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Mandal SN, Sanchez J, Bhowmick R, Bello OR, Van-Beek CR, de Los Reyes BG. Novel genes and alleles of the BTB/POZ protein family in Oryza rufipogon. Sci Rep 2023; 13:15466. [PMID: 37726366 PMCID: PMC10509276 DOI: 10.1038/s41598-023-41269-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O. rufipogon as outcomes of tandem duplication events. Phylogenetic grouping of duplicated OrBTB genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The O. rufipogon genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant, O. sativa ssp. japonica. Comparative sequence analysis and structure comparisons of novel OrBTB genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.
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Affiliation(s)
- Swarupa Nanda Mandal
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jacobo Sanchez
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Rakesh Bhowmick
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, 263601, India
| | - Oluwatobi R Bello
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Coenraad R Van-Beek
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
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Tan M, Chen R, Chen X, Shahid MQ, Liu X, Wu J. In Vitro Induction of Interspecific Hybrid and Polyploidy Derived from Oryza officinalis Wall. PLANTS (BASEL, SWITZERLAND) 2023; 12:3001. [PMID: 37631212 PMCID: PMC10459038 DOI: 10.3390/plants12163001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Oryza officinalis Wall is a potential genetic resource for rice breeding; however, its distant genome limits its crossing ability with cultivated rice. The interspecific hybridization of O. officinalis and cultivated rice, establishment of its tissue culture, and induction of polyploidy are ways to improve O. officinalis's poor crossability. We developed an interspecific hybrid and studied its reproductive pollen development process in this work, and the results showed that abortive pollens (81.94%) and embryo sac abnormalities (91.04%) were the key causes of its high sterility. In order to induce callus formation in interspecific hybrid explants, two different culture media, namely Chu's N-6 medium (N6) and 1/2 Murashig and Skoog medium (1/2 MS), were employed. Additionally, two plant growth regulators (PGRs), namely 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BA), along with L-proline (Pro) and acid hydrolyzed casein, were utilized in the experiment. The optimal N6 medium, supplemented with 2.0 mg·L-1 2,4-D, produced the highest induction rate (80.56 ± 5.44)%. For callus differentiation and proliferation, the MS medium supplemented with 2.0 mg·L-1 BA + 0.2 mg·L-1 NAA produced the highest differentiation rate (75.00 ± 4.97)% and seedling emergence ratio (28.97 ± 4.67)%. The optimal combination for seedling rooting was the 1/2 MS medium supplemented with 2.0 mg L-1 NAA and 0.2 mg L-1 BA, which produced an average of 13.95 roots per plant. For polyploidy induction in the interspecific hybrid, the concentration of colchicine treatment at 400 mg·L-1 for three days is an ideal protocol. We devised tissue culture and interspecific hybrid polyploidy induction to overcome O. officinalis' poor crossability and introduce its favorable features into cultivated rice.
