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Su Y, Fang J, Zeeshan Ul Haq M, Yang W, Yu J, Yang D, Liu Y, Wu Y. Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Peanut ( Arachis hypogea L.) Revealed Its Crucial Role in Growth and Multiple Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2077. [PMID: 39124195 PMCID: PMC11313903 DOI: 10.3390/plants13152077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Casparian strip membrane domain proteins (CASPs), regulating the formation of Casparian strips in plants, serve crucial functions in facilitating plant growth, development, and resilience to abiotic stress. However, little research has focused on the characteristics and functions of AhCASPs in cultivated peanuts. In this study, the genome-wide identification and expression analysis of the AhCASPs gene family was performed using bioinformatics and transcriptome data. Results showed that a total of 80 AhCASPs members on 20 chromosomes were identified and divided into three subclusters, which mainly localized to the cell membrane. Ka/Ks analysis revealed that most of the genes underwent purifying selection. Analysis of cis elements suggested the possible involvement of AhCASPs in hormonal and stress responses, including GA, MeJA, IAA, ABA, drought, and low temperature. Moreover, 20 different miRNAs for 37 different AhCASPs genes were identified by the psRNATarget service. Likewise, transcriptional analysis revealed key AhCASPs responding to various stresses, hormonal processing, and tissue types, including 33 genes in low temperature and drought stress and 41 genes in tissue-specific expression. These results provide an important theoretical basis for the functions of AhCASPs in growth, development, and multiple stress resistance in cultivated peanuts.
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Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jieyun Fang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Wanli Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Hainan University, Haikou 570228, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
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Newman TE, Jacques S, Grime C, Mobegi FM, Kamphuis FL, Khentry Y, Lee R, Kamphuis LG. Genetic dissection of domestication traits in interspecific chickpea populations. THE PLANT GENOME 2024; 17:e20408. [PMID: 37961823 DOI: 10.1002/tpg2.20408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
Chickpea (Cicer arietinum) is a pulse crop that provides an integral source of nutrition for human consumption. The close wild relatives Cicer reticulatum and Cicer echinospermum harbor untapped genetic diversity that can be exploited by chickpea breeders to improve domestic varieties. Knowledge of genomic loci that control important chickpea domestication traits will expedite the development of improved chickpea varieties derived from interspecific crosses. Therefore, we set out to identify genomic loci underlying key chickpea domestication traits by both association and quantitative trait locus (QTL) mapping using interspecific F2 populations. Diverse phenotypes were recorded for various agronomic traits. A total of 11 high-confidence markers were detected on chromosomes 1, 3, and 7 by both association and QTL mapping; these were associated with growth habit, flowering time, and seed traits. Furthermore, we identified candidate genes linked to these markers, which advanced our understanding of the genetic basis of domestication traits and validated known genes such as the FLOWERING LOCUS gene cluster that regulates flowering time. Collectively, this study has elucidated the genetic basis of chickpea domestication traits, which can facilitate the development of superior chickpea varieties.
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Affiliation(s)
- Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Christy Grime
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fredrick M Mobegi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fiona L Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Robert Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia
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Su Y, Zeeshan Ul Haq M, Liu X, Li Y, Yu J, Yang D, Wu Y, Liu Y. A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles. PLANTS (BASEL, SWITZERLAND) 2023; 12:3901. [PMID: 38005798 PMCID: PMC10675793 DOI: 10.3390/plants12223901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Casparian strip membrane domain protein-like (CASPL) genes are key genes for the formation and regulation of the Casparian strip and play an important role in plant abiotic stress. However, little research has focused on the members, characteristics, and biological functions of the patchouli PatCASPL gene family. In this study, 156 PatCASPL genes were identified at the whole-genome level. Subcellular localization predicted that 75.6% of PatCASPL proteins reside on the cell membrane. A phylogenetic analysis categorized PatCASPL genes into five subclusters alongside Arabidopsis CASPL genes. In a cis-acting element analysis, a total of 16 different cis-elements were identified, among which the photo-responsive element was the most common in the CASPL gene family. A transcriptome analysis showed that p-hydroxybenzoic acid, an allelopathic autotoxic substance, affected the expression pattern of PatCASPLs, including a total of 27 upregulated genes and 30 down-regulated genes, suggesting that these PatCASPLs may play an important role in the regulation of patchouli continuous cropping obstacles by affecting the formation and integrity of Casparian strip bands. These results provided a theoretical basis for exploring and verifying the function of the patchouli PatCASPL gene family and its role in continuous cropping obstacles.
