Yang YH, Tan XL. Genome-wide identification of the NPR1-like gene family in Brassica napus and functional characterization of BnaNPR1 in resistance to Sclerotinia sclerotiorum. PLANT CELL REPORTS 2020; 39:709-722. [PMID: 32140767 DOI: 10.1007/s00299-020-02525-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
The BnaNPR1-like gene family was identified in B. napus, and it was revealed that repression of BnaNPR1 significantly reduces resistance toS. sclerotiorum, intensifies ROS accumulation, and changes the expression of genes associated with SA and JA/ET signaling in response to this pathogen. The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) and related NPR1-like genes play an important role in regulating plant defense. Oilseed rape (Brassica napus L.) is an important oilseed crop; however, little is known about the B. napus (Bna) NPR1-like gene family. Here, a total of 19 BnaNPR1-like genes were identified in the B. napus genome, and then named according to their respective best match in Arabidopsis thaliana (At), which led to the determination of B. napus homologs of every AtNPR1-like gene. Analysis of important protein domains and functional motifs indicated the conservation and variation among these homologs. Phylogenetic analysis of these BnaNPR1-like proteins and their Arabidopsis homologs revealed six distinct sub-clades, consequently indicating that their name classification totally conformed to their phylogenetic relationships. Further, B. napus transcriptomic data showed that the expression of three BnaNPR1s was significantly down-regulated in response to infection with Sclerotinia sclerotiorum, the most important pathogen of this crop, whereas BnaNPR2/3/4/5/6s did not show the expression differences in general. Further, we generated B. napus BnaNPR1-RNAi lines to interpret the effect of the down-regulated expression of BnaNPR1s on resistance to S. sclerotiorum. The results showed that BnaNPR1-RNAi significantly decreased this resistance. Further experiments revealed that BnaNPR1-RNAi intensified ROS production and changed defense responses in the interaction of plants with this pathogen. These results indicated that S. sclerotiorum might use BnaNPR1 to regulate specific physiological processes of B. napus, such as ROS production and SA defense response, for the infection.
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Affiliation(s)
- Zheng Wang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Lu-Yue Ma
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Xiao Li
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Feng-Yun Zhao
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Rehman Sarwar
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Jun Cao
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Yu-Long Li
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Li-Na Ding
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Ke-Ming Zhu
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Yan-Hua Yang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China.
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Xu M, Tong Q, Wang Y, Wang Z, Xu G, Elias GK, Li S, Liang Z. Transcriptomic Analysis of the Grapevine LEA Gene Family in Response to Osmotic and Cold Stress Reveals a Key Role for VamDHN3. PLANT & CELL PHYSIOLOGY 2020; 61:775-786. [PMID: 31967299 DOI: 10.1093/pcp/pcaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 01/09/2020] [Indexed: 05/14/2023]
Abstract
Late embryogenesis abundant (LEA) proteins comprise a large family that plays important roles in the regulation of abiotic stress, however, no in-depth analysis of LEA genes has been performed in grapevine to date. In this study, we analyzed a total of 52 putative LEA genes in grapevine at the genomic and transcriptomic level, compiled expression profiles of four selected (V. amurensis) VamLEA genes under cold and osmotic stresses, and studied the potential function of the V. amurensis DEHYDRIN3 (VamDHN3) gene in grapevine callus. The 52 LEA proteins were classified into seven phylogenetic groups. RNA-seq and quantitative real-time PCR results demonstrated that a total of 16 and 23 VamLEA genes were upregulated under cold and osmotic stresses, respectively. In addition, overexpression of VamDHN3 enhanced the stability of the cell membrane in grapevine callus, suggesting that VamDHN3 is involved in osmotic regulation. These results provide fundamental knowledge for the further analysis of the biological roles of grapevine LEA genes in adaption to abiotic stress.
