1
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Ibe CN, Bailey SL, Korolev AV, Brett P, Saunders DGO. Isocitrate lyase promotes Puccinia striiformis f. sp. tritici susceptibility in wheat (Triticum aestivum) by suppressing accumulation of glyoxylate cycle intermediates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2033-2044. [PMID: 38949911 DOI: 10.1111/tpj.16908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Plant fungal parasites manipulate host metabolism to support their own survival. Among the many central metabolic pathways altered during infection, the glyoxylate cycle is frequently upregulated in both fungi and their host plants. Here, we examined the response of the glyoxylate cycle in bread wheat (Triticum aestivum) to infection by the obligate biotrophic fungal pathogen Puccinia striiformis f. sp. tritici (Pst). Gene expression analysis revealed that wheat genes encoding the two unique enzymes of the glyoxylate cycle, isocitrate lyase (TaICL) and malate synthase, diverged in their expression between susceptible and resistant Pst interactions. Focusing on TaICL, we determined that the TaICL B homoeolog is specifically upregulated during early stages of a successful Pst infection. Furthermore, disruption of the B homoeolog alone was sufficient to significantly perturb Pst disease progression. Indeed, Pst infection of the TaICL-B disruption mutant (TaICL-BY400*) was inhibited early during initial penetration, with the TaICL-BY400* line also accumulating high levels of malic acid, citric acid, and aconitic acid. Exogenous application of malic acid or aconitic acid also suppressed Pst infection, with trans-aconitic acid treatment having the most pronounced effect by decreasing fungal biomass 15-fold. Thus, enhanced TaICL-B expression during Pst infection may lower accumulation of malic acid and aconitic acid to promote Pst proliferation. As exogenous application of aconitic acid and malic acid has previously been shown to inhibit other critical pests and pathogens, we propose TaICL as a potential target for disruption in resistance breeding that could have wide-reaching protective benefits for wheat and beyond.
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Affiliation(s)
- Carol N Ibe
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah L Bailey
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Paul Brett
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Abdelrahman M, Gorafi YSA, Sulieman S, Jogaiah S, Gupta A, Tsujimoto H, Nguyen HT, Herrera-Estrella L, Tran LSP. Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1685-1702. [PMID: 38935838 DOI: 10.1111/tpj.16887] [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: 12/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.
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Affiliation(s)
- Mostafa Abdelrahman
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Yasir Serag Alnor Gorafi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kitashirakawa, 606-8502, Kyoto, Japan
| | - Saad Sulieman
- Department of Agronomy, Faculty of Agriculture, University of Khartoum, Khartoum North, 13314, Sudan
| | - Sudisha Jogaiah
- Department of Environmental Science, Central University of Kerala, Periye, Kasaragod, 671316, Kerala, India
| | - Aarti Gupta
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Henry T Nguyen
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, Missouri, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
- Unidad de Genomica Avanzada, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional, Irapuato, 36821, Mexico
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
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3
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Zhao K, Dong J, Xu J, Bai Y, Yin Y, Long C, Wu L, Lin T, Fan L, Wang Y, Edger PP, Xiong Z. Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:11. [PMID: 38110525 DOI: 10.1007/s00122-023-04510-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/18/2023] [Indexed: 12/20/2023]
Abstract
KEY MESSAGE Homoeolog expression bias and the gene dosage effect induce downregulation of genes on chromosome A7, causing a significant increase in the plant height of resynthesized allopolyploid Brassica napus. Gene expression levels in allopolyploid plants are not equivalent to the simple average of the expression levels in the parents and are associated with several non-additive expression phenomena, including homoeolog expression bias. However, hardly any information is available on the effect of homoeolog expression bias on traits. Here, we studied the effects of gene expression-related characteristics on agronomic traits using six isogenic resynthesized Brassica napus lines across the first ten generations. We found a group of genes located on chromosome A7 whose expression levels were significantly negatively correlated with plant height. They were expressed at significantly lower levels than their homoeologous genes, owing to allopolyploidy rather than inheritance from parents. Homoeolog expression bias resulted in resynthesized allopolyploids with a plant height similar to their female Brassica oleracea parent, but significantly higher than that of the male Brassica rapa parent. Notably, aneuploid lines carrying monosomic and trisomic chromosome A7 had the highest and lowest plant heights, respectively, due to changes in the expression bias of homoeologous genes because of alterations in the gene dosage. These findings suggest that the downregulation of the expression of homoeologous genes on a single chromosome can result in the partial improvement of traits to a significant extent in the nascent allopolyploid B. napus.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jing Dong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Chunshen Long
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Longqiu Fan
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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4
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Gruet C, Alaoui M, Gerin F, Prigent-Combaret C, Börner A, Muller D, Moënne-Loccoz Y. Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2023; 46:3933-3948. [PMID: 37614118 DOI: 10.1111/pce.14698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maroua Alaoui
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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5
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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6
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Pan Y, Zhuang Y, Liu T, Chen H, Wang L, Varshney RK, Zhuang W, Wang X. Deciphering peanut complex genomes paves a way to understand its origin and domestication. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2173-2181. [PMID: 37523347 PMCID: PMC10579718 DOI: 10.1111/pbi.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 06/12/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023]
Abstract
Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retention and gene expression. This subgenome bias, extended to sequence variation and point mutation, might be related to the long terminal repeat (LTR) explosions after tetraploidization, especially in At subgenomes. Except that, whole-genome sequences revealed many important genes, for example, fatty acids and triacylglycerols pathway, NBS-LRR (nucleotide-binding site-leucine-rich repeats), and seed size decision genes, were enriched after recursive polyploidization. Each ancestral polyploidy, with old ones having occurred hundreds of thousand years ago, has thousands of duplicated genes in extant genomes, contributing to genetic novelty. Notably, although full genome sequences are available, the actual At subgenome ancestor has still been elusive, highlighted with new debate about peanut origin. Although being an orphan crop lagging behind other crops in genomic resources, the genome sequencing achievement has laid a solid foundation for advancing crop enhancement and system biology research of peanut.