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Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Xiaofeng Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yang Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
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Kozyulina PY, Pavlova OA, Kantsurova (Rudaya) ES, Bovin AD, Shirobokova SA, Dolgikh AV, Dymo AM, Dolgikh EA. Transcriptomic analysis of pea plant responses to chitooligosaccharides' treatment revealed stimulation of mitogen-activated protein kinase cascade. FRONTIERS IN PLANT SCIENCE 2023; 14:1092013. [PMID: 36968377 PMCID: PMC10030943 DOI: 10.3389/fpls.2023.1092013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Since chitooligosaccharides (COs) are water-soluble, biodegradable and nontoxic compounds, their application may be considered as a promising plant-protecting agent. However, the molecular and cellular modes of action of COs are not yet understood. In this study, transcriptional changes in pea roots treated with COs were investigated via RNA sequencing. Pea roots treated with the deacetylated CO8-DA at low concentration (10-5 М) were harvested 24 h after treatment and their expression profiles were compared against medium-treated control plants. We observed 886 differentially expressed genes (fold change ≥ 1; p-value < 0.05) 24 h after treatment with CO8-DA. Gene Ontology term over-representation analysis allowed us to identify the molecular functions of the genes activated in response to CO8-DA treatment and their relation to biological processes. Our findings suggest that calcium signaling regulators and MAPK cascade play a key role in pea plant responses to treatment. Here we found two MAPKKKs, the PsMAPKKK5 and PsMAPKKK20, which might function redundantly in the CO8-DA-activated signaling pathway. In accordance with this suggestion, we showed that PsMAPKKK knockdown decreases resistance to pathogenic Fusarium culmorum fungi. Therefore, analysis showed that typical regulators of intracellular signal transduction pathways involved in triggering of plant responses via CERK1 receptors to chitin/COs in Arabidopsis and rice may also be recruited in legume pea plants.
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Yang X, Xie H, Weng Q, Liang K, Zheng X, Guo Y, Sun X. Rice OsCASP1 orchestrates Casparian strip formation and suberin deposition in small lateral roots to maintain nutrient homeostasis. FRONTIERS IN PLANT SCIENCE 2022; 13:1007300. [PMID: 36600916 PMCID: PMC9807177 DOI: 10.3389/fpls.2022.1007300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis Casparian strip membrane domain proteins (CASPs) form a transmembrane scaffold to recruit lignin biosynthetic enzymes for Casparian strip (CS) formation. Rice is a semi-aquatic plant with a more complex root structure than Arabidopsis to adapt its growing conditions, where the different deposition of lignin and suberin is crucial for adaptive responses. Here, we observed the structure of rice primary and small lateral roots (SLRs), particularly the deposition patterns of lignin and suberin in wild type and Oscasp1 mutants. We found that the appearance time and structure of CS in the roots of rice are different from those of Arabidopsis and observed suberin deposition in the sclerenchyma in wild type roots. Rice CASP1 is highly similar to AtCASPs, but its expression is concentrated in SLR tips and can be induced by salt stress especially in the steles. The loss of OsCASP1 function alters the expression of the genes involved in suberin biosynthesis and the deposition of suberin in the endodermis and sclerenchyma and leads to delayed CS formation and uneven lignin deposition in SLRs. These different depositions may alter nutrient uptake, resulting in ion imbalance in plant, withered leaves, fewer tillers, and reduced tolerance to salt stress. Our findings suggest that OsCASP1 could play an important role in nutrient homeostasis and adaptation to the growth environment.
