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Xia Y, Han Q, Shu J, Jiang S, Kang X. Stomatal density suppressor PagSDD1 is a "generalist" gene that promotes plant growth and improves water use efficiency. Int J Biol Macromol 2024; 262:129721. [PMID: 38296132 DOI: 10.1016/j.ijbiomac.2024.129721] [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: 08/08/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/13/2024]
Abstract
The serine protease SDD1 regulates stomatal density, but its potential impact on plant vegetative growth is unclear. Our study reveals a substantial upregulation of SDD1 in triploid poplar apical buds and leaves, suggesting its possible role in their growth regulation. We cloned PagSDD1 from poplar 84 K (Populus alba × P. glandulosa) and found that overexpression in poplar, soybean, and lettuce led to decreased leaf stomatal density. Furthermore, PagSDD1 represses PagEPF1, PagEPF2, PagEPFL9, PagSPCH, PagMUTE, and PagFAMA expression. In contrast, PagSDD1 promotes the expression of its receptors, PagTMM and PagERECTA. PagSDD1-OE poplars showed stronger drought tolerance than wild-type poplars. Simultaneously, PagSDD1-OE poplar, soybean, and lettuce had vegetative growth advantages. RNA sequencing revealed a significant upregulation of genes PagLHCB2.1 and PagGRF5, correlating positively with photosynthetic rate, and PagCYCA3;4 and PagEXPA8 linked to cell division and differentiation in PagSDD1-OE poplars. This increase promoted leaf photosynthesis, boosted auxin and cytokinin accumulation, and enhanced vegetative growth. SDD1 overexpression can increase the biomass of poplar, soybean, and lettuce by approximately 70, 176, and 155 %, respectively, and increase the water use efficiency of poplar leaves by over 52 %, which is of great value for the molecular design and breeding of plants with growth and water-saving target traits.
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Affiliation(s)
- Yufei Xia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Qiang Han
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Jianghai Shu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Shenxiu Jiang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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2
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Kang L, Li C, Qin A, Liu Z, Li X, Zeng L, Yu H, Wang Y, Song J, Chen R. Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean ( Glycine max) under Various Abiotic Stresses. Int J Mol Sci 2024; 25:1115. [PMID: 38256188 PMCID: PMC10816777 DOI: 10.3390/ijms25021115] [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: 11/11/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3' end of RNA. In plants, NTPs can regulate RNA stability by influencing 3' end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans.
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Affiliation(s)
- Liqing Kang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Changgen Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Aokang Qin
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Zehui Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Xuanyue Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Liming Zeng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Hongyang Yu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Yihua Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Jianbo Song
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
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Wang M, He C, Shi G, Yin Q, Zhang H, Yang W, Yue A, Wang L, Du W. Genome-wide analysis of the SCAMPs gene family of soybean and functional identification of GmSCAMP5 in salt tolerance. BMC PLANT BIOLOGY 2023; 23:628. [PMID: 38062393 PMCID: PMC10704743 DOI: 10.1186/s12870-023-04649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]
Abstract
The effect of salt damage on plants is mainly caused by the toxic effect of Na+. Studies showed that the secretory carrier membrane proteins were associated with the Na+ transport. However, the salt tolerance mechanism of secretory carrier protein (SCAMP) in soybean was yet to be defined. In this study, ten potential SCAMP genes distributed in seven soybean chromosomes were identified in the soybean genome. The phylogenetic tree of SCAMP domain sequences of several plants can divide SCAMPs into two groups. Most GmSCAMPs genes contained multiple Box4, MYB and MYC cis-elements indicated they may respond to abiotic stresses. We found that GmSCAMP1, GmSCAMP2 and GmSCAMP4 expressed in several tissues and GmSCAMP5 was significantly induced by salt stress. GmSCAMP5 showed the same expression patterns under NaCl treatment in salt-tolerant and salt-sensitive soybean varieties, but the induced time of GmSCAMP5 in salt-tolerant variety was earlier than that of salt-sensitive variety. To further study the effect of GmSCAMP5 on the salt tolerance of soybean plants, compared to GmSCAMP5-RNAi and EV-Control plants, GmSCAMP5-OE had less wilted leave and higher SPAD value. Compared to empty vector control, less trypan blue staining was observed in GmSCAMP5-OE leaves while more staining in GmSCAMP5-RNAi leaves. The Na+ of GmSCAMP5-RNAi plants leaves under NaCl stress were significantly higher than that in EV-Control plants, while significantly lower Na+ in GmSCAMP5-OE plants than in that EV-Control plants. The contents of leaves K+ of GmSCAMP5-RNAi, EV-Control, and GmSCAMP5-OE plants under NaCl stress were opposite to that of leaves Na+ content. Finally, salt stress-related genes NHX1, CLC1, TIP1, SOD1, and SOS1 in transformed hairy root changed significantly compared with the empty control. The research will provide novel information for study the molecular regulation mechanism of soybean salt tolerance.
