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Wu X, Yang Z, Zhu Y, Zhan Y, Li Y, Teng W, Han Y, Zhao X. Bioinformatics Identification and Expression Analysis of Acetyl-CoA Carboxylase Reveal Its Role in Isoflavone Accumulation during Soybean Seed Development. Int J Mol Sci 2024; 25:10221. [PMID: 39337707 DOI: 10.3390/ijms251810221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/05/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024] Open
Abstract
Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a key enzyme in fatty acid synthesis and also catalyzes the production of various secondary metabolites. However, information on the ACC gene family in the soybean (Glycine max L. Merr.) genome and the specific members involved in isoflavone biosynthesis is still lacking. In this study, we identified 20 ACC family genes (GmACCs) from the soybean genome and further characterized their evolutionary relationships and expression patterns. Phylogenetic analysis showed that the GmACCs could be divided into five groups, and the gene structures within the same groups were highly conserved, indicating that they had similar functions. The GmACCs were randomly distributed across 12 chromosomes, and collinearity analysis suggested that many GmACCs originated from tandem and segmental duplications, with these genes being under purifying selection. In addition, gene expression pattern analysis indicated that there was functional divergence among GmACCs in different tissues. The GmACCs reached their peak expression levels during the early or middle stages of seed development. Based on the transcriptome and isoflavone content data, a weighted gene co-expression network was constructed, and three candidate genes (Glyma.06G105900, Glyma.13G363500, and Glyma.13G057400) that may positively regulate isoflavone content were identified. These results provide valuable information for the further functional characterization and application of GmACCs in isoflavone biosynthesis in soybean.
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Affiliation(s)
- Xu Wu
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Zhenhong Yang
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Yina Zhu
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
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Wang S, Wang X, Yue L, Li H, Zhu L, Dong Z, Long Y. Genome-Wide Identification and Characterization of Lignin Synthesis Genes in Maize. Int J Mol Sci 2024; 25:6710. [PMID: 38928419 PMCID: PMC11203529 DOI: 10.3390/ijms25126710] [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: 04/01/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Lignin is a crucial substance in the formation of the secondary cell wall in plants. It is widely distributed in various plant tissues and plays a significant role in various biological processes. However, the number of copies, characteristics, and expression patterns of genes involved in lignin biosynthesis in maize are not fully understood. In this study, bioinformatic analysis and gene expression analysis were used to discover the lignin synthetic genes, and two representative maize inbred lines were used for stem strength phenotypic analysis and gene identification. Finally, 10 gene families harboring 117 related genes involved in the lignin synthesis pathway were retrieved in the maize genome. These genes have a high number of copies and are typically clustered on chromosomes. By examining the lignin content of stems and the expression patterns of stem-specific genes in two representative maize inbred lines, we identified three potential stem lodging resistance genes and their interactions with transcription factors. This study provides a foundation for further research on the regulation of lignin biosynthesis and maize lodging resistance genes.
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Affiliation(s)
| | | | | | | | | | - Zhenying Dong
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and Agriculture, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (S.W.); (X.W.); (L.Y.); (H.L.); (L.Z.)
| | - Yan Long
- Zhongzhi International Institute of Agricultural Biosciences, Research Institute of Biology and Agriculture, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (S.W.); (X.W.); (L.Y.); (H.L.); (L.Z.)