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Affiliation(s)
- Meilong Xu
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of the Seedling Bioengineering, Yinchuan 750004, China
| | - Qian Tong
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zemin Wang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guangzhao Xu
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gathunga Kirabi Elias
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Lohani N, Jain D, Singh MB, Bhalla PL. Engineering Multiple Abiotic Stress Tolerance in Canola, Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:3. [PMID: 32161602 PMCID: PMC7052498 DOI: 10.3389/fpls.2020.00003] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Impacts of climate change like global warming, drought, flooding, and other extreme events are posing severe challenges to global crop production. Contribution of Brassica napus towards the oilseed industry makes it an essential component of international trade and agroeconomics. Consequences from increasing occurrences of multiple abiotic stresses on this crop are leading to agroeconomic losses making it vital to endow B. napus crop with an ability to survive and maintain yield when faced with simultaneous exposure to multiple abiotic stresses. For an improved understanding of the stress sensing machinery, there is a need for analyzing regulatory pathways of multiple stress-responsive genes and other regulatory elements such as non-coding RNAs. However, our understanding of these pathways and their interactions in B. napus is far from complete. This review outlines the current knowledge of stress-responsive genes and their role in imparting multiple stress tolerance in B. napus. Analysis of network cross-talk through omics data mining is now making it possible to unravel the underlying complexity required for stress sensing and signaling in plants. Novel biotechnological approaches such as transgene-free genome editing and utilization of nanoparticles as gene delivery tools are also discussed. These can contribute to providing solutions for developing climate change resilient B. napus varieties with reduced regulatory limitations. The potential ability of synthetic biology to engineer and modify networks through fine-tuning of stress regulatory elements for plant responses to stress adaption is also highlighted.
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Affiliation(s)
| | | | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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41
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Genome-wide identification and characterization of late embryogenesis abundant protein-encoding gene family in wheat: Evolution and expression profiles during development and stress. Gene 2020; 736:144422. [PMID: 32007584 DOI: 10.1016/j.gene.2020.144422] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Late embryogenesis abundant (LEA) proteins are involved in plant stress responses and osmotic regulation, and they are accumulated in the late embryonic stage. There have been no previous genome-wide analyses of the LEA gene family members in wheat and its close relatives. In this study, 281, 53, 151, 89, 99, and 99 LEA genes were identified in wheat (Triticum aestivum), Triticum urartu, Triticum dicoccoides, Aegilops tauschii, barley, and Brachypodium distachyon, respectively. The wheat LEA gene family (TaLEA genes) was divided into eight subfamilies according to the conserved domains. All TaLEA genes contain very few introns (<3) and they are unevenly distributed on the 21 chromosomes. We identified 39 pairs of tandem duplication genes and 9 pairs of segmental duplication genes in the wheat LEA gene family. This proved that the tandem duplication and segmental duplication played an important role in the expansion of the TaLEA gene family. According to published transcriptome data and qRT-PCR analysis, the TaLEA genes exhibit different tissue expression patterns and they are regulated by various abiotic stresses, especially salt and cold stress. This study provides a comprehensive understanding of the wheat LEA gene family.
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Farooq N, Nawaz MA, Mukhtar Z, Ali I, Hundleby P, Ahmad N. Investigating the In Vitro Regeneration Potential of Commercial Cultivars of Brassica. PLANTS (BASEL, SWITZERLAND) 2019; 8:E558. [PMID: 31795525 PMCID: PMC6963692 DOI: 10.3390/plants8120558] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 01/11/2023]
Abstract
In vitro regeneration is a pre-requisite for developing transgenic plants through tissue culture-based genetic engineering approaches. Huge variations among different genotypes of the genus Brassica necessitate the identification of a set of regeneration conditions for a genotype, which can be reliably used in transformation experiments. In this study, we evaluated the morphogenesis potential of four commercial cultivars (Faisal canola, Punjab canola, Aari canola, Nifa Gold) and one model, Westar, from four different explants namely cotyledons, hypocotyls, petioles and roots on three different Brassica regeneration protocols, BRP-I, -II and -III. The regeneration efficiency was observed in the range of 6-73%, 4-79.3%, 0-50.6%, and 0-42.6% from cotyledons, petioles, hypocotyls and roots, respectively, whereas, the regeneration response in terms of average shoots per explant was found to be 0.76-10.9, 0.2-3.2, 0-3.4 and 0-2.7 from these explants. Of the commercial varieties tested, almost all varieties showed poorer regeneration than Westar except Aari canola. In comparison to Westar, its regeneration frequency from cotyledons was up to 7.5-fold higher on BRP-I, while it produced up to 21.9-fold more shoots per explant. Our data show that the explant has strong influence on the regeneration response, ranging from 24% to 92%. While the growth of commercial cultivars was least affected by the regeneration conditions provided, the effect on Westar was twice that of the commercial cultivars. After determining the optimal explant type and regeneration conditions, we also determined the minimum kanamycin concentration levels required to selectively inhibit the growth of untransformed cells for these cultivars. Regenerated shoots of Aari canola could be successfully grown to maturity within 16-18 weeks, with no altered phenotype noted and normal seed yields obtained. Therefore, the commercial variety, Aari canola, could be a good candidate for future genetic transformation studies.