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Affiliation(s)
- Min Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Chuanrong He
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Guangcheng Shi
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Qiukai Yin
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Hanyue Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Wanmin Yang
- Department of Biological Science and Technology, Jinzhong University, Yuci, 030619, China
| | - Aiqin Yue
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Lixiang Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
- Houji laboratory in Shanxi Province, Shanxi Agricultural University, Taigu, 030801, China.
| | - Weijun Du
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
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Jolliffe JB, Pilati S, Moser C, Lashbrooke JG. Beyond skin-deep: targeting the plant surface for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6468-6486. [PMID: 37589495 PMCID: PMC10662250 DOI: 10.1093/jxb/erad321] [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: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
The above-ground plant surface is a well-adapted tissue layer that acts as an interface between the plant and its surrounding environment. As such, its primary role is to protect against desiccation and maintain the gaseous exchange required for photosynthesis. Further, this surface layer provides a barrier against pathogens and herbivory, while attracting pollinators and agents of seed dispersal. In the context of agriculture, the plant surface is strongly linked to post-harvest crop quality and yield. The epidermal layer contains several unique cell types adapted for these functions, while the non-lignified above-ground plant organs are covered by a hydrophobic cuticular membrane. This review aims to provide an overview of the latest understanding of the molecular mechanisms underlying crop cuticle and epidermal cell formation, with focus placed on genetic elements contributing towards quality, yield, drought tolerance, herbivory defence, pathogen resistance, pollinator attraction, and sterility, while highlighting the inter-relatedness of plant surface development and traits. Potential crop improvement strategies utilizing this knowledge are outlined in the context of the recent development of new breeding techniques.
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Affiliation(s)
- Jenna Bryanne Jolliffe
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Stefania Pilati
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Justin Graham Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
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5
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Doll Y, Koga H, Tsukaya H. Experimental validation of the mechanism of stomatal development diversification. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5667-5681. [PMID: 37555400 PMCID: PMC10540739 DOI: 10.1093/jxb/erad279] [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: 03/22/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023]
Abstract
Stomata are the structures responsible for gas exchange in plants. The established framework for stomatal development is based on the model plant Arabidopsis, but diverse patterns of stomatal development have been observed in other plant lineages and species. The molecular mechanisms behind these diversified patterns are still poorly understood. We recently proposed a model for the molecular mechanisms of the diversification of stomatal development based on the genus Callitriche (Plantaginaceae), according to which a temporal shift in the expression of key stomatal transcription factors SPEECHLESS and MUTE leads to changes in the behavior of meristemoids (stomatal precursor cells). In the present study, we genetically manipulated Arabidopsis to test this model. By altering the timing of MUTE expression, we successfully generated Arabidopsis plants with early differentiation or prolonged divisions of meristemoids, as predicted by the model. The epidermal morphology of the generated lines resembled that of species with prolonged or no meristemoid divisions. Thus, the evolutionary process can be reproduced by varying the SPEECHLESS to MUTE transition. We also observed unexpected phenotypes, which indicated the participation of additional factors in the evolution of the patterns observed in nature. This study provides novel experimental insights into the diversification of meristemoid behaviors.
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Affiliation(s)
- Yuki Doll
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Koga
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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6
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Yu L, Zhang H, Guan R, Li Y, Guo Y, Qiu L. Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean. Genes (Basel) 2023; 14:1150. [PMID: 37372330 DOI: 10.3390/genes14061150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.