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Li L, Zang X, Liu J, Ren J, Wang Z, Yang D. Integrated physiological and weighted gene co-expression network analysis reveals the hub genes engaged in nitrate-regulated alleviation of ammonium toxicity at the seedling stage in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1012966. [PMID: 36466221 PMCID: PMC9713819 DOI: 10.3389/fpls.2022.1012966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Wheat has a specific preference for NO3 - and shows toxicity symptoms under high NH4 + concentrations. Increasing the nitrate supply may alleviate ammonium stress. Nevertheless, the mechanisms underlying the nitrate regulation of wheat root growth to alleviate ammonium toxicity remain unclear. In this study, we integrated physiological and weighted gene co-expression network analysis (WGCNA) to identify the hub genes involved in nitrate alleviation of ammonium toxicity at the wheat seedling stage. Five NH4 +/NO3 - ratio treatments, including 100/0 (Na), 75/25 (Nr1), 50/50 (Nr2), 25/75 (Nr3), and 0/100 (Nn) were tested in this study. The results showed that sole ammonium treatment (Na) increased the lateral root number but reduced root biomass. Increasing the nitrate supply significantly increased the root biomass. Increasing nitrate levels decreased abscisic acid (ABA) content and increased auxin (IAA) content. Furthermore, we identified two modules (blue and turquoise) using transcriptome data that were significantly related to root physiological growth indicators. TraesCS6A02G178000 and TraesCS2B02G056300 were identified as hub genes in the two modules which coded for plastidic ATP/ADP-transporter and WRKY62 transcription factors, respectively. Additionally, network analysis showed that in the blue module, TraesCS6A02G178000 interacts with downregulated genes that coded for indolin-2-one monooxygenase, SRG1, DETOXIFICATION, and wall-associated receptor kinase. In the turquoise module, TraesCS2B02G056300 was highly related to the genes that encoded ERD4, ERF109, CIGR2, and WD40 proteins, and transcription factors including WRKY24, WRKY22, MYB30, and JAMYB, which were all upregulated by increasing nitrate supply. These studies suggest that increasing the nitrate supply could improve root growth and alleviate ammonium toxicity through physiological and molecular regulation networks, including ROS, hormonal crosstalk, and transcription factors.
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Cao D, Wang D, Li S, Li Y, Hao M, Liu B. Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1705-1715. [PMID: 35244733 DOI: 10.1007/s00122-022-04064-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The genetic diversity and loci underlying agronomic traits were analyzed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions. Triticale (× Triticosecale Wittmack) is an economically important grain forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.
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Affiliation(s)
- Dong Cao
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Dongxia Wang
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, Xining, 810016, People's Republic of China
| | - Shiming Li
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China
| | - Yun Li
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
| | - Baolong Liu
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China.
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People's Republic of China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Li X, Hu H, Hu X, Wang G, Du X, Li L, Wang F, Fu J, Wang G, Wang J, Gu R. Transcriptome Analysis of Near-Isogenic Lines Provides Novel Insights into Genes Associated with Seed Low-Temperature Germination Ability in Maize ( Zea mays L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070887. [PMID: 35406867 PMCID: PMC9002958 DOI: 10.3390/plants11070887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/13/2022] [Accepted: 03/22/2022] [Indexed: 05/14/2023]
Abstract
Maize originated from tropical regions and is extremely sensitive to low temperature during germination. Our previous work identified a major QTL, qp1ER1-1, for low temperature germination ability (LTGA) of maize. Here, we introgressed qp1ER1-1 from the tolerant line L220 into the sensitive line PH4CV to generate two near isogenic lines NIL220-3 and NIL220-25. When germinated under cold temperature for 25 days (Cold-25), the NILs showed similar seedling root length and shoot length to L220, but significantly higher than PH4CV. However, when germinated under cold temperature for 15 days (Cold-15) or under normal temperature (25 °C) for 3 days (CK-3), all lines showed similar seedling performance, indicating that introgression of qp1ER1-1 from L220 into PH4CV could improve LTGA of NIL220-3 and NIL220-25. The whole seedlings, including root and shoot, of Cold-15 and CK-3 were harvested for transcriptome analysis, when both stayed at a similar developmental stage. Dry seed embryo was sequenced as a non-germination control (CK-0). Compared with PH4CV, the tolerant line (L220, NIL220-3, and NIL220-25) specifically expressed genes (different expressed genes, DEGs) were identified for CK-0, Cold-15, and CK-3. Then, DEGs identified from Cold-15, but not from CK-0 or CK-3, were defined as tolerant line specifically expressed LTGA genes. Finally, 1786, 174, and 133 DEGs were identified as L220, NIL220-3, and NIL220-25 specifically expressed LTGA genes, respectively. Of them, 27 were common LTGA genes that could be identified from all three tolerant lines, with two (Zm00001d031209 and Zm00001d031292) locating in the confidence interval of qp1ER1-1. In addition, GO analysis revealed that L220 specifically expressed LTGA genes were majorly enriched in the cell division process and plasma membrane related categories. Taken together, these results provided new insight into the molecular mechanism of maize seed LTGA and facilitated the cloning of the qp1ER1-1 gene.