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Affiliation(s)
- Yuxin Pan
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yuhui Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tao Liu
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Hua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Wang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, and Centre for Crop & Food InnovationFood Futures InstituteMurdoch UniversityMurdochWest AustraliaAustralia
| | - Weijian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiyin Wang
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
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7
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Fang C, Yang M, Tang Y, Zhang L, Zhao H, Ni H, Chen Q, Meng F, Jiang J. Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean. Proc Natl Acad Sci U S A 2023; 120:e2303836120. [PMID: 37871213 PMCID: PMC10622917 DOI: 10.1073/pnas.2303836120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase-hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9-mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation of cis-regulatory elements (CREs) within the ACRs can change the balance of the expression level and/or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
| | - Mingyu Yang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Yuecheng Tang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Ling Zhang
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun130033, China
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
| | - Hejia Ni
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Qingshan Chen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Fanli Meng
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
- Department of Horticulture, Michigan State University, East Lansing, MI48824
- Michigan State University AgBioResearch, East Lansing, MI48824
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8
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Zhang Z, Lv R, Wang B, Xun H, Liu B, Xu C. Effects of Allopolyploidization and Homoeologous Chromosomal Segment Exchange on Homoeolog Expression in a Synthetic Allotetraploid Wheat under Variable Environmental Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:3111. [PMID: 37687357 PMCID: PMC10490264 DOI: 10.3390/plants12173111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Allopolyploidy through the combination of divergent genomes into a common nucleus at doubled dosage is known as a potent genetic and evolutionary force. As a macromutation, a striking feature of allopolyploidy in comparison with other mutational processes is that 'genome shock' can be evoked, thereby generating rapid and saltational biological consequences. A major manifestation of genome shock is genome-wide gene expression rewiring, which previously remained to be fully elucidated. Here, using a large set of RNAseq-based transcriptomic data of a synthetic allotetraploid wheat (genome AADD) and its parental species, we performed in-depth analyses of changes in the genome-wide gene expression under diverse environmental conditions at the subgenome (homoeolog) level and investigated the additional effects of homoeologous chromosomal segment exchanges (abbreviated HEs). We show that allopolyploidy caused large-scale changes in gene expression that were variable across the conditions and exacerbated by both stresses and HEs. Moreover, although both subgenomes (A and D) showed clear commonality in the changes, they responded differentially under variable conditions. The subgenome- and condition-dependent differentially expressed genes were enriched for different gene ontology terms implicating different biological functions. Our results provide new insights into the direct impacts of allopolyploidy on condition-dependent changes in subgenome expression and the additional effects of HEs in nascent allopolyploidy.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences (CAS), Changchun 130102, China
| | - Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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9
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Vasudevan A, Lévesque-Lemay M, Edwards T, Cloutier S. Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat. Commun Biol 2023; 6:426. [PMID: 37069312 PMCID: PMC10110605 DOI: 10.1038/s42003-023-04781-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
Synthetic hexaploid wheat (SHW) lines are created as pre-breeding germplasm to diversify the D subgenome of hexaploid wheat and capitalize upon the untapped genetic diversity of the Aegilops tauschii gene pool. However, the phenotypes observed in the Ae. tauschii parents are not always recovered in the SHW lines, possibly due to inter-subgenome interactions. To elucidate this post-polyploidization genome reprogramming phenomenon, we performed RNA-seq of four SHW lines and their corresponding tetraploid and diploid parents, across ten tissues and three biological replicates. Homoeologue expression bias (HEB) analysis using more than 18,000 triads suggests massive suppression of homoeoalleles of the D subgenome in SHWs. Comparative transcriptome analysis of the whole-genome gene set further corroborated this finding. Alternative splicing analysis of the high-confidence genes indicates an additional layer of complexity where all five splice events are identified, and retained intron is predominant. Homoeologue expression upon resynthesis of hexaploid wheat has implications to the usage and handling of this germplasm in breeding as it relates to capturing the effects of epistatic interaction across subgenomes upon polyploidization. Special considerations must be given to this germplasm in pre-breeding activities to consider the extent of the inter-subgenome interactions on gene expression and their impact on traits for crop improvement.
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Affiliation(s)
- Akshaya Vasudevan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Tara Edwards
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada.
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
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10
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de Jong GW, Adams KL. Subgenome-dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:142-158. [PMID: 36710652 DOI: 10.1111/tpj.16127] [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: 03/14/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both resynthesized and natural lines of polyploid Brassica napus, along with the progenitors Brassica rapa and Brassica oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12 709 DAS events) and lower in resynthesized B. napus (8863 DAS events). Natural B. napus had more upregulated events and fewer downregulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus, this resulted in a disproportionate C subgenome contribution to the pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in resynthesized and natural B. napus.