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Zhang J, Yue Y, Hu M, Yi F, Chen J, Lai J, Xin B. Dynamic transcriptome landscape of maize pericarp development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1574-1591. [PMID: 37970738 DOI: 10.1111/tpj.16548] [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: 04/24/2023] [Revised: 10/09/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023]
Abstract
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome-wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA-seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non-seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp-specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene-related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
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Affiliation(s)
- Jihong Zhang
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Yang Yue
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Mingjian Hu
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Fei Yi
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, P. R. China
| | - Jian Chen
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Beibei Xin
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
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Yi X, Chen W, Guan J, Zhu J, Zhang Q, Yang H, Yang H, Zhong S, Chen C, Tan F, Ren T, Luo P. Genome-Wide Analysis of the Polygalacturonase Gene Family Sheds Light on the Characteristics, Evolutionary History, and Putative Function of Akebia trifoliata. Int J Mol Sci 2023; 24:16973. [PMID: 38069295 PMCID: PMC10707396 DOI: 10.3390/ijms242316973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Polygalacturonase (PG) is one of the largest families of hydrolytic enzymes in plants. It is involved in the breakdown of pectin in the plant cell wall and even contributes to peel cracks. Here, we characterize PGs and outline their expression profiles using the available reference genome and transcriptome of Akebia trifoliata. The average length and exon number of the 47 identified AktPGs, unevenly assigned on 14 chromosomes and two unassembled contigs, were 5399 bp and 7, respectively. The phylogenetic tree of 191 PGs, including 47, 57, 51, and 36 from A. trifoliata, Durio zibethinus, Actinidia chinensis, and Vitis vinifera, respectively, showed that AktPGs were distributed in all groups except group G and that 10 AktPGs in group E were older, while the remaining 37 AktPGs were younger. Evolutionarily, all AktPGs generally experienced whole-genome duplication (WGD)/segmental repeats and purifying selection. Additionally, the origin of conserved domain III was possibly associated with a histidine residue (H) substitute in motif 8. The results of both the phylogenetic tree and expression profiling indicated that five AktPGs, especially AktPG25, could be associated with the cracking process. Detailed information and data on the PG family are beneficial for further study of the postharvest biology of A. trifoliata.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (W.C.); (J.G.); (J.Z.); (Q.Z.); (H.Y.); (H.Y.); (S.Z.); (C.C.); (F.T.); (T.R.)
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Li H, Li Y, Wang X, Jiao Z, Zhang W, Long Y. Characterization of Glycosyltransferase Family 1 (GT1) and Their Potential Roles in Anthocyanin Biosynthesis in Maize. Genes (Basel) 2023; 14:2099. [PMID: 38003042 PMCID: PMC10671782 DOI: 10.3390/genes14112099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Glycosyltransferase family 1 (GT1) is a large group of proteins that play critical roles in secondary metabolite biosynthesis in plants. However, the GT1 family is not well studied in maize. In this study, 107 GT1 unigenes were identified in the maize reference genome and classified into 16 groups according to their phylogenetic relationship. GT1s are unevenly distributed across all ten maize chromosomes, occurring as gene clusters in some chromosomes. Collinearity analysis revealed that gene duplication events, whole-genome or segmental duplication, and tandem duplication occurred at a similar frequency, indicating that both types of gene duplication play notable roles in the expansion of the GT1 gene family. Expression analysis showed GT1s expressing in all tissues with specific expression patterns of each GT1, suggesting that they might participate in multiple biological processes during the whole growth and development stages. Furthermore, 16 GT1s were identified to have similar expression patterns to those of anthocyanidin synthase (ANS), the critical enzyme in anthocyanin biosynthesis. Molecular docking was carried out to examine the affinity of GT1s with substrates in anthocyanin biosynthesis. This study provides valuable information on the GT1s of maize and will promote the development of research on their biological functions in the biosynthesis of other secondary metabolites.
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Affiliation(s)
- Huangai Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
| | - Yiping Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
| | - Xiaofang Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
| | - Ziwei Jiao
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; (Z.J.); (W.Z.)
| | - Wei Zhang
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; (Z.J.); (W.Z.)
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
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Hou Q, Wang L, Qi Y, Yan T, Zhang F, Zhao W, Wan X. A systematic analysis of the subtilase gene family and expression and subcellular localization investigation of anther-specific members in maize. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108041. [PMID: 37722281 DOI: 10.1016/j.plaphy.2023.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/20/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Subtilases (SBTs), also known as Subtilisin-like serine proteases, are extracellular alkaline protease proteins. SBTs function in all stages of plant growth, development and stress responses. Maize (Zea mays L.) is a crop widely used worldwide as food, feed, and industrial materials. However, information about the members and their functions of the SBT proteins in maize is lacking. In this study, we identified 58 ZmSBT genes from the maize genome and conducted a comprehensive investigation of ZmSBTs by phylogenetic, gene duplication event, gene structure, and protein conserved motif analyses. The ZmSBT proteins were phylogenetically classified into seven groups, and collinearity analysis indicated that many ZmSBTs originate from tandem or segmental duplications. Structural and homolog protein comparison revealed ZmSBTs have conserved protein structures with reported subtilase proteins, suggesting the conserved functions. Further analysis showed that ZmSBTs are expressed in different tissues, and many are responses to specific abiotic stress. Analysis of the anther-specific ZmSBT genes showed their expression peaked at different developmental stages of maize anthers. Subcellular localization analysis of selected maize ZmSBTs showed they are located in different cellular compartments. The information provided in this study is valuable for further functional study of ZmSBTs.