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Affiliation(s)
- Xuhui Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou 510316, China
| | - Hairui Hu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
| | - Xinmin Hu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
| | - Guihua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
| | - Li Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
| | - Feng Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.F.); (G.W.)
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.F.); (G.W.)
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
- Correspondence: (J.W.); (R.G.)
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (X.L.); (H.H.); (X.H.); (G.W.); (X.D.); (L.L.); (F.W.)
- Correspondence: (J.W.); (R.G.)
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Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, Karimi M, Soorni A. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 2021; 22:704. [PMID: 34587906 PMCID: PMC8482690 DOI: 10.1186/s12864-021-07989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07989-1.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Marzieh Karimi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, Shahrekord, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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Boher P, Soler M, Fernández-Piñán S, Torrent X, Müller SY, Kelly KA, Serra O, Figueras M. Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress. BMC PLANT BIOLOGY 2021; 21:409. [PMID: 34493224 PMCID: PMC8424952 DOI: 10.1186/s12870-021-03141-z] [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: 01/21/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. RESULTS To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue. CONCLUSIONS The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.
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Affiliation(s)
- Pau Boher
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Marçal Soler
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sandra Fernández-Piñán
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Xènia Torrent
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sebastian Y. Müller
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Olga Serra
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Mercè Figueras
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
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11
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Huang WX, Zhang DM, Cao YQ, Dang BJ, Jia W, Xu ZC, Han D. Differential cadmium translocation and accumulation between Nicotiana tabacum L. and Nicotiana rustica L. by transcriptome combined with chemical form analyses. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111412. [PMID: 33039872 DOI: 10.1016/j.ecoenv.2020.111412] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 05/17/2023]
Abstract
Cadmium (Cd) is a severely toxic and carcinogenic heavy metal. Cigarette smoking is one of the major source of Cd exposure in humans. Nicotiana tabacum is primarily a leaf Cd accumulator, while Nicotiana rustica is a root Cd accumulator among Nicotiana species. However, little is known about the mechanisms of differential Cd translocation and accumulation in Nicotiana. To find the key factors, Cd concentration, Cd chemical forms, and transcriptome analysis were comparatively studied between N. tabacum and N. rustica under control or 10 μM Cd stress. The leaf/root Cd concentration ratio of N. tabacum was 2.26 and that of N. rustica was 0.14. The Cd concentration in xylem sap of N. tabacum was significantly higher than that of N. rustica. The root of N. tabacum had obviously higher proportion of ethanol extractable Cd (40%) and water extractable Cd (16%) than those of N. rustica (16% and 6%). Meanwhile the proportion of sodium chloride extracted Cd in N. rustica (71%) was significantly higher than that in N. tabacum (30%). A total of 30710 genes expressed differentially between the two species at control, while this value was 30,294 under Cd stress, among which 27,018 were collective genes, manifesting the two species existed enormous genetic differences. KEGG pathway analysis showed the phenylpropanoid biosynthesis pathway was overrepresented between the two species under Cd stress. Several genes associated with pectin methylesterase, suberin and lignin synthesis, and heavy metal transport were discovered to be differential expressed genes between two species. The results suggested that the higher accumulation of Cd in the leaf of N. tabacum depends on a comprehensive coordination of Cd transport, including less cell wall binding, weaker impediment by the Casparian strip, and efficient xylem loading.
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Affiliation(s)
- Wu-Xing Huang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Duo-Min Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Yu-Qiao Cao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Bing-Jun Dang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Wei Jia
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Zi-Cheng Xu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Dan Han
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China.
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12
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Sapkota S, Boatwright JL, Jordan K, Boyles R, Kresovich S. Identification of Novel Genomic Associations and Gene Candidates for Grain Starch Content in Sorghum. Genes (Basel) 2020; 11:E1448. [PMID: 33276449 PMCID: PMC7760202 DOI: 10.3390/genes11121448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.