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Affiliation(s)
- Grant W de Jong
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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11
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Ma Y, Yu H, Lu Y, Gao S, Fatima M, Ming R, Yue J. Transcriptome analysis of sugarcane reveals rapid defense response of SES208 to Xanthomonas albilineans in early infection. BMC PLANT BIOLOGY 2023; 23:52. [PMID: 36694139 PMCID: PMC9872421 DOI: 10.1186/s12870-023-04073-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Diseases are the major factor affecting the quality and yield of sugarcane during its growth and development. However, our knowledge about the factors regulating disease responses remain limited. The present study focuses on identifying genes regulating transcriptional mechanisms responsible for resistance to leaf scald caused by Xanthomonas albilineans in S. spontaneum and S. officinarum. RESULTS After inoculation of the two sugarcane varieties SES208 (S. spontaneum) and LA Purple (S. officinarum) with Xanthomonas albilineans, SES208 exhibited significantly greater resistance to leaf scald caused by X. albilineans than did LA Purple. Using transcriptome analysis, we identified a total of 4323 and 1755 differentially expressed genes (DEGs) in inoculated samples of SES208 and LA Purple, respectively. Significantly, 262 DEGs were specifically identified in SES208 that were enriched for KEGG pathway terms such as plant-pathogen interaction, MAPK signaling pathway, and plant hormone signal transduction. Furthermore, we built a transcriptional regulatory co-expression network that specifically identified 16 and 25 hub genes in SES208 that were enriched for putative functions in plant-pathogen interactions, MAPK signaling, and plant hormone signal transduction. All of these essential genes might be significantly involved in resistance-regulating responses in SES208 after X. albilineans inoculation. In addition, we found allele-specific expression in SES208 that was associated with the resistance phenotype of SES208 when infected by X. albilineans. After infection with X. albilineans, a great number of DEGs associated with the KEGG pathways 'phenylpropanoid biosynthesis' and 'flavonoid biosynthesis' exhibited significant expression changes in SES208 compared to LA Purple that might contribute to superior leaf scald resistance in SES208. CONCLUSIONS We provided the first systematical transcriptome map that the higher resistance of SES208 is associated with and elicited by the rapid activation of multiple clusters of defense response genes after infection by X. albilineans and not merely due to changes in the expression of genes generically associated with stress resistance. These results will serve as the foundation for further understanding of the molecular mechanisms of resistance against X. albilineans in S. spontaneum.
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Affiliation(s)
- Yaying Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hongying Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yijing Lu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sanji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jingjing Yue
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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12
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Pootakham W, Sonthirod C, Naktang C, Yundaeng C, Yoocha T, Kongkachana W, Sangsrakru D, Somta P, Tangphatsornruang S. Genome assemblies of Vigna reflexo-pilosa (créole bean) and its progenitors, Vigna hirtella and Vigna trinervia, revealed homoeolog expression bias and expression-level dominance in the allotetraploid. Gigascience 2022; 12:giad050. [PMID: 37470496 PMCID: PMC10357499 DOI: 10.1093/gigascience/giad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Vigna reflexo-pilosa (créole bean) is a wild legume belonging to the subgenus Ceratoropis and is widely distributed in Asia. Créole bean is the only tetraploid species in the genus Vigna, and it has been shown to derive from the hybridization of Vigna hirtella and Vigna trinervia. In this study, we combined the long-read PacBio technology with the chromatin contact mapping (Hi-C) technique to obtain a chromosome-level assembly of V. reflexo-pilosa. The final assembly contained 998,724,903 bases with an N50 length of 42,545,650 bases. Our gene prediction recovered 99.4% of the highly conserved orthologs based on the BUSCO analysis. To investigate homoeolog expression bias and expression level dominance in the tetraploid, we also sequenced and assembled the genomes of its progenitors. Overall, the majority of the homoeolog pairs (72.9%) displayed no expression bias, and among those that exhibited biased expression, 16.3% showed unbalanced homoeolog expression bias toward the V. trinervia subgenome. Moreover, 41.2% and 36.2% of the expressed gene pairs exhibited transgressive expression and expression level dominance, respectively. Interestingly, the genome-wide expression level dominance in the tetraploid was biased toward the V. trinervia subgenome. The analysis of methylation patterns also revealed that the average methylation levels in coding regions were higher in the V. hirtella subgenome than those in the V. trinervia subgenome. The genomic/transcriptomic resources for these three species are useful not only for the development of elite cultivars in Vigna breeding programs but also to researchers studying comparative genomics and investigating genomic/epigenomic changes following polyploid events.
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Affiliation(s)
- Wirulda Pootakham
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chutima Sonthirod
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chaiwat Naktang
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chutintorn Yundaeng
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Thippawan Yoocha
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Duangjai Sangsrakru
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
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13
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Lin Z, Li H, Luo W, Xu Y, Xu G, Ji R, Liu Z, Zhang H, Lin Z, Li G, Qiu Y, Qiu S, Tang H. Genome sequence resource of Pectobacterium polaris QK413-1 that causes blackleg on potato in Fujian Province, China. PLANT DISEASE 2022; 107:1151-1158. [PMID: 36510425 DOI: 10.1094/pdis-08-22-1861-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Pectobacterium pathogens cause soft rot and blackleg diseases on many plants and crops, including potatoes. Here we first report a high-quality genome assembly and announcement of the P. polaris strain QK413-1, which causes blackleg disease in potatoes in China. The QK413-1 genome was sequenced and assembled using the PacBio Sequel II and Illumina sequencing platform. The assembled genome has a total size of 5,005,507bp with a GC content of 51.81%, encoding 4782 open reading frames, including 639 virulence genes, 273 drug resistance genes, and 416 secreted proteins. The QK413-1 genome sequence provides a valuable resource for the control of potato blackleg and research into its mechanism.