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Affiliation(s)
- Quancan Hou
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Zhongzhi lnternational lnstitute of Agricultural Biosciences, Beijing, 100192, China
| | - Linlin Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yuchen Qi
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tingwei Yan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Fan Zhang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Wei Zhao
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Zhongzhi lnternational lnstitute of Agricultural Biosciences, Beijing, 100192, China.
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He P, Zhang J, Lv Z, Cui P, Xu X, George MS, Lu G. Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato. BMC PLANT BIOLOGY 2023; 23:300. [PMID: 37270475 PMCID: PMC10239142 DOI: 10.1186/s12870-023-04272-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/07/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND Polygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants' developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sweetpotato (Ipomoea batatas) have not been extensively identified. RESULTS In this study, there were 103 PG genes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed these PGs according to their locations of the chromosomes. The investigation of collinearity between the PGs in sweetpotato and other four species, contained Arabidopsis thaliana, Solanum lycopersicum, Malus domestica and Ziziphus jujuba, revealed important clues about the potential evolution of the PG family in sweetpotato. Gene duplication analysis showed that IbPGs with collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins contained cis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103 IbPGs were differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment). IbPG038 and IbPG039 were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found that IbPG006, IbPG034 and IbPG099 had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes. CONCLUSION A total of 103 IbPGs were identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested that IbPG006, IbPG034 and IbPG099 might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of the IbPGs.
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Affiliation(s)
- Peiwen He
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jingzhen Zhang
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Zunfu Lv
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Cui
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ximing Xu
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Melvin Sidikie George
- Crop Science Department, Njala University, Njala Campus. Private Mail bag, Freetown, 999127, Sierra Leone
| | - Guoquan Lu
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
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Ma Y, Xue M, Zhang X, Chen S. Genome-wide analysis of the metallothionein gene family in cassava reveals its role in response to physiological stress through the regulation of reactive oxygen species. BMC PLANT BIOLOGY 2023; 23:227. [PMID: 37118665 PMCID: PMC10142807 DOI: 10.1186/s12870-023-04174-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cassava (Manihot esculenta Crantz) is widely planted in tropical and several subtropical regions in which drought, high temperatures, and other abiotic stresses occur. Metallothionein (MT) is a group of conjugated proteins with small molecular weight and rich in cysteine. These proteins play a substantial role in response to physiological stress through the regulation of reactive oxygen species (ROS). However, the biological functions of MT genes in cassava are unknown. RESULTS A total of 10 MeMT genes were identified in the cassava genome. The MeMTs were divided into 3 groups (Types 2-4) based on the contents and distribution of Cys residues. The MeMTs exhibited tissue-specific expression and located on 7 chromosomes. The MeMT promoters contain some hormones regulatory and stresses responsiveness elements. MeMTs were upregulated under hydrogen peroxide (H2O2) treatment and in respond to post-harvest physiological deterioration (PPD). The results were consistent with defense-responsive cis-acting elements in the MeMT promoters. Further, four of MeMTs were selected and silenced by using the virus-induced gene silencing (VIGS) method to evaluate their functional characterization. The results of gene-silenced cassava suggest that MeMTs are involved in oxidative stress resistance, as ROS scavengers. CONCLUSION We identified the 10 MeMT genes, and explore their evolutionary relationship, conserved motif, and tissue-specific expression. The expression profiles of MeMTs under three kinds of abiotic stresses (wounding, low-temperature, and H2O2) and during PPD were analyzed. The tissue-specific expression and the response to abiotic stresses revealed the role of MT in plant growth and development. Furthermore, silenced expression of MeMTs in cassava leaves decreased its tolerance to ROS, consistent with its predicted role as ROS scavengers. In summary, our results suggest an important role of MeMTs in response to physiological stress as well as species adaptation via the regulation of ROS homeostasis.
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Affiliation(s)
- Yanyan Ma
- School of Life Sciences, Hainan University, Haikou, 570228, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, 571101, China
| | - Maofu Xue
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, 571101, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and CIAT, Cali, 763537, Colombia
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, 571101, China.