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Affiliation(s)
- Meimei Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Ruoxin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xingran Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Tian Q, Gong Y, Liu S, Ji M, Tang R, Kong D, Xue Z, Wang L, Hu F, Huang L, Qin S. Endophytic bacterial communities in wild rice ( Oryza officinalis) and their plant growth-promoting effects on perennial rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1184489. [PMID: 37645460 PMCID: PMC10461003 DOI: 10.3389/fpls.2023.1184489] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. Oryza officinalis is a unique perennial wild rice species in China with rich genetic resources. However, endophytic bacterial communities of this species and their plant growth-promoting (PGP) traits remain largely unknown. In this study, endophytic bacteria in the root, stem, and leaf tissues of O. officinalis were characterized using 16S rRNA gene Illumina sequencing. Culturable bacterial endophytes were also isolated from O. officinalis tissues and characterized for their PGP traits. The microbiome analysis showed a more complex structure and powerful function of the endophytic bacterial community in roots compared with those in other tissue compartments. Each compartment had its specific endophytic bacterial biomarkers, including Desulfomonile and Ruminiclostridium for roots; Lactobacillus, Acinetobacter, Cutibacterium and Dechloromonas for stems; and Stenotrophomonas, Chryseobacterium, Achromobacter and Methylobacterium for leaves. A total of 96 endophytic bacterial strains with PGP traits of phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, and siderophore or indole-3-acetic acid (IAA) production were isolated from O. officinalis. Among them, 11 strains identified as Enterobacter mori, E. ludwigii, E. cloacae, Bacillus amyloliquefaciens, B. siamensis, Pseudomonas rhodesiae and Kosakonia oryzae were selected for inoculation of perennial rice based on their IAA production traits. These strains showed promising PGP effects on perennial rice seedlings. They promoted plants to form a strong root system, stimulate biomass accumulation, and increase chlorophyll content and nitrogen uptake, which could fulfil the ecologically sustainable cultivation model of perennial rice. These results provide insights into the bacterial endosphere of O. officinalis and its application potential in perennial rice. There is the prospect of mining beneficial endophytic bacteria from wild rice species, which could rewild the microbiome of cultivated rice varieties and promote their growth.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fengyi Hu
- Key Laboratory of Biology and Germplasm Innovation of Perennial Rice From Ministry of Agriculture and Rural Affairs, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Liyu Huang
- Key Laboratory of Biology and Germplasm Innovation of Perennial Rice From Ministry of Agriculture and Rural Affairs, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Shiwen Qin
- Key Laboratory of Biology and Germplasm Innovation of Perennial Rice From Ministry of Agriculture and Rural Affairs, School of Agriculture, Yunnan University, Kunming, Yunnan, China
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Huang Y, Li F, Yi J, Yan H, He Z, Li X. Transcriptomic and physio-biochemical features in rice (Oryza sativa L.) in response to mercury stress. CHEMOSPHERE 2022; 309:136612. [PMID: 36179923 DOI: 10.1016/j.chemosphere.2022.136612] [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: 05/24/2022] [Revised: 09/24/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Mercury (Hg) is a toxic and nonessential element for organisms, and its contamination in the environment is a global concern. Previous research has shown that Hg stress may cause severe damage to rice roots; however, the transcriptomic changes in roots and physio-biochemical responses in leaves to different levels of Hg stress are not fully understood. In the present study, rice seedlings were exposed to 20, 80, and 160 μM HgCl2 for three days in hydroponic experiments. The results showed that the majority of Hg was accumulated in rice roots after Hg exposure, and the 80- and 160-μM Hg stresses significantly increased the root-to-shoot translocation factors relative to 20-μM Hg stress, resulting in elevated Hg concentrations in rice shoots. Only the 160-μM Hg stress significantly inhibited root growth compared with the control, while photosynthesis capacity in leaves was significantly reduced under Hg stress. RNA transcriptome sequencing analyses of the roots showed that common responsive differentially expressed genes were strongly associated with glutathione metabolism, amino acid biosynthesis, and secondary metabolite metabolism, which may play significant roles in Hg accumulation by rice plants. Nine crucial genes identified by protein-protein interaction network analysis may be used as candidate target genes for further investigation of the detoxification mechanism, encoding proteins involved in jasmonic acid synthesis, sugar metabolism, allene oxide synthase, glutathione peroxidase, dismutase, and catalase. Furthermore, physio-biochemical analyses of the leaves indicated that higher production of reactive oxygen species was induced by Hg stress, while glutathione and antioxidant enzymes may play crucial roles in Hg detoxification. Our findings provide transcriptomic and physio-biochemical features of rice roots and shoots, which advance our understanding of the responsive and detoxification mechanisms in rice under different levels of Hg stress.
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Affiliation(s)
- Yingmei Huang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Jicai Yi
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huili Yan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhenyan He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, China.