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Affiliation(s)
| | - Huawei Li
- Xifeng Road 100Fuzhou, Fujian, China, 350013;
| | | | | | | | | | | | | | | | | | | | | | - Hao Tang
- Fujian Academy of Agricultural Sciences, 107629, Institute of Crop Sciences, Fuzhou, Fujian, China;
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14
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Zheng M, Li J, Zeng C, Liu X, Chu W, Lin J, Wang F, Wang W, Guo W, Xin M, Yao Y, Peng H, Ni Z, Sun Q, Hu Z. Subgenome-biased expression and functional diversification of a Na +/H + antiporter homoeologs in salt tolerance of polyploid wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1072009. [PMID: 36570929 PMCID: PMC9768589 DOI: 10.3389/fpls.2022.1072009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is an allohexaploid species combines the D genome from Ae. tauschii and with the AB genomes from tetraploid wheat (Triticum turgidum). Compared with tetraploid wheat, hexaploid wheat has wide-ranging adaptability to environmental adversity such as salt stress. However, little is known about the molecular basis underlying this trait. The plasma membrane Na+/H+ transporter Salt Overly Sensitive 1 (SOS1) is a key determinant of salt tolerance in plants. Here we show that the upregulation of TaSOS1 expression is positively correlated with salt tolerance variation in polyploid wheat. Furthermore, both transcriptional analysis and GUS staining on transgenic plants indicated TaSOS1-A and TaSOS1-B exhibited higher basal expression in roots and leaves in normal conditions and further up-regulated under salt stress; while TaSOS1-D showed markedly lower expression in roots and leaves under normal conditions, but significant up-regulated in roots but not leaves under salt stress. Moreover, transgenic studies in Arabidopsis demonstrate that three TaSOS1 homoeologs display different contribution to salt tolerance and TaSOS1-D plays the prominent role in salt stress. Our findings provide insights into the subgenomic homoeologs variation potential to broad adaptability of natural polyploidy wheat, which might effective for genetic improvement of salinity tolerance in wheat and other crops.
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Affiliation(s)
- Mei Zheng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Chaowu Zeng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Xinjiang Academy of Agricultural Sciences, Urumuqi, China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Wei Chu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Fengzhi Wang
- Hebei Key Laboratory of Crop Salt-alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou Academy of Agriculture and Forestry Science, Cangzhou, China
| | - Weiwei Wang
- Hebei Key Laboratory of Crop Salt-alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou Academy of Agriculture and Forestry Science, Cangzhou, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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15
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Batyrshina ZS, Shavit R, Yaakov B, Bocobza S, Tzin V. The transcription factor TaMYB31 regulates the benzoxazinoid biosynthetic pathway in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5634-5649. [PMID: 35554544 PMCID: PMC9467655 DOI: 10.1093/jxb/erac204] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/10/2022] [Indexed: 05/13/2023]
Abstract
Benzoxazinoids are specialized metabolites that are highly abundant in staple crops, such as maize and wheat. Although their biosynthesis has been studied for several decades, the regulatory mechanisms of the benzoxazinoid pathway remain unknown. Here, we report that the wheat transcription factor MYB31 functions as a regulator of benzoxazinoid biosynthesis genes. A transcriptomic analysis of tetraploid wheat (Triticum turgidum) tissue revealed the up-regulation of two TtMYB31 homoeologous genes upon aphid and caterpillar feeding. TaMYB31 gene silencing in the hexaploid wheat Triticum aestivum significantly reduced benzoxazinoid metabolite levels and led to susceptibility to herbivores. Thus, aphid progeny production, caterpillar body weight gain, and spider mite oviposition significantly increased in TaMYB31-silenced plants. A comprehensive transcriptomic analysis of hexaploid wheat revealed that the TaMYB31 gene is co-expressed with the target benzoxazinoid-encoded Bx genes under several biotic and environmental conditions. Therefore, we analyzed the effect of abiotic stresses on benzoxazinoid levels and discovered a strong accumulation of these compounds in the leaves. The results of a dual fluorescence assay indicated that TaMYB31 binds to the Bx1 and Bx4 gene promoters, thereby activating the transcription of genes involved in the benzoxazinoid pathway. Our finding is the first report of the transcriptional regulation mechanism of the benzoxazinoid pathway in wheat.
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Affiliation(s)
- Zhaniya S Batyrshina
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 8499000, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 8499000, Israel
| | - Samuel Bocobza
- Department of Ornamentals and Biotechnology, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 Hamakabim Road, 7528809, Rishon LeZion, Israel
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16
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Wang R, Chen Y, Kaur G, Wu X, Nguyen HT, Shen R, Pandey AK, Lan P. Differentially reset transcriptomes and genome bias response orchestrate wheat response to phosphate deficiency. PHYSIOLOGIA PLANTARUM 2022; 174:e13767. [PMID: 36281840 DOI: 10.1111/ppl.13767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is an essential macronutrient for all organisms. Phosphate (Pi) deficiency reduces grain yield and quality in wheat. Understanding how wheat responds to Pi deficiency at the global transcriptional level remains limited. We revisited the available RNA-seq transcriptome from Pi-starved wheat roots and shoots subjected to Pi starvation. Genome-wide transcriptome resetting was observed under Pi starvation, with a total of 917 and 2338 genes being differentially expressed in roots and shoots, respectively. Chromosomal distribution analysis of the gene triplets and differentially expressed genes (DEGs) revealed that the D genome displayed genome induction bias and, specifically, the chromosome 2D might be a key contributor to Pi-limiting triggered gene expression response. Alterations in multiple metabolic pathways pertaining to secondary metabolites, transcription factors and Pi uptake-related genes were evidenced. This study provides genomic insight and the dynamic landscape of the transcriptional changes contributing to the hexaploid wheat during Pi starvation. The outcomes of this study and the follow-up experiments have the potential to assist the development of Pi-efficient wheat cultivars.