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Affiliation(s)
- Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Smit ME, Vatén A, Mair A, Northover CAM, Bergmann DC. Extensive embryonic patterning without cellular differentiation primes the plant epidermis for efficient post-embryonic stomatal activities. Dev Cell 2023; 58:506-521.e5. [PMID: 36931268 DOI: 10.1016/j.devcel.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/12/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
Plant leaves feature epidermal stomata that are organized in stereotyped patterns. How does the pattern originate? We provide transcriptomic, imaging, and genetic evidence that Arabidopsis embryos engage known stomatal fate and patterning factors to create regularly spaced stomatal precursor cells. Analysis of embryos from 36 plant species indicates that this trait is widespread among angiosperms. Embryonic stomatal patterning in Arabidopsis is established in three stages: first, broad SPEECHLESS (SPCH) expression; second, coalescence of SPCH and its targets into discrete domains; and third, one round of asymmetric division to create stomatal precursors. Lineage progression is then halted until after germination. We show that the embryonic stomatal pattern enables fast stomatal differentiation and photosynthetic activity upon germination, but it also guides the formation of additional stomata as the leaf expands. In addition, key stomatal regulators are prevented from driving the fate transitions they can induce after germination, identifying stage-specific layers of regulation that control lineage progression during embryogenesis.
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Affiliation(s)
- Margot E Smit
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Andrea Mair
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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Mano NA, Madore B, Mickelbart MV. Different Leaf Anatomical Responses to Water Deficit in Maize and Soybean. Life (Basel) 2023; 13:life13020290. [PMID: 36836647 PMCID: PMC9966819 DOI: 10.3390/life13020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
The stomata on leaf surfaces control gas exchange and water loss, closing during dry periods to conserve water. The distribution and size of stomatal complexes is determined by epidermal cell differentiation and expansion during leaf growth. Regulation of these processes in response to water deficit may result in stomatal anatomical plasticity as part of the plant acclimation to drought. We quantified the leaf anatomical plasticity under water-deficit conditions in maize and soybean over two experiments. Both species produced smaller leaves in response to the water deficit, partly due to the reductions in the stomata and pavement cell size, although this response was greater in soybean, which also produced thicker leaves under severe stress, whereas the maize leaf thickness did not change. The stomata and pavement cells were smaller with the reduced water availability in both species, resulting in higher stomatal densities. Stomatal development (measured as stomatal index, SI) was suppressed in both species at the lowest water availability, but to a greater extent in maize than in soybean. The result of these responses is that in maize leaves, the stomatal area fraction (fgc) was consistently reduced in the plants grown under severe but not moderate water deficit, whereas the fgc did not decrease in the water-stressed soybean leaves. The water deficit resulted in the reduced expression of one of two (maize) or three (soybean) SPEECHLESS orthologs, and the expression patterns were correlated with SI. The vein density (VD) increased in both species in response to the water deficit, although the effect was greater in soybean. This study establishes a mechanism of stomatal development plasticity that can be applied to other species and genotypes to develop or investigate stomatal development plasticity.
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Affiliation(s)
- Noel Anthony Mano
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Bethany Madore
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Michael V. Mickelbart
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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López-Cordova A, Ramírez-Medina H, Silva-Martinez GA, González-Cruz L, Bernardino-Nicanor A, Huanca-Mamani W, Montero-Tavera V, Tovar-Aguilar A, Ramírez-Pimentel JG, Durán-Figueroa NV, Acosta-García G. LEA13 and LEA30 Are Involved in Tolerance to Water Stress and Stomata Density in Arabidopsis thaliana. PLANTS 2021; 10:plants10081694. [PMID: 34451739 PMCID: PMC8400336 DOI: 10.3390/plants10081694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022]
Abstract
Late embryogenesis abundant (LEA) proteins are a large protein family that mainly function in protecting cells from abiotic stress, but these proteins are also involved in regulating plant growth and development. In this study, we performed a functional analysis of LEA13 and LEA30 from Arabidopsis thaliana. The results showed that the expression of both genes increased when plants were subjected to drought-stressed conditions. The insertional lines lea13 and lea30 were identified for each gene, and both had a T-DNA element in the regulatory region, which caused the genes to be downregulated. Moreover, lea13 and lea30 were more sensitive to drought stress due to their higher transpiration and stomatal spacing. Microarray analysis of the lea13 background showed that genes involved in hormone signaling, stomatal development, and abiotic stress responses were misregulated. Our results showed that LEA proteins are involved in drought tolerance and participate in stomatal density.