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Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC PLANT BIOLOGY 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
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Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
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Sanchez J, Kaur PP, Pabuayon ICM, Karampudi NBR, Kitazumi A, Sandhu N, Catolos M, Kumar A, de Los Reyes BG. DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds. THE PLANT GENOME 2022; 15:e20168. [PMID: 34806842 DOI: 10.1002/tpg2.20168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.
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Affiliation(s)
- Jacobo Sanchez
- Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, USA
| | | | | | | | - Ai Kitazumi
- Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, USA
| | - Nitika Sandhu
- International Rice Research Institute, Los Banos, Philippines
- Current address: School of Agricultural Biotechnology, Punjab Agricultural Univ., Ludhiana, India
| | | | - Arvind Kumar
- International Rice Research Institute, Los Banos, Philippines
- Current address: International Crops Research Institute for the Semi-Arid Tropics, Petancheru, India
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Yang J, Wu Y, Li L, Li C. Comprehensive analysis of the BES1 gene family and its expression under abiotic stress and hormone treatment in Populus trichocarpa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 173:1-13. [PMID: 35085861 DOI: 10.1016/j.plaphy.2022.01.019] [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: 10/28/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The BRI1 EMS SUPPRESSOR 1/BRASSINAZOLE RESISTANT 1 (BES1/BZR1) plays a vital role in plant growth and development and stress responses, but there are few studies on poplar BES1 genes. In this study, we identified 14 BES1 genes in the Populus trichocarpa genome and analyzed the expression under hormone treatment and abiotic stress. The PtrBES1 genes were classified into seven subgroups (I-VII) through phylogenetic analysis. All the paralogous gene pairs were shown to be subjected to expansion by segment duplication and purification selection during the PtrBES1 family evolution. Promoter cis-element analysis showed that the PtrBES1 promoter contains stress related cis-elements including ABRE-motif, MBS and TC-rich elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the PtrBES1 genes were upregulated upon NaCl, Polyethylene glycol 6000 (PEG6000) stress as well as the major stress hormone abscisic acid (ABA) treatment. Under the three treatments, PtrBES1-7 showed high expression levels in leaves and roots. Physiological experiments showed that the overexpression PtrBES1-7 line could enhance tolerance to drought stress in P. trichocarpa by improving the ability to scavenge ROS (reactive oxygen species). This is specifically reflected in the fact that the overexpression line contains less ROS (O2- and H2O2) and more antioxidant enzymes (1.42 times SOD and 1.5 times POD) than the control line. The preliminary results of this study provided a solid basis for the future functional studies of the BES1 gene family in P. trichocarpa.
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Affiliation(s)
- Jia Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Ye Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Lu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation. PLoS One 2021; 16:e0256324. [PMID: 34710139 PMCID: PMC8553054 DOI: 10.1371/journal.pone.0256324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022] Open
Abstract
Because of the continuous rise of foodborne illnesses caused by the consumption of raw fruits and vegetables, effective post-harvest anti-microbial strategies are necessary. The aim of this study was to evaluate the anti-microbial efficacy of ozone (O3) against two common causes of fresh produce contamination, the Gram-negative Escherichia coli O157:H7 and Gram-positive Listeria monocytogenes, and to relate its effects to potential mechanisms of xenobiosis by transcriptional network modeling. The study on non-host tomato environment correlated the dose × time aspects of xenobiosis by examining the correlation between bacterial survival in terms of log-reduction and defense responses at the level of gene expression. In E. coli, low (1 μg O3/g of fruit) and moderate (2 μg O3/g of fruit) doses caused insignificant reduction in survival, while high dose (3 μg/g of fruit) caused significant reduction in survival in a time-dependent manner. In L. monocytogenes, moderate dose caused significant reduction even with short-duration exposure. Distinct responses to O3 xenobiosis between E. coli and L. monocytogenes are likely related to differences in membrane and cytoplasmic structure and components. Transcriptome profiling by RNA-Seq showed that primary defenses in E. coli were attenuated after exposure to a low dose, while the responses at moderate dose were characterized by massive upregulation of pathogenesis and stress-related genes, which implied the activation of defense responses. More genes were downregulated during the first hour at high dose, with a large number of such genes getting significantly upregulated after 2 hr and 3 hr. This trend suggests that prolonged exposure led to potential adaptation. In contrast, massive downregulation of genes was observed in L. monocytogenes regardless of dose and exposure duration, implying a mechanism of defense distinct from that of E. coli. The nature of bacterial responses revealed by this study should guide the selection of xenobiotic agents for eliminating bacterial contamination on fresh produce without overlooking the potential risks of adaptation.