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Affiliation(s)
- Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinglong Chen
- UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Xiaoba Wu
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Henry T Nguyen
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
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17
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Aljuaid BS, Mukherjee S, Sayed AN, El-Gabry YAEG, Omar MMA, Mahmoud SF, Alsubeie MS, Darwish DBE, Al-Qahtani SM, Al-Harbi NA, Alzuaibr FM, Basahi MA, Hamada MMA. Folic Acid Reinforces Maize Tolerance to Sodic-Alkaline Stress through Modulation of Growth, Biochemical and Molecular Mechanisms. Life (Basel) 2022; 12:life12091327. [PMID: 36143364 PMCID: PMC9506096 DOI: 10.3390/life12091327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
The mechanism by which folic acid (FA) or its derivatives (folates) mediates plant tolerance to sodic-alkaline stress has not been clarified in previous literature. To apply sodic-alkaline stress, maize seedlings were irrigated with 50 mM of a combined solution (1:1) of sodic-alkaline salts (NaHCO3 and Na2CO3; pH 9.7). Maize seedlings under stressed and non-stressed conditions were sprayed with folic acid (FA) at 0 (distilled water as control), 0.05, 0.1, and 0.2 mM. Under sodic-alkaline stress, FA applied at 0.2 mM significantly improved shoot fresh weight (95%), chlorophyll (Chl a (41%), Chl b (57%), and total Chl (42%)), and carotenoids (27%) compared to the untreated plants, while root fresh weight was not affected compared to the untreated plants. This improvement was associated with a significant enhancement in the cell-membrane stability index (CMSI), relative water content (RWC), free amino acids (FAA), proline, soluble sugars, K, and Ca. In contrast, Na, Na/K ratio, H2O2, malondialdehyde (MDA), and methylglycoxal (MG) were significantly decreased. Moreover, seedlings treated with FA demonstrated significantly higher activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POX), catalase (CAT), and ascorbate peroxidase (APX) compared to the untreated plants. The molecular studies using RT-qPCR demonstrated that FA treatments, specifically at 0.2 mM, enhanced the K+/Na+ selectivity and the performance of photosynthesis under alkaline-stress conditions. These responses were observed through up-regulation of the expression of the high-affinity potassium-transporter protein (ZmHKT1), the major core protein of photosystem II (D2-Protein), and the activity of the first enzyme of carbon fixation cycle in C4 plants (PEP-case) by 74, 248, and 225% over the untreated plants, respectively. Conversely, there was a significant down-regulation in the expression ZmSOS1 and ZmNHX1 by 48.2 and 27.8%, respectively, compared to the untreated plants.
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Affiliation(s)
- Bandar S. Aljuaid
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, Kalyani 742213, India
- Correspondence: (S.M.); (M.M.A.H.)
| | - Amany N. Sayed
- Department of Agronomy, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | | | - Mohamed M. A. Omar
- Department of Biochemistry, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Samy F. Mahmoud
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Moodi Saham Alsubeie
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Doaa Bahaa Eldin Darwish
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35511, Egypt
- Biology Department, Faculty of Science, Tabuk University, Tabuk 71491, Saudi Arabia
| | - Salem Mesfir Al-Qahtani
- Biology Department, University College of Tayma, University of Tabuk, P.O. Box 741, Tabuk 47512, Saudi Arabia
| | - Nadi Awad Al-Harbi
- Biology Department, University College of Tayma, University of Tabuk, P.O. Box 741, Tabuk 47512, Saudi Arabia
| | - Fahad Mohammed Alzuaibr
- Department of Biology, Faculty of Science, University of Tabuk, P.O. Box 741, Tabuk 71491, Saudi Arabia
| | - Mohammed A. Basahi
- College of Science and Arts Sajir, Shaqra University, P.O. Box 33, Shaqra 11961, Saudi Arabia
| | - Maha M. A. Hamada
- Department of Agronomy, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
- Correspondence: (S.M.); (M.M.A.H.)
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18
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Dong Y, Hu G, Grover CE, Miller ER, Zhu S, Wendel JF. Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:872-887. [PMID: 35686631 PMCID: PMC9540634 DOI: 10.1111/tpj.15863] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.
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Affiliation(s)
- Yating Dong
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang455 000China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen518 120China
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Shuijin Zhu
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
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19
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Alsamadany H, Mansour H, Elkelish A, Ibrahim MFM. Folic Acid Confers Tolerance against Salt Stress-Induced Oxidative Damages in Snap Beans through Regulation Growth, Metabolites, Antioxidant Machinery and Gene Expression. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111459. [PMID: 35684231 PMCID: PMC9182733 DOI: 10.3390/plants11111459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 06/01/2023]
Abstract
Although the effect of folic acid (FA) and its derivatives (folates) have been extensively studied in humans and animals, their effects are still unclear in most plant species, specifically under various abiotic stress conditions. Here, the impact of FA as a foliar application at 0, 0.1, and 0.2 mM was studied on snap bean seedlings grown under non-saline and salinity stress (50 mM NaCl) conditions. The results indicated that under salinity stress, FA-treated plants revealed a significant (p ≤ 0.05) increase in growth parameters (fresh and dry weight of shoot and root). A similar trend was observed in chlorophyll (Chl b), total chlorophyll, carotenoids, leaf relative water content (RWC), proline, free amino acids (FAA), soluble sugars, cell membrane stability index (CMSI), and K, Ca, and K/Na ratio compared to the untreated plants. In contrast, a significant decrease was observed in Na and salinity-induced oxidative damage as indicated by reduced H2O2 production (using biochemical and histochemical detection methods) and rate of lipid peroxidation (malondialdehyde; MDA). This enhancement was correlated by increasing the activities of antioxidant enzymes, i.e., superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (G-POX), and ascorbate peroxidase (APX). Gene expression analyses conducted using qRT-PCR demonstrated that genes coding for the Na+/H+ antiporter protein Salt Overly Sensitive 1 (SOS1), the tonoplast-localized Na+/H+ antiporter protein (NHX1), and the multifunctional osmotic protective protein (Osmotin) were significantly up-regulated in the FA-treated plants under both saline and non-saline treatments. Generally, treatment with 0.2 mM FA was more potent than 0.1 mM and can be recommended to improve snap bean tolerance to salinity stress.