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Affiliation(s)
- Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - J. Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Kathleen Jordan
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
| | - Richard Boyles
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
- Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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13
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Ghaemi R, Pourjam E, Safaie N, Verstraeten B, Mahmoudi SB, Mehrabi R, De Meyer T, Kyndt T. Molecular insights into the compatible and incompatible interactions between sugar beet and the beet cyst nematode. BMC PLANT BIOLOGY 2020; 20:483. [PMID: 33092522 PMCID: PMC7583174 DOI: 10.1186/s12870-020-02706-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 10/18/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Sugar beet (Beta vulgaris subsp. vulgaris) is an economically important crop that provides nearly one third of the global sugar production. The beet cyst nematode (BCN), Heterodera schachtii, causes major yield losses in sugar beet and other crops worldwide. The most effective and economic approach to control this nematode is growing tolerant or resistant cultivars. To identify candidate genes involved in susceptibility and resistance, the transcriptome of sugar beet and BCN in compatible and incompatible interactions at two time points was studied using mRNA-seq. RESULTS In the susceptible cultivar, most defense-related genes were induced at 4 dai while suppressed at 10 dai but in the resistant cultivar Nemakill, induction of genes involved in the plant defense response was observed at both time points. In the compatible interaction, alterations in phytohormone-related genes were detected. The effect of exogenous application of Methyl Jasmonate and ET-generator ethephon on susceptible plants was therefore investigated and the results revealed significant reduction in plant susceptibility. Genes putatively involved in the resistance of Nemakill were identified, such as genes involved in phenylpropanoid pathway and genes encoding CYSTM domain-containing proteins, F-box proteins, chitinase, galactono-1,4-lactone dehydrogenase and CASP-like protein. Also, the transcriptome of the BCN was analyzed in infected root samples and several novel potential nematode effector genes were found. CONCLUSIONS Our data provides detailed insights into the plant and nematode transcriptional changes occurring during compatible and incompatible interactions between sugar beet and BCN. Many important genes playing potential roles in susceptibility or resistance of sugar beet against BCN, as well as some BCN effectors with a potential role as avr proteins were identified. In addition, our findings indicate the effective role of jasmonate and ethylene in enhancing sugar beet defense response against BCN. This research provides new molecular insights into the plant-nematode interactions that can be used to design novel management strategies against BCN.
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Affiliation(s)
- Razieh Ghaemi
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ebrahim Pourjam
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Bruno Verstraeten
- Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Seyed Bagher Mahmoudi
- Sugar Beet Seed Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, P.O. Box 8415683111, Isfahan, Iran
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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14
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Wang X, Zhang Y, Wang L, Pan Z, He S, Gao Q, Chen B, Gong W, Du X. Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth. BMC Genomics 2020; 21:340. [PMID: 32366264 PMCID: PMC7199351 DOI: 10.1186/s12864-020-6723-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/06/2020] [Indexed: 11/28/2022] Open
Abstract
Background Root systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) are responsible for the formation of Casparian strips. Results To investigate the function of CASPs in cotton, we identified and characterized 48, 54, 91 and 94 CASPs from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively, at the genome-wide level. However, only 29 common homologous CASP genes were detected in the four Gossypium species. A collinearity analysis revealed that whole genome duplication (WGD) was the primary reason for the expansion of the genes of the CASP family in the four cotton species. However, dispersed duplication could also contribute to the expansion of the GaCASPs gene family in the ancestors of G. arboreum. Phylogenetic analysis was used to cluster a total of 85 CASP genes from G. arboreum and Arabidopsis into six distinct groups, while the genetic structure and motifs of CASPs were conserved in the same group. Most GaCASPs were expressed in diverse tissues, with the exception of that five GaCASPs (Ga08G0113, Ga08G0114, Ga08G0116, Ga08G0117 and Ga08G0118) that were highly expressed in root tissues. Analyses of the tissue and subcellular localization suggested that GaCASP27 genes (Ga08G0117) are membrane protein genes located in the root. In the GaCASP27 silenced plants and the Arabidopsis mutants, the lateral root number significantly increased. Furthermore, GaMYB36, which is related to root development was found to regulate lateral root growth by targeting GaCASP27. Conclusions This study provides a fundamental understanding of the CASP gene family in cotton and demonstrates the regulatory role of GaCASP27 on lateral root growth and development.