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Shenton M, Kobayashi M, Terashima S, Ohyanagi H, Copetti D, Hernández-Hernández T, Zhang J, Ohmido N, Fujita M, Toyoda A, Ikawa H, Fujiyama A, Furuumi H, Miyabayashi T, Kubo T, Kudrna D, Wing R, Yano K, Nonomura KI, Sato Y, Kurata N. Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. Genome Biol Evol 2021; 12:413-428. [PMID: 32125373 PMCID: PMC7531200 DOI: 10.1093/gbe/evaa037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
The Oryza officinalis complex is the largest species group in
Oryza, with more than nine species from four continents, and is a
tertiary gene pool that can be exploited in breeding programs for the improvement of
cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using
a new reference C genome for the diploid species O. officinalis, and
draft genomes for two other C genome diploid species Oryza eichingeri and
Oryza rhizomatis, we examine the influence of transposable elements on
genome structure and provide a detailed phylogeny and evolutionary history of the
Oryza C genomes. The O. officinalis genome is 1.6
times larger than the A genome of cultivated Oryza sativa, mostly due to
proliferation of Gypsy type long-terminal repeat transposable elements,
but overall syntenic relationships are maintained with other Oryza
genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species,
Oryza eichingeri and Oryza rhizomatis, and short-read
resequencing of a series of other C genome species and accessions reveal that after the
divergence of the C genome progenitor, there was still a substantial degree of variation
within the C genome species through proliferation and loss of both DNA and long-terminal
repeat transposable elements. We provide a detailed phylogeny and evolutionary history of
the Oryza C genomes and a genomic resource for the exploitation of the
Oryza tertiary gene pool.
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Affiliation(s)
| | | | | | - Hajime Ohyanagi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | | | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Nobuko Ohmido
- Division of the Living Environment, Kobe University, Japan
| | | | | | | | | | | | | | - Takahiko Kubo
- National Institute of Genetics, Mishima, Japan.,Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - David Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Rod Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines.,Biological and Environment Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Kentaro Yano
- School of Agriculture, Meiji University, Tokyo, Japan
| | | | - Yutaka Sato
- National Institute of Genetics, Mishima, Japan
| | - Nori Kurata
- National Institute of Genetics, Mishima, Japan
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Kakei Y, Masuda H, Nishizawa NK, Hattori H, Aung MS. Elucidation of Novel cis-Regulatory Elements and Promoter Structures Involved in Iron Excess Response Mechanisms in Rice Using a Bioinformatics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:660303. [PMID: 34149757 PMCID: PMC8207140 DOI: 10.3389/fpls.2021.660303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/06/2021] [Indexed: 05/24/2023]
Abstract
Iron (Fe) excess is a major constraint on crop production in flooded acidic soils, particularly in rice cultivation. Under Fe excess, plants activate a complex mechanism and network regulating Fe exclusion by roots and isolation in various tissues. In rice, the transcription factors and cis-regulatory elements (CREs) that regulate Fe excess response mechanisms remain largely elusive. We previously reported comprehensive microarray analyses of several rice tissues in response to various levels of Fe excess stress. In this study, we further explored novel CREs and promoter structures in rice using bioinformatics approaches with this microarray data. We first performed network analyses to predict Fe excess-related CREs through