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Affiliation(s)
- Nisma Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Muhammad Asif Nawaz
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Iftikhar Ali
- Nuclear Institute for Agriculture and Biology, Faisalabad 38000, Pakistan
| | - Penny Hundleby
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Niaz Ahmad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
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Liang Y, Kang K, Gan L, Ning S, Xiong J, Song S, Xi L, Lai S, Yin Y, Gu J, Xiang J, Li S, Wang B, Li M. Drought-responsive genes, late embryogenesis abundant group3 (LEA3) and vicinal oxygen chelate, function in lipid accumulation in Brassica napus and Arabidopsis mainly via enhancing photosynthetic efficiency and reducing ROS. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2123-2142. [PMID: 30972883 PMCID: PMC6790364 DOI: 10.1111/pbi.13127] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/18/2019] [Accepted: 04/04/2019] [Indexed: 05/10/2023]
Abstract
Drought is an abiotic stress that affects plant growth, and lipids are the main economic factor in the agricultural production of oil crops. However, the molecular mechanisms of drought response function in lipid metabolism remain little known. In this study, overexpression (OE) of different copies of the drought response genes LEA3 and VOC enhanced both drought tolerance and oil content in Brassica napus and Arabidopsis. Meanwhile, seed size, membrane stability and seed weight were also improved in OE lines. In contrast, oil content and drought tolerance were decreased in the AtLEA3 mutant (atlea3) and AtVOC-RNAi of Arabidopsis and in both BnLEA-RNAi and BnVOC-RNAi B. napus RNAi lines. Hybrids between two lines with increased or reduced expression (LEA3-OE with VOC-OE, atlea3 with AtVOC-RNAi) showed corresponding stronger trends in drought tolerance and lipid metabolism. Comparative transcriptomic analysis revealed the mechanisms of drought response gene function in lipid accumulation and drought tolerance. Gene networks involved in fatty acid (FA) synthesis and FA degradation were up- and down-regulated in OE lines, respectively. Key genes in the photosynthetic system and reactive oxygen species (ROS) metabolism were up-regulated in OE lines and down-regulated in atlea3 and AtVOC-RNAi lines, including LACS9, LIPASE1, PSAN, LOX2 and SOD1. Further analysis of photosynthetic and ROS enzymatic activities confirmed that the drought response genes LEA3 and VOC altered lipid accumulation mainly via enhancing photosynthetic efficiency and reducing ROS. The present study provides a novel way to improve lipid accumulation in plants, especially in oil production crops.
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Affiliation(s)
- Yu Liang
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Kai Kang
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Lu Gan
- Center for Plant Science Innovation and Department of BiochemistryUniversity of Nebraska LincolnLincolnNEUSA
| | - Shaobo Ning
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Jinye Xiong
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Shuyao Song
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Lingzhi Xi
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Senying Lai
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Yongtai Yin
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Jianwei Gu
- Hubei Research Institute of New Socialist Countryside DevelopmentHubei Engineering UniversityXiaoganChina
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive UtilizationHubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie MountainsHuanggang Normal UniversityHuanggangChina
| | - Shisheng Li
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive UtilizationHubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie MountainsHuanggang Normal UniversityHuanggangChina
| | - Baoshan Wang
- College of Life ScienceShandong Normal UniversityJinanChina
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive UtilizationHubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie MountainsHuanggang Normal UniversityHuanggangChina
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Zheng J, Su H, Lin R, Zhang H, Xia K, Jian S, Zhang M. Isolation and characterization of an atypical LEA gene (IpLEA) from Ipomoea pes-caprae conferring salt/drought and oxidative stress tolerance. Sci Rep 2019; 9:14838. [PMID: 31619699 PMCID: PMC6796003 DOI: 10.1038/s41598-019-50813-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 09/18/2019] [Indexed: 12/23/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins belong to a large family that exists widely in plants and is mainly involved in desiccation processes during plant development or in the response to abiotic stresses. Here, we reported on an atypical LEA gene (IpLEA) related to salt tolerance from Ipomoea pes-caprae L. (Convolvulaceae). Sequence analysis revealed that IpLEA belongs to the LEA_2 (PF03168) group. IpLEA was shown to have a cytoplasmic localization pattern. Quantitative reverse transcription PCR analysis showed that IpLEA was widely expressed in different organs of the I. pes-caprae plants, and the expression levels increased following salt, osmotic, oxidative, freezing, and abscisic acid treatments. Analysis of the 1,495 bp promoter of IpLEA identified distinct cis-acting regulatory elements involved in abiotic stress. Induction of IpLEA improved Escherichia coli growth performance compared with the control under abiotic stresses. To further assess the function of IpLEA in plants, transgenic Arabidopsis plants overexpressing IpLEA were generated. The IpLEA-overexpressing Arabidopsis seedlings and adult plants showed higher tolerance to salt and drought stress than the wild-type. The transgenic plants also showed higher oxidative stress tolerance than the wild-type Arabidopsis. Furthermore, the expression patterns of a series of stress-responsive genes were affected. The results indicate that IpLEA is involved in the plant response to salt and drought, probably by mediating water homeostasis or by acting as a reactive oxygen species scavenger, thereby influencing physiological processes under various abiotic stresses in microorganisms and plants.