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Affiliation(s)
- Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, College of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia;
- Botany Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt;
| | - Amr Elkelish
- Botany Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt;
| | - Mohamed F. M. Ibrahim
- Department of Agricultural Botany, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
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20
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Correr FH, Furtado A, Franco Garcia AA, Henry RJ, Rodrigues Alves Margarido G. Allele expression biases in mixed-ploid sugarcane accessions. Sci Rep 2022; 12:8778. [PMID: 35610293 PMCID: PMC9130122 DOI: 10.1038/s41598-022-12725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, genes showing ASE (ASEGs) were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.
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Affiliation(s)
- Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Antonio Augusto Franco Garcia
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
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21
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Xie Y, Chen Y, Li Z, Zhu J, Liu M, Zhang Y, Dong Z. Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat. Genome Biol 2022; 23:109. [PMID: 35501845 PMCID: PMC9063354 DOI: 10.1186/s13059-022-02675-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/18/2022] [Indexed: 12/15/2022] Open
Abstract
The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat genome. We find that genes associated with transcriptional enhancers are expressed at significantly higher levels, and enhancer RNA is more precise and robust in predicting enhancer activity compared to chromatin features. We demonstrate that sub-genome-biased enhancer transcription could drive sub-genome-biased gene expression. This study highlights enhancer transcription as a hallmark in regulating gene expression in wheat.
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Affiliation(s)
- Yilin Xie
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiafu Zhu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Min Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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22
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Kumar A, Kaur G, Singh P, Meena V, Sharma S, Tiwari M, Bauer P, Pandey AK. Strategies and Bottlenecks in Hexaploid Wheat to Mobilize Soil Iron to Grains. FRONTIERS IN PLANT SCIENCE 2022; 13:863849. [PMID: 35574143 PMCID: PMC9100831 DOI: 10.3389/fpls.2022.863849] [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: 01/27/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Our knowledge of iron (Fe) uptake and mobilization in plants is mainly based on Arabidopsis and rice. Although multiple players of Fe homeostasis have been elucidated, there is a significant gap in our understanding of crop species, such as wheat. It is, therefore, imperative not only to understand the different hurdles for Fe enrichment in tissues but also to address specifically the knowns/unknowns involved in the plausible mechanism of Fe sensing, signaling, transport, and subsequent storage in plants. In the present review, a unique perspective has been described in light of recent knowledge generated in wheat, an economically important crop. The strategies to boost efficient Fe uptake, transcriptional regulation, and long-distance mobilization in grains have been discussed, emphasizing recent biotechnological routes to load Fe in grains. This article also highlights the new elements of physiological and molecular genetics that underpin the mechanistic insight for the identified Fe-related genes and discusses the bottlenecks in unloading the Fe in grains. The information presented here will provide much-needed resources and directions to overcome challenges and design efficient strategies to enhance the Fe density in wheat grains.
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Affiliation(s)
- Anil Kumar
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Palvinder Singh
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Varsha Meena
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Shivani Sharma
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Manish Tiwari
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
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23
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Wang Z, Yang J, Cheng F, Li P, Xin X, Wang W, Yu Y, Zhang D, Zhao X, Yu S, Zhang F, Dong Y, Su T. Subgenome dominance and its evolutionary implications in crop domestication and breeding. HORTICULTURE RESEARCH 2022; 9:uhac090. [PMID: 35873727 PMCID: PMC9297153 DOI: 10.1093/hr/uhac090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 05/29/2023]
Abstract
Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.
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Affiliation(s)
| | | | | | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
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24
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Shavit R, Batyrshina ZS, Yaakov B, Florean M, Köllner TG, Tzin V. The wheat dioxygenase BX6 is involved in the formation of benzoxazinoids in planta and contributes to plant defense against insect herbivores. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111171. [PMID: 35151455 DOI: 10.1016/j.plantsci.2021.111171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/22/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Benzoxazinoids are plant specialized metabolites with defense properties, highly abundant in wheat (Triticum), one of the world's most important crops. The goal of our study was to characterize dioxygenase BX6 genes in tetraploid and hexaploid wheat genotypes and to elucidate their effects on defense against herbivores. Phylogenetic analysis revealed four BX6 genes in the hexaploid wheat T. aestivum, but only one ortholog was found in the tetraploid (T. turgidum) wild emmer wheat and the cultivated durum wheat. Transcriptome sequencing of durum wheat plants, damaged by either aphids or caterpillars, revealed that several BX genes, including TtBX6, were upregulated upon caterpillar feeding, relative to the undamaged control plants. A virus-induced gene silencing approach was used to reduce the expression of BX6 in T. aestivum plants, which exhibited both reduced transcript levels and reduced accumulation of different benzoxazinoids. To elucidate the effect of BX6 on plant defense, bioassays with different herbivores feeding on BX6-silenced leaves were conducted. The results showed that plants with silenced BX6 were more susceptible to aphids and the two-spotted spider mite than the control. Overall, our study indicates that wheat BX6 is involved in benzoxazinoid formation in planta and contributes to plant resistance against insect herbivores.