the categorization of the gene expression patterns of Fe excess-responsive transcriptional regulons, and found four major expression clusters: Fe storage type, Fe chelator type, Fe uptake type, and WRKY and other co-expression type. Next, we explored CREs within these four clusters of gene expression types using a machine-learning method called microarray-associated motif analyzer (MAMA), which we previously established. Through a comprehensive bioinformatics approach, we identified a total of 560 CRE candidates extracted by MAMA analyses and 42 important conserved sequences of CREs directly related to the Fe excess response in various rice tissues. We explored several novel cis-elements as candidate Fe excess CREs including GCWGCWGC, CGACACGC, and Myb binding-like motifs. Based on the presence or absence of candidate CREs using MAMA and known PLACE CREs, we found that the Boruta-XGBoost model explained expression patterns with high accuracy of about 83%. Enriched sequences of both novel MAMA CREs and known PLACE CREs led to high accuracy expression patterns. We also found new roles of known CREs in the Fe excess response, including the DCEp2 motif, IDEF1-, Zinc Finger-, WRKY-, Myb-, AP2/ERF-, MADS- box-, bZIP and bHLH- binding sequence-containing motifs among Fe excess-responsive genes. In addition, we built a molecular model and promoter structures regulating Fe excess-responsive genes based on new finding CREs. Together, our findings about Fe excess-related CREs and conserved sequences will provide a comprehensive resource for discovery of genes and transcription factors involved in Fe excess-responsive pathways, clarification of the Fe excess response mechanism in rice, and future application of the promoter sequences to produce genotypes tolerant of Fe excess.
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Affiliation(s)
- Yusuke Kakei
- Institute of Vegetable and Floriculture Science, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Hiroshi Masuda
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - Naoko K. Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Hiroyuki Hattori
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - May Sann Aung
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
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11
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Sato Y, Tsuda K, Yamagata Y, Matsusaka H, Kajiya-Kanegae H, Yoshida Y, Agata A, Ta KN, Shimizu-Sato S, Suzuki T, Nosaka-Takahashi M, Kubo T, Kawamoto S, Nonomura KI, Yasui H, Kumamaru T. Collection, preservation and distribution of Oryza genetic resources by the National Bioresource Project RICE (NBRP-RICE). BREEDING SCIENCE 2021; 71:291-298. [PMID: 34776736 PMCID: PMC8573556 DOI: 10.1270/jsbbs.21005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/15/2021] [Indexed: 05/26/2023]
Abstract
Biological resources are the basic infrastructure of bioscience research. Rice (Oryza sativa L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding. The availability of genetic materials, including mutants, is important for rice research. In addition, Oryza species are attractive to researchers for both finding useful genes for breeding and for understanding the mechanism of genome evolution that enables wild plants to adapt to their own habitats. NBRP-RICE contributes to rice research by promoting the usage of genetic materials, especially wild Oryza accessions and mutant lines. Our activity includes collection, preservation and distribution of those materials and the provision of basic information on them, such as morphological and physiological traits and genomic information. In this review paper, we introduce the activities of NBRP-RICE and our database, Oryzabase, which facilitates the access to NBRP-RICE resources and their genomic sequences as well as the current situation of wild Oryza genome sequencing efforts by NBRP-RICE and other institutes.