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Affiliation(s)
- Jiexuan Zheng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100039, P.R. China
| | - Huaxiang Su
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100039, P.R. China
| | - Ruoyi Lin
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China.,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100039, P.R. China
| | - Hui Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100039, P.R. China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Shuguang Jian
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Mei Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China.
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Jin X, Cao D, Wang Z, Ma L, Tian K, Liu Y, Gong Z, Zhu X, Jiang C, Li Y. Genome-wide identification and expression analyses of the LEA protein gene family in tea plant reveal their involvement in seed development and abiotic stress responses. Sci Rep 2019; 9:14123. [PMID: 31575979 PMCID: PMC6773783 DOI: 10.1038/s41598-019-50645-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/16/2019] [Indexed: 11/18/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are widely known to be present in higher plants and are believed to play important functional roles in embryonic development and abiotic stress responses. However, there is a current lack of systematic analyses on the LEA protein gene family in tea plant. In this study, a total of 48 LEA genes were identified using Hidden Markov Model profiles in C. sinensis, and were classified into seven distinct groups based on their conserved domains and phylogenetic relationships. Genes in the CsLEA_2 group were found to be the most abundant. Gene expression analyses revealed that all the identified CsLEA genes were expressed in at least one tissue, and most had higher expression levels in the root or seed relative to other tested tissues. Nearly all the CsLEA genes were found to be involved in seed development, and thirty-nine might play an important role in tea seed maturation concurrent with dehydration. However, only sixteen CsLEA genes were involved in seed desiccation, and furthermore, most were suppressed. Additionally, forty-six CsLEA genes could be induced by at least one of the tested stress treatments, and they were especially sensitive to high temperature stress. Furthermore, it was found that eleven CsLEA genes were involved in tea plant in response to all tested abiotic stresses. Overall, this study provides new insights into the formation of CsLEA gene family members and improves our understanding on the potential roles of these genes in normal development processes and abiotic stress responses in tea plant, particularly during seed development and desiccation. These results are beneficial for future functional studies of CsLEA genes that will help preserve the recalcitrant tea seeds for a long time and genetically improve tea plant.
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Affiliation(s)
- Xiaofang Jin
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Dan Cao
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zhongjie Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Linlong Ma
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Kunhong Tian
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Liu
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Ziming Gong
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Xiangxiang Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Changjun Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
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Genome-wide identification of and functional insights into the late embryogenesis abundant (LEA) gene family in bread wheat (Triticum aestivum). Sci Rep 2019; 9:13375. [PMID: 31527624 PMCID: PMC6746774 DOI: 10.1038/s41598-019-49759-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are involved in the responses and adaptation of plants to various abiotic stresses, including dehydration, salinity, high temperature, and cold. Here, we report the first comprehensive survey of the LEA gene family in “Chinese Spring” wheat (Triticum aestivum). A total of 179 TaLEA genes were identified in T. aestivum and classified into eight groups. All TaLEA genes harbored the LEA conserved motif and had few introns. TaLEA genes belonging to the same group exhibited similar gene structures and chromosomal locations. Our results revealed that most TaLEA genes contained abscisic acid (ABA)-responsive elements (ABREs) and various cis-acting elements associated with the stress response in the promoter region and were induced under ABA and abiotic stress treatments. In addition, 8 genes representing each group were introduced into E. coli and yeast to investigate the protective function of TaLEAs under heat and salt stress. TaLEAs enhanced the tolerance of E. coli and yeast to salt and heat, indicating that these proteins have protective functions in host cells under stress conditions. These results increase our understanding of LEA genes and provide robust candidate genes for future functional investigations aimed at improving the stress tolerance of wheat.
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47
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Liang Z, Li M, Liu Z, Wang J. Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed ( Brassica napus L.) compared with its diploid progenitors. PeerJ 2019; 7:e7511. [PMID: 31497395 PMCID: PMC6707343 DOI: 10.7717/peerj.7511] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/17/2019] [Indexed: 11/27/2022] Open
Abstract
Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions.