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Affiliation(s)
- Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Zhaniya S Batyrshina
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Matilde Florean
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, D-07745, Jena, Germany
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, D-07745, Jena, Germany
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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25
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Guan J, Wang Z, Liu S, Kong X, Wang F, Sun G, Geng S, Mao L, Zhou P, Li A. Transcriptome Analysis of Developing Wheat Grains at Rapid Expanding Phase Reveals Dynamic Gene Expression Patterns. BIOLOGY 2022; 11:biology11020281. [PMID: 35205147 PMCID: PMC8869726 DOI: 10.3390/biology11020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/30/2022] [Accepted: 02/06/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Understanding the regulatory mechanism underlying grain development is essential for wheat improvement. The early grain expanding phase boasts critical biological events like embryogenesis and initiation of grain filling. RNA sequencing analysis of this developmental stage revealed dynamic expressions of genes related to cell division, starch biosynthesis, and hormone biosynthesis. An unbalanced expression among triads may play critical roles as shown by multiple enriched metabolic pathways. Our work demonstrated complex regulation mechanisms in early grain development and provided useful information for future wheat improvement. Abstract Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. The wheat grain expanding phase is the early process involving the rapid morphological changes and initiation of grain filling. However, little is known about the molecular basis of grain development at this stage. Here, we provide a time-series transcriptome profile of developing wheat grain at 0, 2, 4, 6, 8, and 10 days after pollination of the wheat landrace Chinese Spring. A total of 26,892 differentially expressed genes, including 1468 transcription factors, were found between adjacent time points. Co-expression cluster analysis and Gene Ontology enrichment revealed dynamic expressions of cell division and starch biosynthesis related structural genes and transcription factors. Moreover, diverse, differential and drastically varied expression trends of the key genes related to hormone metabolism were identified. Furthermore, ~30% of triads showed unbalanced expression patterns enriching for genes in multiple pivotal metabolic pathways. Hormone metabolism related genes, such as YUC10 (YUCCA flavin-containing monooxygenase 10), AOS2 (allene oxide synthase 2), CYP90D2 (cytochrome P450 90D2), and CKX1 (cytokinin dehydrogenase 1), were dominantly contributed by A or D homoeologs of the triads. Our study provided a systematic picture of transcriptional regulation of wheat grains at the early grain expanding phase which should deepen our understanding of wheat grain development and help in wheat yield improvement.
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Affiliation(s)
- Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Shaoshuai Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Xingchen Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Sino-Agro Research Station for Salt Tolerant Crops, Yellow River Delta, Kenli District, Dongying 257500, China
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Guoliang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Sino-Agro Research Station for Salt Tolerant Crops, Yellow River Delta, Kenli District, Dongying 257500, China
- Correspondence: (L.M.); (P.Z.); (A.L.)
| | - Peng Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Correspondence: (L.M.); (P.Z.); (A.L.)
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Correspondence: (L.M.); (P.Z.); (A.L.)
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26
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Khan D, Ziegler DJ, Kalichuk JL, Hoi V, Huynh N, Hajihassani A, Parkin IAP, Robinson SJ, Belmonte MF. Gene expression profiling reveals transcription factor networks and subgenome bias during Brassica napus seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:477-489. [PMID: 34786793 DOI: 10.1111/tpj.15587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 05/22/2023]
Abstract
We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole-genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive-lethal phenotype. Global mRNA profiling revealed lower accumulation of Cn subgenome transcripts relative to the An subgenome. Subgenome-specific transcription factor networks identified distinct transcription factor families enriched in each of the An and Cn subgenomes early in seed development. Analysis of laser-microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the An subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cn subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the An and Cn genomes of the whole B. napus seed can identify valuable targets for seed development research and that -omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.
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Affiliation(s)
- Deirdre Khan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Dylan J Ziegler
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Jenna L Kalichuk
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Vanessa Hoi
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Nina Huynh
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Abolfazl Hajihassani
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
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27
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Margarido GRA, Correr FH, Furtado A, Botha FC, Henry RJ. Limited allele-specific gene expression in highly polyploid sugarcane. Genome Res 2022; 32:297-308. [PMID: 34949669 PMCID: PMC8805727 DOI: 10.1101/gr.275904.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/19/2021] [Indexed: 12/04/2022]
Abstract
Polyploidy is widespread in plants, allowing the different copies of genes to be expressed differently in a tissue-specific or developmentally specific way. This allele-specific expression (ASE) has been widely reported, but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole-genome level in the highly polyploid sugarcane genome. Very high depth whole-genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single-copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.
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Affiliation(s)
- Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
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Ma X, Zhang Z, Li G, Gou X, Bian Y, Zhao Y, Wang B, Lang M, Wang T, Xie K, Liu X, Liu B, Gong L. Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD). FRONTIERS IN PLANT SCIENCE 2022; 13:887133. [PMID: 35651770 PMCID: PMC9150853 DOI: 10.3389/fpls.2022.887133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/08/2022] [Indexed: 05/15/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to "transcriptome shock. " However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors Triticum urartu and Aegilops tauschii. We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the cis-only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in cis elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T. urartu may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.
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Affiliation(s)
- Xintong Ma
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yao Bian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Yue Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Man Lang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Kun Xie
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaoming Liu
- Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang, China
- *Correspondence: Xiaoming Liu
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Bao Liu
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Lei Gong
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29
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Zhang L, He J, He H, Wu J, Li M. Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica. HORTICULTURE RESEARCH 2021; 8:246. [PMID: 34848691 PMCID: PMC8633066 DOI: 10.1038/s41438-021-00672-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 05/04/2023]
Abstract
Raphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongsheng He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiangsheng Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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30
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Malla KB, Thapa G, Doohan FM. Mitochondrial phosphate transporter and methyltransferase genes contribute to Fusarium head blight Type II disease resistance and grain development in wheat. PLoS One 2021; 16:e0258726. [PMID: 34648604 PMCID: PMC8516198 DOI: 10.1371/journal.pone.0258726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Fusarium head blight (FHB) is an economically important disease of wheat that results in yield loss and grain contaminated with fungal mycotoxins that are harmful to human and animal health. Herein we characterised two wheat genes involved in the FHB response in wheat: a wheat mitochondrial phosphate transporter (TaMPT) and a methyltransferase (TaSAM). Wheat has three sub-genomes (A, B, and D) and gene expression studies demonstrated that TaMPT and TaSAM homoeologs were differentially expressed in response to FHB infection and the mycotoxigenic Fusarium virulence factor deoxynivalenol (DON) in FHB resistant wheat cv. CM82036 and susceptible cv. Remus. Virus-induced gene silencing (VIGS) of either TaMPT or TaSAM enhanced the susceptibility of cv. CM82036 to FHB disease, reducing disease spread (Type II disease resistance). VIGS of TaMPT and TaSAM significantly reduced grain number and grain weight. This indicates TaSAM and TaMPT genes also contribute to grain development in wheat and adds to the increasing body of evidence linking FHB resistance genes to grain development. Hence, Fusarium responsive genes TaSAM and TaMPT warrant further study to determine their potential to enhance both disease resistance and grain development in wheat.