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Affiliation(s)
- Yutaka Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Hiromi Kajiya-Kanegae
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Chiyoda-ku, Tokyo 100-0013, Japan
| | - Yuri Yoshida
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Ayumi Agata
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Kim Nhung Ta
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Sae Shimizu-Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Misuzu Nosaka-Takahashi
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Takahiko Kubo
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Shoko Kawamoto
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Ken-Ichi Nonomura
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
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12
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Pabuayon ICM, Kitazumi A, Cushman KR, Singh RK, Gregorio GB, Dhatt B, Zabet-Moghaddam M, Walia H, de los Reyes BG. Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects. FRONTIERS IN PLANT SCIENCE 2021; 12:615277. [PMID: 33708229 PMCID: PMC7940525 DOI: 10.3389/fpls.2021.615277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/03/2021] [Indexed: 06/01/2023]
Abstract
The phenomenon of transgressive segregation, where a small minority of recombinants are outliers relative to the range of parental phenotypes, is commonly observed in plant breeding populations. While this phenomenon has been attributed to complementation and epistatic effects, the physiological and developmental synergism involved have not been fully illuminated by the QTL mapping approach alone, especially for stress-adaptive traits involving highly complex interactions. By systems-level profiling of the IR29 × Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salinity tolerance phenotypes are created by reconfigured physiological networks due to positive or negative coupling-uncoupling of developmental and physiological attributes of each parent. Real-time growth and hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. Large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The synergism uncovered by the phenomics approach in this study supports the modern views of the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study also supports a breeding paradigm rooted on genomic modeling from multi-dimensional genetic, physiological, and phenotypic profiles to create novel adaptive traits for new crop varieties of the 21st century.
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Affiliation(s)
- Isaiah C. M. Pabuayon
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Kevin R. Cushman
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | | | | | - Balpreet Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Masoud Zabet-Moghaddam
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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13
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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14
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Pabuayon ICM, Kitazumi A, Gregorio GB, Singh RK, de los Reyes BG. Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks. Front Genet 2020; 11:594569. [PMID: 33193743 PMCID: PMC7644915 DOI: 10.3389/fgene.2020.594569] [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: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
Genetic novelties are important nucleators of adaptive speciation. Transgressive segregation is a major mechanism that creates genetic novelties with morphological and developmental attributes that confer adaptive advantages in certain environments. This study examined the morpho-developmental and physiological profiles of recombinant inbred lines (RILs) from the salt-sensitive IR29 and salt-tolerant Pokkali rice, representing the total range of salt tolerance including the outliers at both ends of the spectrum. Morpho-developmental and physiological profiles were integrated with a hypothesis-driven interrogation of mRNA and miRNA transcriptomes to uncover the critical genetic networks that have been rewired for novel adaptive architecture. The transgressive super-tolerant FL510 had a characteristic small tiller angle and wider, more erect, sturdier, and darker green leaves. This unique morphology resulted in lower transpiration rate, which also conferred a special ability to retain water more efficiently for osmotic avoidance. The unique ability for water retention conferred by such adaptive morphology appeared to enhance the efficacy of defenses mediated by Na+ exclusion mechanism (SalTol-effects) inherited from Pokkali. The super-tolerant FL510 and super-sensitive FL499 had the smallest proportions of differentially expressed genes with little overlaps. Genes that were steadily upregulated in FL510 comprised a putative cytokinin-regulated genetic network that appeared to maintain robust growth under salt stress through well-orchestrated cell wall biogenesis and cell expansion, likely through major regulatory (OsRR23, OsHK5) and biosynthetic (OsIPT9) genes in the cytokinin signaling pathway. Meanwhile, a constitutively expressed cluster in FL510 prominently featured two transcription factors (OsIBH1, TAC3) that control tiller angle and growth habit through the brassinosteroid signaling pathway. Both the putative cytokinin-mediated and brassinosteroid-mediated clusters appeared to function as highly coordinated network synergies in FL510. In contrast, both networks appeared to be sub-optimal and inferior in the other RILs and parents as they were disjointed and highly fragmented. Transgressively expressed miRNAs (miR169, miR397, miR827) were also identified as prominent signatures of FL510, with functional implications to mechanisms that support robust growth, homeostasis, and osmotic stress avoidance. Results of this study demonstrate how genetic recombination creates novel morphology that complements inducible defenses hence transgressive adaptive phenotypes.