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Affiliation(s)
- Abigael López-Cordova
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/IT de Celaya, Antonio García Cubas Pte. #600 esq. Av. Tecnológico, Celaya 38010, Guanajuato, Mexico; (A.L.-C.); (H.R.-M.); (G.-A.S.-M.); (L.G.-C.); (A.B.-N.)
| | - Humberto Ramírez-Medina
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/IT de Celaya, Antonio García Cubas Pte. #600 esq. Av. Tecnológico, Celaya 38010, Guanajuato, Mexico; (A.L.-C.); (H.R.-M.); (G.-A.S.-M.); (L.G.-C.); (A.B.-N.)
| | - Guillermo-Antonio Silva-Martinez
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/IT de Celaya, Antonio García Cubas Pte. #600 esq. Av. Tecnológico, Celaya 38010, Guanajuato, Mexico; (A.L.-C.); (H.R.-M.); (G.-A.S.-M.); (L.G.-C.); (A.B.-N.)
| | - Leopoldo González-Cruz
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/IT de Celaya, Antonio García Cubas Pte. #600 esq. Av. Tecnológico, Celaya 38010, Guanajuato, Mexico; (A.L.-C.); (H.R.-M.); (G.-A.S.-M.); (L.G.-C.); (A.B.-N.)
| | - Aurea Bernardino-Nicanor
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/IT de Celaya, Antonio García Cubas Pte. #600 esq. Av. Tecnológico, Celaya 38010, Guanajuato, Mexico; (A.L.-C.); (H.R.-M.); (G.-A.S.-M.); (L.G.-C.); (A.B.-N.)
| | - Wilson Huanca-Mamani
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile;
| | - Víctor Montero-Tavera
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya 38110, Guanajuato, Mexico;
| | - Andrea Tovar-Aguilar
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, México City 07340, Mexico; (A.T.-A.); (N.-V.D.-F.)
| | | | - Noé-Valentín Durán-Figueroa
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, México City 07340, Mexico; (A.T.-A.); (N.-V.D.-F.)
| | - Gerardo Acosta-García
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/IT de Celaya, Antonio García Cubas Pte. #600 esq. Av. Tecnológico, Celaya 38010, Guanajuato, Mexico; (A.L.-C.); (H.R.-M.); (G.-A.S.-M.); (L.G.-C.); (A.B.-N.)
- Correspondence: ; Tel.: +52-4616117575 (ext. 5471)
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Zhang H, Hu Z, Yang Y, Liu X, Lv H, Song BH, An YQC, Li Z, Zhang D. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics 2021; 22:453. [PMID: 34134624 PMCID: PMC8207594 DOI: 10.1186/s12864-021-07783-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. RESULTS In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. CONCLUSIONS Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.
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Affiliation(s)
- Hengyou Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haiyan Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zhimin Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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11
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Arellano-Villagómez FC, Guevara-Olvera L, Zuñiga-Mayo VM, E. Cerbantez-Bueno V, Verdugo-Perales M, R. Medina H, De Folter S, Acosta-García G. Arabidopsis cysteine-rich receptor-like protein kinase CRK33 affects stomatal density and drought tolerance. PLANT SIGNALING & BEHAVIOR 2021; 16:1905335. [PMID: 33769202 PMCID: PMC8143253 DOI: 10.1080/15592324.2021.1905335] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 05/19/2023]
Abstract
Cysteine-rich receptor-like protein kinases (CRKs) are transmembrane proteins containing two domains of unknown function 26 (DUF26) RLKs in their ectodomain. Despite that CRKs control important aspects of plant development, only few proteins have functionally been characterized. In this work, we analyzed the function of CRK33 by characterizing two insertional lines. The stomatal density and stomatal index were decreased in crk33-2 and crk33-3 plants in comparison to wild-type plants, correlating with a decreased transpiration in transgenic plants and a higher drought tolerance. Furthermore, photosynthesis and stomatal conductance changed. Finally, all four stomata cell fate genes were upregulated, especially the expression of TMM and SPCH in the mutant background, suggesting a role for CRK33 in stomatal spacing.