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Affiliation(s)
- Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.,Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liyuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiong Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. .,Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Ministry of Education, Changsha, 410004, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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15
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Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. Int J Mol Sci 2019; 21:E3. [PMID: 31861318 PMCID: PMC6982007 DOI: 10.3390/ijms21010003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover, GO enrichment analyses suggest an ongoing gene birth-death-innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes.
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Affiliation(s)
- Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Ana Paula Moraes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo 09606-070, Brazil;
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Maria H. M. Julião
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Douglas S. Domingues
- Departamento de Botânica, Instituto de Biociências, UNESP—Universidade Estadual Paulista, Rio Claro 13506-900, Brazil;
| | | | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
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16
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Lee M, Jeon HS, Kim SH, Chung JH, Roppolo D, Lee H, Cho HJ, Tobimatsu Y, Ralph J, Park OK. Lignin-based barrier restricts pathogens to the infection site and confers resistance in plants. EMBO J 2019; 38:e101948. [PMID: 31559647 PMCID: PMC6885736 DOI: 10.15252/embj.2019101948] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/10/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pathogenic bacteria invade plant tissues and proliferate in the extracellular space. Plants have evolved the immune system to recognize and limit the growth of pathogens. Despite substantial progress in the study of plant immunity, the mechanism by which plants limit pathogen growth remains unclear. Here, we show that lignin accumulates in Arabidopsis leaves in response to incompatible interactions with bacterial pathogens in a manner dependent on Casparian strip membrane domain protein (CASP)-like proteins (CASPLs). CASPs are known to be the organizers of the lignin-based Casparian strip, which functions as a diffusion barrier in roots. The spread of invading avirulent pathogens is prevented by spatial restriction, which is disturbed by defects in lignin deposition. Moreover, the motility of pathogenic bacteria is negatively affected by lignin accumulation. These results suggest that the lignin-deposited structure functions as a physical barrier similar to the Casparian strip, trapping pathogens and thereby terminating their growth.
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Affiliation(s)
| | | | - Seu Ha Kim
- Department of Life SciencesKorea UniversitySeoulKorea
| | | | - Daniele Roppolo
- Institute of Plant SciencesUniversity of BernBernSwitzerland
- Present address:
European Society for Clinical Microbiology and Infectious DiseaseBaselSwitzerland
| | - Hye‐Jung Lee
- Department of Life SciencesKorea UniversitySeoulKorea
| | - Hong Joo Cho
- Department of Life SciencesKorea UniversitySeoulKorea
- Present address:
Cutigen Research InstituteTegoscience Inc.SeoulKorea
| | - Yuki Tobimatsu
- Research Institute for Sustainable HumanosphereKyoto UniversityUjiKyotoJapan
| | - John Ralph
- Department of Biochemistry, and US Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of WisconsinMadisonWIUSA
| | - Ohkmae K Park
- Department of Life SciencesKorea UniversitySeoulKorea
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17
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Pradhan S, Babar MA, Robbins K, Bai G, Mason RE, Khan J, Shahi D, Avci M, Guo J, Maksud Hossain M, Bhatta M, Mergoum M, Asseng S, Amand PS, Gezan S, Baik BK, Blount A, Bernardo A. Understanding the Genetic Basis of Spike Fertility to Improve Grain Number, Harvest Index, and Grain Yield in Wheat Under High Temperature Stress Environments. FRONTIERS IN PLANT SCIENCE 2019; 10:1481. [PMID: 31850009 PMCID: PMC6895025 DOI: 10.3389/fpls.2019.01481] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/25/2019] [Indexed: 05/22/2023]
Abstract
Moderate heat stress accompanied by short episodes of extreme heat during the post-anthesis stage is common in most US wheat growing areas and causes substantial yield losses. Sink strength (grain number) is a key yield limiting factor in modern wheat varieties. Increasing spike fertility (SF) and improving the partitioning of assimilates can optimize sink strength which is essential to improve wheat yield potential under a hot and humid environment. A genome-wide association study (GWAS) allows identification of novel quantitative trait loci (QTLs) associated with SF and other partitioning traits that can assist in marker assisted breeding. In this study, GWAS was performed on a soft wheat association mapping panel (SWAMP) comprised of 236 elite lines using 27,466 single nucleotide polymorphisms (SNPs). The panel was phenotyped in two heat stress locations over 3 years. GWAS identified 109 significant marker-trait associations (MTAs) (p ≤ 9.99 x 10-5) related to eight phenotypic traits including SF (a major component of grain number) and spike harvest index (SHI, a major component of grain weight). MTAs detected on chromosomes 1B, 3A, 3B, and 5A were associated with multiple traits and are potentially important targets for selection. More than half of the significant MTAs (60 out of 109) were found in genes encoding different types of proteins related to metabolism, disease, and abiotic stress including heat stress. These MTAs could be potential targets for further validation study and may be used in marker-assisted breeding for improving wheat grain yield under post-anthesis heat stress conditions. This is the first study to identify novel QTLs associated with SF and SHI which represent the major components of grain number and grain weight, respectively, in wheat.