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Affiliation(s)
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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15
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Shu X, Singh M, Karampudi NBR, Bridges DF, Kitazumi A, Wu VCH, De Los Reyes BG. Xenobiotic Effects of Chlorine Dioxide to Escherichia coli O157:H7 on Non-host Tomato Environment Revealed by Transcriptional Network Modeling: Implications to Adaptation and Selection. Front Microbiol 2020; 11:1122. [PMID: 32582084 PMCID: PMC7286201 DOI: 10.3389/fmicb.2020.01122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli serotype O157:H7 is one of the major agents of pathogen outbreaks associated with fresh fruits and vegetables. Gaseous chlorine dioxide (ClO2) has been reported to be an effective intervention to eliminate bacterial contamination on fresh produce. Although remarkable positive effects of low doses of ClO2 have been reported, the genetic regulatory machinery coordinating the mechanisms of xenobiotic effects and the potential bacterial adaptation remained unclear. This study examined the temporal transcriptome profiles of E. coli O157:H7 during exposure to different doses of ClO2 in order to elucidate the genetic mechanisms underlying bacterial survival under such harsh conditions. Dosages of 1 μg, 5 μg, and 10 μg ClO2 per gram of tomato fruits cause different effects with dose-by-time dynamics. The first hour of exposure to 1 μg and 5 μg ClO2 caused only partial killing with significant growth reduction starting at the second hour, and without further significant reduction at the third hour. However, 10 μg ClO2 exposure led to massive bacterial cell death at 1 h with further increase in cell death at 2 and 3 h. The first hour exposure to 1 μg ClO2 caused activation of primary defense and survival mechanisms. However, the defense response was attenuated during the second and third hours. Upon treatment with 5 μg ClO2, the transcriptional networks showed massive downregulation of pathogenesis and stress response genes at the first hour of exposure, with decreasing number of differentially expressed genes at the second and third hours. In contrast, more genes were further downregulated with exposure to 10 μg ClO2 at the first hour, with the number of both upregulated and downregulated genes significantly decreasing at the second hour. A total of 810 genes were uniquely upregulated at the third hour at 10 μg ClO2, suggesting that the potency of xenobiotic effects had led to potential adaptation. This study provides important knowledge on the possible selection of target molecules for eliminating bacterial contamination on fresh produce without overlooking potential risks of adaptation.
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Affiliation(s)
- Xiaomei Shu
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Manavi Singh
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | | | - David F Bridges
- Produce Safety and Microbiology Research, Western Regional Research Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA, United States
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vivian C H Wu
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States.,Produce Safety and Microbiology Research, Western Regional Research Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA, United States
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16
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de Los Reyes BG. Genomic and epigenomic bases of transgressive segregation - New breeding paradigm for novel plant phenotypes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110213. [PMID: 31521221 DOI: 10.1016/j.plantsci.2019.110213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/17/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
For a holistic approach in developing the stress-resilient crops of the 21st century, modern genomic biology will need to re-envision the underappreciated phenomena in classical genetics, and incorporate them into the new plant breeding paradigm. Advances in evolutionary genomics support a theory that genetic recombination under genome shock during hybridization of widely divergent parents is an important driver of adaptive speciation, by virtue of the novelties of rare hybrids and recombinants. The enormous potential of genetic network rewiring to generate developmental or physiological novelties with adaptive advantage to special ecological niches has been appreciated. Developmental and physiological reconfiguration through network rewiring involves intricate molecular synergies controlled both at the genetic and epigenetic levels, as typified by the phenomenon of transgressive segregation, observed in both natural and breeding populations. This paper presents modern views on the possible molecular underpinnings of transgressive phenotypes as they are created in plant breeding, expanded from classical explanations through the Omnigenic Theory for quantitative traits and modern paradigms of epigenetics. Perspectives on how genomic biology can fully exploit this phenomenon to create novel phenotypes beyond what could be achieved through the more reductionist approach of functional genomics are presented in context of genomic modeling.
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Affiliation(s)
- Benildo G de Los Reyes
- Department of Plant and Soil Science Texas Tech University 215 Experimental Sciences Building, Lubbock, TX 806-834-6421, USA.
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