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Affiliation(s)
| | - Lorenzo Guevara-Olvera
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
| | - Víctor M. Zuñiga-Mayo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro De Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
- Instituto de Fitosanidad, Colegio de Postgraduados, Campus Montecillo, Texcoco, Estado de México, México
| | - Vincent E. Cerbantez-Bueno
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro De Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
| | - Mercedes Verdugo-Perales
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
| | - Humberto R. Medina
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
| | - Stefan De Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro De Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
| | - Gerardo Acosta-García
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
- CONTACT Gerardo Acosta-García Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
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12
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Reddy VRP, Das S, Dikshit HK, Mishra GP, Aski M, Meena SK, Singh A, Pandey R, Singh MP, Tripathi K, Gore PG, Priti, Bhagat TK, Kumar S, Nair R, Sharma TR. Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean ( Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach. FRONTIERS IN PLANT SCIENCE 2020; 11:537766. [PMID: 33193476 PMCID: PMC7658405 DOI: 10.3389/fpls.2020.537766] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/18/2020] [Indexed: 10/10/2023]
Abstract
Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.
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Affiliation(s)
| | - Shouvik Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gyan Prakash Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Surendra Kumar Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Division of Basic Science, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Padmavati Ganpat Gore
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Priti
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | | | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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13
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Wang Y, Chen ZH. Does Molecular and Structural Evolution Shape the Speedy Grass Stomata? FRONTIERS IN PLANT SCIENCE 2020; 11:333. [PMID: 32373136 PMCID: PMC7186404 DOI: 10.3389/fpls.2020.00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/05/2020] [Indexed: 05/03/2023]
Abstract
It has been increasingly important for breeding programs to be aimed at crops that are capable of coping with a changing climate, especially with regards to higher frequency and intensity of drought events. Grass stomatal complex has been proposed as an important factor that may enable grasses to adapt to water stress and variable climate conditions. There are many studies focusing on the stomatal morphology and development in the eudicot model plant Arabidopsis and monocot model plant Brachypodium. However, the comprehensive understanding of the distinction of stomatal structure and development between monocots and eudicots, especially between grasses and eudicots, are still less known at evolutionary and comparative genetic levels. Therefore, we employed the newly released version of the One Thousand Plant Transcriptome (OneKP) database and existing databases of green plant genome assemblies to explore the evolution of gene families that contributed to the formation of the unique structure and development of grass stomata. This review emphasizes the differential stomatal morphology, developmental mechanisms, and guard cell signaling in monocots and eudicots. We provide a summary of useful molecular evidences for the high water use efficiency of grass stomata that may offer new horizons for future success in breeding climate resilient crops.
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Affiliation(s)
- Yuanyuan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
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14
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Ortega A, de Marcos A, Illescas-Miranda J, Mena M, Fenoll C. The Tomato Genome Encodes SPCH, MUTE, and FAMA Candidates That Can Replace the Endogenous Functions of Their Arabidopsis Orthologs. FRONTIERS IN PLANT SCIENCE 2019; 10:1300. [PMID: 31736989 PMCID: PMC6828996 DOI: 10.3389/fpls.2019.01300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/18/2019] [Indexed: 05/22/2023]
Abstract
Stomatal abundance determines the maximum potential for gas exchange between the plant and the atmosphere. In Arabidopsis, it is set during organ development through complex genetic networks linking epidermal differentiation programs with environmental response circuits. Three related bHLH transcription factors, SPCH, MUTE, and FAMA, act as positive drivers of stomata differentiation. Mutant alleles of some of these genes sustain different stomatal numbers in the mature organs and have potential to modify plant performance under different environmental conditions. However, knowledge about stomatal genes in dicotyledoneous crops is scarce. In this work, we identified the Solanum lycopersicum putative orthologs of these three master regulators and assessed their functional orthology by their ability to complement Arabidopsis loss-of-function mutants, the epidermal phenotypes elicited by their conditional overexpression, and the expression patterns of their promoter regions in Arabidopsis. Our results indicate that the tomato proteins are functionally equivalent to their Arabidopsis counterparts and that the tomato putative promoter regions display temporal and spatial expression domains similar to those reported for the Arabidopsis genes. In vivo tracking of tomato stomatal lineages in developing cotyledons revealed cell division and differentiation histories similar to those of Arabidopsis. Interestingly, the S. lycopersicum genome harbors a FAMA-like gene, expressed in leaves but functionally distinct from the true FAMA orthologue. Thus, the basic program for stomatal development in S. lycopersicum uses key conserved genetic determinants. This opens the possibility of modifying stomatal abundance in tomato through previously tested Arabidopsis alleles conferring altered stomata abundance phenotypes that correlate with physiological traits related to water status, leaf cooling, or photosynthesis.