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Affiliation(s)
- Ziwei Liang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhengyi Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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48
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Liu D, Sun J, Zhu D, Lyu G, Zhang C, Liu J, Wang H, Zhang X, Gao D. Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat ( Triticum aestivum L.). Genes (Basel) 2019; 10:genes10090696. [PMID: 31510067 PMCID: PMC6770980 DOI: 10.3390/genes10090696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022] Open
Abstract
Late embryogenesis-abundant (LEA) genes play important roles in plant growth and development, especially the cellular dehydration tolerance during seed maturation. In order to comprehensively understand the roles of LEA family members in wheat, we carried out a series of analyses based on the latest genome sequence of the bread wheat Chinese Spring. 121 Triticum aestivum L. LEA (TaLEA) genes, classified as 8 groups, were identified and characterized. TaLEA genes are distributed in all chromosomes, most of them with a low number of introns (≤3). Expression profiles showed that most TaLEA genes expressed specifically in grains. By qRT-PCR analysis, we confirmed that 12 genes among them showed high expression levels during late stage grain maturation in two spring wheat cultivars, Yangmai16 and Yangmai15. For most genes, the peak of expression appeared earlier in Yangmai16. Statistical analysis indicated that expression level of 8 genes in Yangmai 16 were significantly higher than Yangmai 15 at 25 days after anthesis. Taken together, our results provide more knowledge for future functional analysis and potential utilization of TaLEA genes in wheat breeding.
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Affiliation(s)
- Datong Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Jing Sun
- Yangzhou University, Yangzhou 225009, China.
| | - Dongmei Zhu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Guofeng Lyu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Chunmei Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Jian Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Hui Wang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Xiao Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Derong Gao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
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49
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Liu M, Wen Y, Sun W, Ma Z, Huang L, Wu Q, Tang Z, Bu T, Li C, Chen H. Genome-wide identification, phylogeny, evolutionary expansion and expression analyses of bZIP transcription factor family in tartaty buckwheat. BMC Genomics 2019; 20:483. [PMID: 31185893 PMCID: PMC6560858 DOI: 10.1186/s12864-019-5882-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome. Results In this study, 96 FtbZIP genes named from FtbZIP1 to FtbZIP96 were identified and divided into 11 subfamilies according to their genetic relationship with 70 bZIPs of A. thaliana. FtbZIP genes are not evenly distributed on the chromosomes, and we found tandem and segmental duplication events of FtbZIP genes on 8 tartary buckwheat chromosomes. According to the results of gene and motif composition, FtbZIP located in the same group contained analogous intron/exon organizations and motif composition. By qRT-PCR, we quantified the expression of FtbZIP members in stem, root, leaf, fruit, and flower and during fruit development. Exogenous ABA treatment increased the weight of tartary buckwheat fruit and changed the expressions of FtbZIP genes in group A. Conclusions Through our study, we identified 96 FtbZIP genes in tartary buckwheat and synthetically further analyzed the structure composition, evolution analysis and expression pattern of FtbZIP proteins. The expression pattern indicates that FtbZIP is important in the course of plant growth and development of tartary buckwheat. Through comprehensively analyzing fruit weight and FtbZIP genes expression after ABA treatment and endogenous ABA content of tartary buckwheat fruit, ABA may regulate downstream gene expression by regulating the expression of FtPinG0003523300.01 and FtPinG0003196200.01, thus indirectly affecting the fruit development of tartary buckwheat. This will help us to further study the function of FtbZIP genes in the tartary buckwheat growth and improve the fruit of tartary buckwheat. Electronic supplementary material The online version of this article (10.1186/s12864-019-5882-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moyang Liu
- Sichuan Agricultural University, College of Life Science, Ya'an, China.,Shanghai Jiao Tong University, School of Agriculture and Biolog, Shanghai, China
| | - Yongdi Wen
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Wenjun Sun
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Zhaotang Ma
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Li Huang
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Qi Wu
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Zizhong Tang
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Tongliang Bu
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Chenglei Li
- Sichuan Agricultural University, College of Life Science, Ya'an, China
| | - Hui Chen
- Sichuan Agricultural University, College of Life Science, Ya'an, China.
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50
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Wu C, Ding X, Ding Z, Tie W, Yan Y, Wang Y, Yang H, Hu W. The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. Int J Mol Sci 2019; 20:ijms20112730. [PMID: 31163686 PMCID: PMC6600411 DOI: 10.3390/ijms20112730] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/27/2023] Open
Abstract
The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.
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Affiliation(s)
- Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yu Wang
- Beijing Commerce and Trade School, Beijing 100162, China.
| | - Hai Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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