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Affiliation(s)
- Sumit Pradhan
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Md Ali Babar
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Kelly Robbins
- School of Integrative Plant Science, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | - Richard Esten Mason
- Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Jahangir Khan
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Dipendra Shahi
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Muhsin Avci
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Jia Guo
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | | | - Madhav Bhatta
- Department of Agronomy, University of Wisconsin, Madison, WI, United States
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Senthold Asseng
- Agricultural and Biological Engineering, University of Florida, Gainesville, FL, United States
| | | | - Salvador Gezan
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | | | - Ann Blount
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Amy Bernardo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
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18
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Root hairs enhance Arabidopsis seedling survival upon soil disruption. Sci Rep 2019; 9:11181. [PMID: 31371805 PMCID: PMC6671945 DOI: 10.1038/s41598-019-47733-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/23/2019] [Indexed: 12/18/2022] Open
Abstract
Root hairs form a substantial portion of the root surface area. Compared with their nutritional function, the physical function of root hairs has been poorly characterised. This study investigates the physical role of root hairs of Arabidopsis thaliana seedlings in interaction of the root with water and soil and in plant survival upon soil disruption. Five transgenic lines with different root hair lengths were used to assess the physical function of root hairs. Upon soil disruption by water falling from a height (mimicking rainfall), long-haired lines showed much higher anchorage rates than short-haired lines. The root-pulling test revealed that a greater amount of soil adhered to long-haired roots than to short-haired roots. When seedlings were pulled out and laid on the soil surface for 15 d, survival rates of long-haired seedlings were higher than those of short-haired seedlings. Moreover, the water holding capacity of roots was much greater among long-haired seedlings than short-haired seedlings. These results suggest that root hairs play a significant role in plant survival upon soil disruption which could be fatal for young seedlings growing on thin soil surface with a short primary root and root hairs as the only soil anchoring system.
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19
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Rafique S. Differential expression of leaf proteome of tolerant and susceptible maize ( Zea mays L.) genotypes in response to multiple abiotic stresses. Biochem Cell Biol 2019; 97:581-588. [PMID: 30807207 DOI: 10.1139/bcb-2018-0338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In the present work, tropical maize genotypes were evaluated for multiple stresses (drought × low-N and waterlogging × low-N) applied simultaneously to 30-day-old maize seedlings. Two-dimensional gel electrophoresis was used to examine the protein changes induced by combined stress, in leaves, of tolerant and susceptible genotypes. Moreover, physiological and biochemical parameters were assessed to understand the physiological status of tolerant and susceptible genotypes under combined stress. The results show that up-regulated proteins of the tolerant genotype have a significant role in activating defense response, restoration of plant growth, and to maintain metabolic homeostasis under stressful conditions. Therefore, they contribute to improve and maintain the state of acclimation of the genotype under stress. Alternatively in the susceptible genotype, the up-regulated proteins are representative biomarkers of stress or are involved in the defense against pathogens and efforts to maintain energy metabolism. Thus, protecting the survival of the genotype under multiple stress conditions. We conclude that depending on the given stress treatment, tolerant and susceptible genotypes differed in stress-enduring approaches. Therefore, the study provides insight to comprehend the response of tolerant and susceptible genotypes under combined stress conditions, which could be valuable for further research and will demonstrate that it is advantageous to select combined stress-tolerant genotypes.
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Affiliation(s)
- Suphia Rafique
- Department of Biotechnology, Faculty of Chemicals and Life Sciences, Jamia Hamdard, New Delhi, 110062, India.,Department of Biotechnology, Faculty of Chemicals and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
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Liu W, Cheng C, Chen F, Ni S, Lin Y, Lai Z. High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans). BMC PLANT BIOLOGY 2018; 18:308. [PMID: 30486778 PMCID: PMC6263057 DOI: 10.1186/s12870-018-1483-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/15/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas. RESULT Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana. CONCLUSIONS In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas.