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Affiliation(s)
| | | | | | - Montaña Mena
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, Toledo, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, Toledo, Spain
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15
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Wu Z, Chen L, Yu Q, Zhou W, Gou X, Li J, Hou S. Multiple transcriptional factors control stomata development in rice. THE NEW PHYTOLOGIST 2019; 223:220-232. [PMID: 30825332 DOI: 10.1111/nph.15766] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/23/2019] [Indexed: 05/07/2023]
Abstract
Grass stomata can balance gas exchange and evaporation effectively in rapidly changing environments via their unique anatomical features. Although the key components of stomatal development in Arabidopsis have been largely elucidated over the past decade, the molecular mechanisms that govern stomatal development in grasses are poorly understood. Via the genome editing system and T-DNA insertion lines, the key transcriptional factors (TFs) regulating stomatal development in rice (Oryza sativa) were knocked out. A combination of genetic and biochemical assays subsequently revealed the functions of these TFs. OsSPCH/OsICE is essential for the initiation of stomatal lineage. OsMUTE/OsICE determines meristemoid to guard mother cell (GMC) transition. OsFAMA/OsICE influences subsidiary mother cell asymmetric division and mature stoma differentiation. OsFLP regulates the orientation of GMC symmetrical division. More importantly, we found that OsSCR/OsSHR controls the initiation of stomatal lineage cells and the formation of subsidiary cells. The transcription of OsSCR is activated by OsSPCH and OsMUTE. This study characterised the functions of master regulatory TFs that control each stomatal developmental stage in rice. Our findings are helpful for elucidating how various species reprogramme the molecular mechanisms to generate different stomatal types during evolution.
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Affiliation(s)
- Zhongliang Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Liang Chen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qi Yu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenqi Zhou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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16
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McCabe CE, Cianzio SR, O'Rourke JA, Graham MA. Leveraging RNA-Seq to Characterize Resistance to Brown Stem Rot and the Rbs3 Locus in Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1083-1094. [PMID: 30004290 DOI: 10.1094/mpmi-01-18-0009-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Brown stem rot, caused by the fungus Phialophora gregata, reduces soybean yield by up to 38%. Although three dominant resistance loci have been identified (Rbs1 to Rbs3), the gene networks responsible for pathogen recognition and defense remain unknown. Further, identification and characterization of resistant and susceptible germplasm remains difficult. We conducted RNA-Seq of infected and mock-infected leaf, stem, and root tissues of a resistant (PI 437970, Rbs3) and susceptible (Corsoy 79) genotype. Combining historical mapping data with genotype expression differences allowed us to identify a cluster of receptor-like proteins that are candidates for the Rbs3 resistance gene. Reads mapping to the Rbs3 locus were used to identify potential novel single-nucleotide polymorphisms within candidate genes that could improve phenotyping and breeding efficiency. Comparing responses to infection revealed little overlap in differential gene expression between genotypes or tissues. Gene networks associated with defense, DNA replication, and iron homeostasis are hallmarks of resistance to P. gregata. This novel research demonstrates the utility of combining contrasting genotypes, gene expression, and classical genetic studies to characterize complex disease resistance loci.
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Affiliation(s)
- Chantal E McCabe
- 1 United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-1010, U.S.A. and Department of Agronomy, Iowa State University, Ames; and
| | | | - Jamie A O'Rourke
- 1 United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-1010, U.S.A. and Department of Agronomy, Iowa State University, Ames; and
| | - Michelle A Graham
- 1 United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-1010, U.S.A. and Department of Agronomy, Iowa State University, Ames; and
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17
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Wu YF, Zhao Y, Liu XY, Gao S, Cheng AX, Lou HX. A bHLH Transcription Factor Regulates Bisbibenzyl Biosynthesis in the Liverwort Plagiochasma appendiculatum. PLANT & CELL PHYSIOLOGY 2018. [PMID: 29528434 DOI: 10.1093/pcp/pcy053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Liverworts, a section of the bryophyte plants which pioneered the colonization of terrestrial habitats, produce cyclic bisbibenzyls as secondary metabolites. These compounds are generated via the phenylpropanoid pathway, similar to flavonoid biosynthesis, for which basic helix-loop-helix (bHLH) transcription factors have been identified as one of the important regulators in higher plants. Here, a bHLH gene homolog (PabHLH) was isolated from the liverwort species Plagiochasma appendiculatum and its contribution to bisbibenzyl biosynthesis was explored. Variation in the abundance of PabHLH transcript mirrored that of tissue bisbibenzyl content in three different liverwort tissues. A phylogenetic analysis based on the bHLH domain sequence suggested that the gene encodes a member of bHLH subgroup IIIf, which clusters proteins involved in flavonoid synthesis. The gene's transient expression in onion epidermal cells implied that its product localized to the nucleus, and a transactivation assays in yeast showed that it was able to activate transcription. In both callus and thallus, the overexpression of PabHLH boosted bisbibenzyl accumulation, while also up-regulating PaPAL, Pa4CL1, PaSTCS1 and two genes encoding P450 cytochromes, and its RNA interference (RNAi)-induced suppression down-regulated the same set of genes and reduced the accumulation of bisbibenzyls. The abundance of PaCHS and PaFNSI transcript was related to flavonoid accumulation in transgenic thallus. PabHLH represents a candidate for the metabolic engineering of bisbibenzyl content.