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Wang D, Wang Y, Zhang L, Yang Y, Wu Q, Hu G, Wang W, Li J, Huang Z. Integrated transcriptomic and proteomic analysis of a cytoplasmic male sterility line and associated maintainer line in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1098125. [PMID: 36818857 PMCID: PMC9933710 DOI: 10.3389/fpls.2023.1098125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Heterosis is a critical phenomenon in crop improvement. Cytoplasmic male sterility (CMS) and Restorer gene (Rf) systems are essential components for heterosis-based breeding. However, the molecular mechanism underlying CMS remains largely unclear in soybean. METHODS We integrated a morphological investigation with comparative analyses of transcriptomic and proteomic changes in pollen from the CMS line W931A and its maintainer line, W931B, at the uninucleate microspore (UM) and binucleate pollen (BP) stages. RESULTS Compared to W931B, which had healthy, oval pollen grains, W931A showed shrunken or degraded pollen grains with an irregularly thickened endothelium and decreased starch accumulation. Transcriptomic comparisons revealed a total of 865 differentially expressed genes (DEGs) in W931A over the two stages. These genes were primarily associated with pentose and glucuronate interconversions, sphingolipid metabolism, and glycerolipid metabolism. Proteomic analysis revealed 343 differentially expressed proteins (DEPs), which were mainly involved in carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism. Consistently, Gene Ontology (GO) biological process terms related to pollen development were enriched among DEGs at the UM and BP stages. Notably, four genes with demonstrated roles in pollen development were differentially expressed, including AGAMOUS-LIKE 104, PROTEIN-TYROSINE-PHOSPHATASE 1, and PHOSPHOLIPASE A2. A total of 53 genes and the corresponding proteins were differentially expressed in W931A at both the UM and BP stages, and many of these were pectinesterases, polygalacturonases, peroxidases, and ATPases. DISCUSSION The results of this study suggest that pollen development in W931A is likely regulated through suppression of the identified DEGs and DEPs. These findings increase our understanding of the molecular mechanism underlying CMS in soybean, aiding future research into soybean fertility and promoting the efficient use of heterosis for soybean improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiekun Li
- *Correspondence: Zhiping Huang, ; Jiekun Li,
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Ibrahim S, Li K, Ahmad N, Kuang L, Sadau SB, Tian Z, Huang L, Wang X, Dun X, Wang H. Genetic Dissection of Mature Root Characteristics by Genome-Wide Association Studies in Rapeseed ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122569. [PMID: 34961040 PMCID: PMC8705616 DOI: 10.3390/plants10122569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Roots are complicated quantitative characteristics that play an essential role in absorbing water and nutrients. To uncover the genetic variations for root-related traits in rapeseed, twelve mature root traits of a Brassica napus association panel were investigated in the field within three environments. All traits showed significant phenotypic variation among genotypes, with heritabilities ranging from 55.18% to 79.68%. Genome-wide association studies (GWAS) using 20,131 SNPs discovered 172 marker-trait associations, including 103 significant SNPs (-log10 (p) > 4.30) that explained 5.24-20.31% of the phenotypic variance. With the linkage disequilibrium r2 > 0.2, these significant associations were binned into 40 quantitative trait loci (QTL) clusters. Among them, 14 important QTL clusters were discovered in two environments and/or with phenotypic contributions greater than 10%. By analyzing the genomic regions within 100 kb upstream and downstream of the peak SNPs within the 14 loci, 334 annotated genes were found. Among these, 32 genes were potentially associated with root development according to their expression analysis. Furthermore, the protein interaction network using the 334 annotated genes gave nine genes involved in a substantial number of interactions, including a key gene associated with root development, BnaC09g36350D. This research provides the groundwork for deciphering B. napus' genetic variations and improving its root system architecture.
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Affiliation(s)
- Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
- Department of Plant Biology, Faculty of Life Sciences, College of Physical and Pharmaceutical Sciences, Bayero University, Kano, P.M.B. 3011, Kano 700006, Nigeria
| | - Keqi Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Salisu Bello Sadau
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Lintao Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan 430062, China; (S.I.); (K.L.); (N.A.); (L.K.); (Z.T.); (L.H.); (X.W.); (H.W.)
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