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Affiliation(s)
- Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Chongqing Normal University, Daxuecheng Middle Rd, Chongqing, Shapingba Qu China
| | - Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Fanglan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shanshan Ni
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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The Casparian strip-one ring to bring cell biology to lignification? Curr Opin Biotechnol 2018; 56:121-129. [PMID: 30502636 DOI: 10.1016/j.copbio.2018.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 11/20/2022]
Abstract
Lignin research has long been motivated by the outstanding importance of wood for human societies. The annual, non-woody Arabidopsis thaliana, has nevertheless contributed greatly to our understanding of lignification, due to its unrivalled genetic resources. Arabidopsis is also great for cell and developmental biology, allowing precise imaging and tracking of cell types. Root endodermis differentiation involves the precise lignification of the Casparian Strip, as an apoplastic barrier; while barrier damage triggers a less localized, compensatory lignification. Transcriptional reprogramming and peptide-induced signalling emerge as promising tools for the study of endodermal lignification. We argue that endodermis lignification is an attractive model complementary to equally powerful, cellular xylem differentiation systems, as it might better represent the restricted - often localized - lignification seen in non-vascular cells.
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Man Y, Zhao Y, Ye R, Lin J, Jing Y. In vivo cytological and chemical analysis of Casparian strips using stimulated Raman scattering microscopy. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:136-144. [PMID: 29175545 DOI: 10.1016/j.jplph.2017.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 05/26/2023]
Abstract
The Casparian strip, a barrier to the apoplastic movement of solutes from the cortex to the stele, is essential for the exclusion of salts, selective nutrient uptake, and many other processes. To date, extensive studies have focused on the physiological functions of endodermal Casparian strips. However, the chemical deposition nature of Casparian strips, as well as its relevance with respect to diffusion barrier functions, remains to be further elucidated. Here, we revealed three developmental stages of Casparian strips in maize primary roots using a traditional fluorescent staining method. Apoplastic permeability tests demonstrated that the barrier function of Casparian strips is largely related to their developmental stage and the pattern of lignin and suberin deposits. Fourier transform infrared (FTIR) analysis showed that the Casparian strips from the roots exhibited significant absorption bands characteristic of lignin and suberin, implying that the Casparian strips in maize primary roots consist largely of lignin and suberin. Furthermore, we developed a new method for label-free, in vivo structural, and biochemical analysis of Casparian strips based on stimulated Raman scattering (SRS) microscopy. Using SRS microscopy, we found that lignin and suberin accumulate simultaneously during the Casparian strip formation process. Based on these results, we propose a potential application of SRS for the chemical composition analysis of plant Casparian strips in situ.
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Affiliation(s)
- Yi Man
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuanyuan Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Rong Ye
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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Li P, Yang M, Chang J, Wu J, Zhong F, Rahman A, Qin H, Wu S. Spatial Expression and Functional Analysis of Casparian Strip Regulatory Genes in Endodermis Reveals the Conserved Mechanism in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:832. [PMID: 29988388 PMCID: PMC6024017 DOI: 10.3389/fpls.2018.00832] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/29/2018] [Indexed: 05/20/2023]
Abstract
Casparian strip (CS) is an impregnation of endodermal cell wall, forming an apoplastic diffusion barrier which forces the symplastic and selective transport of nutrients across endodermis. This extracellular structure can be found in the roots of all higher plants and is thought to provide the protection of vascular tissues. In Arabidopsis, a genetic toolbox regulating the formation of Casparian strips has emerged recently. However, Arabidopsis has the stereotypical root which is much simpler than most other plant species. To understand the Casparian strip formation in a more complex root system, we examined CS regulatory pathways in tomato. Our results reveal a spatiotemporally conserved expression pattern of most essential components of CS machinery in tomato. Further functional analyses verify the role of homologous CS genes in the Casparian strip formation in tomato, indicating the functional conservation of CS regulatory cascade in tomato.
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Affiliation(s)
- Pengxue Li
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meina Yang
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiang Chang
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junqing Wu
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fenglin Zhong
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Abidur Rahman
- Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Haiyang Qin
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuang Wu
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Shuang Wu,
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