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Affiliation(s)
- Yi-Feng Wu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Yu Zhao
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Xin-Yan Liu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Shuai Gao
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
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18
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Sepiol CJ, Yu J, Dhaubhadel S. Genome-Wide Identification of Chalcone Reductase Gene Family in Soybean: Insight into Root-Specific GmCHRs and Phytophthora sojae Resistance. FRONTIERS IN PLANT SCIENCE 2017; 8:2073. [PMID: 29270182 PMCID: PMC5725808 DOI: 10.3389/fpls.2017.02073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/20/2017] [Indexed: 05/02/2023]
Abstract
Soybean (Glycine max [L.] Merr) is one of the main grain legumes worldwide. Soybean farmers lose billions of dollars' worth of yield annually due to root and stem rot disease caused by the oomycete Phytophthora sojae. Many strategies have been developed to combat the disease, however, these methods have proven ineffective in the long term. A more cost effective and durable approach is to select a trait naturally found in soybean that can increase resistance. One such trait is the increased production of phytoalexin glyceollins in soybean. Glyceollins are isoflavonoids, synthesized via the legume-specific branch of general phenylpropanoid pathway. The first key enzyme exclusively involved in glyceollin synthesis is chalcone reductase (CHR) which coacts with chalcone synthase for the production of isoliquiritigenin, the precursor for glyceollin biosynthesis. Here we report the identification of 14 putative CHR genes in soybean where 11 of them are predicted to be functional. Our results show that GmCHRs display tissue-specific gene expression, and that only root-specific GmCHRs are induced upon P. sojae infection. Among 4 root-specific GmCHRs, GmCHR2A is located near a QTL that is linked to P. sojae resistance suggesting GmCHR2A as a novel locus for partial resistance that can be utilized for resistance breeding.
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Affiliation(s)
- Caroline J. Sepiol
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Jaeju Yu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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19
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Redekar N, Pilot G, Raboy V, Li S, Saghai Maroof MA. Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2017; 8:2029. [PMID: 29250090 PMCID: PMC5714895 DOI: 10.3389/fpls.2017.02029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/14/2017] [Indexed: 05/26/2023]
Abstract
A dominant loss of function mutation in myo-inositol phosphate synthase (MIPS) gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified a set of putative candidate transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling, and seed dormancy. We evaluated the performance of our unsupervised network inference method by comparing the predicted regulatory network with published regulatory interactions in Arabidopsis. Some contrasting regulatory interactions were observed in low phytic acid mutants compared to non-mutant lines. These findings provide important hypotheses on expression regulation of myo-inositol metabolism and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at https://lilabatvt.github.io/LPANetwork/.
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Affiliation(s)
- Neelam Redekar
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Guillaume Pilot
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States
| | - Victor Raboy
- National Small Grains Germplasm Research Center, Agricultural Research Service (USDA), Aberdeen, ID, United States
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - M. A. Saghai Maroof
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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20
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Lin JY, Le BH, Chen M, Henry KF, Hur J, Hsieh TF, Chen PY, Pelletier JM, Pellegrini M, Fischer RL, Harada JJ, Goldberg RB. Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc Natl Acad Sci U S A 2017; 114:E9730-E9739. [PMID: 29078418 PMCID: PMC5692608 DOI: 10.1073/pnas.1716758114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar methylation patterns, whether the genes are active or repressed. Our results suggest that methylation does not play a significant role in regulating large numbers of genes important for programming seed development in both soybean and Arabidopsis. We conclude that understanding the mechanisms controlling seed development will require determining how cis-regulatory elements and their cognate transcription factors are organized in genetic regulatory networks.
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Affiliation(s)
- Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Jungim Hur
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pao-Yang Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Julie M Pelletier
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, CA 95616
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - John J Harada
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, CA 95616
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
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21
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An YQC, Goettel W, Han Q, Bartels A, Liu Z, Xiao W. Dynamic Changes of Genome-Wide DNA Methylation during Soybean Seed Development. Sci Rep 2017; 7:12263. [PMID: 28947812 PMCID: PMC5613027 DOI: 10.1038/s41598-017-12510-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023] Open
Abstract
Seed development is programmed by expression of many genes in plants. Seed maturation is an important developmental process to soybean seed quality and yield. DNA methylation is a major epigenetic modification regulating gene expression. However, little is known about the dynamic nature of DNA methylation and its effects on gene expression during plant development. Through whole-genome bisulfite sequencing, we showed that DNA methylation went through dynamic changes during seed maturation. An average of 66% CG, 45% CHG and 9% CHH contexts was methylated in cotyledons. CHH methylation levels in cotyledons changed greatly from 6% at the early stage to 11% at the late stage. Transcribed genes were approximately two-fold more likely to be differentially methylated than non-transcribed genes. We identified 40, 66 and 2136 genes containing differentially methylated regions (DMRs) with negative correlation between their expression and methylation in the CG, CHG and CHH contexts, respectively. The majority of the DMR genes in the CHH context were transcriptionally down-regulated as seeds mature: 99% of them during early maturation were down-regulated, and preferentially associated with DNA replication and cell division. The results provide novel insights into the dynamic nature of DNA methylation and its relationship with gene regulation in seed development.
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Affiliation(s)
- Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
| | - Wolfgang Goettel
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA
| | - Zongrang Liu
- US Department of Agriculture, Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.
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22
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Zhang Y, Li X, Yang S, Feng X. Identification of ZOUPI Orthologs in Soybean Potentially Involved in Endosperm Breakdown and Embryogenic Development. FRONTIERS IN PLANT SCIENCE 2017; 8:139. [PMID: 28228767 PMCID: PMC5296293 DOI: 10.3389/fpls.2017.00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/23/2017] [Indexed: 05/18/2023]
Abstract
Soybean (Glycine max Merr.) is the world's most widely grown legume and provides an important source of protein and oil. Improvement of seed quality requires deep insights into the genetic regulation of seed development. The endosperm serves as a temporary source of nutrients that are transported from maternal to filial tissues, and it also generates signals for proper embryo formation. Endosperm cell death is associated with the processes of nutrient transfer and embryo expansion. The bHLH domain transcription factor AtZHOUPI (AtZOU) plays a key role in both the lysis of the transient endosperm and the formation of embryo cuticle in Arabidopsis thaliana. There are two copies of soybean GmZOU (GmZOU-1 and GmZOU-2), which fall into the same phylogenetic clade as AtZOU. These two copies share the same transcription orientation and are the result of tandem duplication. The expression of GmZOUs is limited to the endosperm, where it peaks during the heart embryo stage. When the exogenous GmZOU-1 and GmZOU-2 were expressed in the zou-4 mutant of Arabidopsis, only GmZOU-1 partially complemented the zou mutant phenotype, as indicated by endosperm breakdown and embryo cuticle formation in the transgenic lines. This research confirmed that the GmZOU-1 is a ZOU ortholog that may be responsible for endosperm breakdown and embryo cuticle formation in soybean.
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Affiliation(s)
| | | | - Suxin Yang
- *Correspondence: Suxin Yang, Xianzhong Feng,
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23
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de Marcos A, Triviño M, Fenoll C, Mena M. Too many faces for TOO MANY MOUTHS? THE NEW PHYTOLOGIST 2016; 210:779-785. [PMID: 26742543 DOI: 10.1111/nph.13827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Alberto de Marcos
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, 45071, Toledo, Spain
| | - Magdalena Triviño
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, 45071, Toledo, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, 45071, Toledo, Spain
| | - Montaña Mena
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-la Mancha, 45071, Toledo, Spain
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