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Affiliation(s)
- Keshav B. Malla
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| | - Ganesh Thapa
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| | - Fiona M. Doohan
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
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31
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Wang H, Dang J, Wu D, Xie Z, Yan S, Luo J, Guo Q, Liang G. Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica). PLANT METHODS 2021; 17:93. [PMID: 34479588 PMCID: PMC8418031 DOI: 10.1186/s13007-021-00792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/24/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. RESULTS We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. CONCLUSIONS qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Zhongyi Xie
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Shuang Yan
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jingnan Luo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China.
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32
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Wang P, Li G, Li G, Yuan S, Wang C, Xie Y, Guo T, Kang G, Wang D. TaPHT1;9-4B and its transcriptional regulator TaMYB4-7D contribute to phosphate uptake and plant growth in bread wheat. THE NEW PHYTOLOGIST 2021; 231:1968-1983. [PMID: 34096624 PMCID: PMC8489284 DOI: 10.1111/nph.17534] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/25/2021] [Indexed: 05/19/2023]
Abstract
Efficient phosphate (Pi) uptake and utilisation are essential for promoting crop yield. However, the underlying molecular mechanism is still poorly understood in complex crop species such as hexaploid wheat. Here we report that TaPHT1;9-4B and its transcriptional regulator TaMYB4-7D function in Pi acquisition, translocation and plant growth in bread wheat. TaPHT1;9-4B, a high-affinity Pi transporter highly upregulated in roots by Pi deficiency, was identified using quantitative proteomics. Disruption of TaPHT1;9-4B function by BSMV-VIGS or CRISPR editing impaired wheat tolerance to Pi deprivation, whereas transgenic expression of TaPHT1;9-4B in rice improved Pi uptake and plant growth. Using yeast-one-hybrid assay, we isolated TaMYB4-7D, a R2R3 MYB transcription factor that could activate TaPHT1;9-4B expression by binding to its promoter. Silencing TaMYB4-7D decreased TaPHT1;9-4B expression, Pi uptake and plant growth. Four promoter haplotypes were identified for TaPHT1;9-4B, with Hap3 showing significant positive associations with TaPHT1;9-4B transcript level, growth performance and phosphorus (P) content in wheat plants. A functional marker was therefore developed for tagging Hap3. Collectively, our data shed new light on the molecular mechanism controlling Pi acquisition and utilisation in bread wheat. TaPHT1;9-4B and TaMYB4-7D may aid further research towards the development of P efficient crop cultivars.
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Affiliation(s)
- Pengfei Wang
- The National Engineering Research Center for Wheat, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, 450046, China
| | - Gezi Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guangwei Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shasha Yuan
- The National Engineering Research Center for Wheat, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, 450046, China
| | - Chenyang Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingxin Xie
- The National Engineering Research Center for Wheat, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, 450046, China
| | - Tiancai Guo
- The National Engineering Research Center for Wheat, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, 450046, China
| | - Guozhang Kang
- The National Engineering Research Center for Wheat, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, 450046, China
- The State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Daowen Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
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Zheng M, Lin J, Liu X, Chu W, Li J, Gao Y, An K, Song W, Xin M, Yao Y, Peng H, Ni Z, Sun Q, Hu Z. Histone acetyltransferase TaHAG1 acts as a crucial regulator to strengthen salt tolerance of hexaploid wheat. PLANT PHYSIOLOGY 2021; 186:1951-1969. [PMID: 33890670 PMCID: PMC8331135 DOI: 10.1093/plphys/kiab187] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/08/2021] [Indexed: 05/22/2023]
Abstract
Polyploidy occurs prevalently and plays an important role during plant speciation and evolution. This phenomenon suggests polyploidy could develop novel features that enable them to adapt wider range of environmental conditions compared with diploid progenitors. Bread wheat (Triticum aestivum L., BBAADD) is a typical allohexaploid species and generally exhibits greater salt tolerance than its tetraploid wheat progenitor (BBAA). However, little is known about the underlying molecular basis and the regulatory pathway of this trait. Here, we show that the histone acetyltransferase TaHAG1 acts as a crucial regulator to strengthen salt tolerance of hexaploid wheat. Salinity-induced TaHAG1 expression was associated with tolerance variation in polyploidy wheat. Overexpression, silencing, and CRISPR-mediated knockout of TaHAG1 validated the role of TaHAG1 in salinity tolerance of wheat. TaHAG1 contributed to salt tolerance by modulating reactive oxygen species (ROS) production and signal specificity. Moreover, TaHAG1 directly targeted a subset of genes that are responsible for hydrogen peroxide production, and enrichment of TaHAG1 triggered increased H3 acetylation and transcriptional upregulation of these loci under salt stress. In addition, we found the salinity-induced TaHAG1-mediated ROS production pathway is involved in salt tolerance difference of wheat accessions with varying ploidy. Our findings provide insight into the molecular mechanism of how an epigenetic regulatory factor facilitates adaptability of polyploidy wheat and highlights this epigenetic modulator as a strategy for salt tolerance breeding in bread wheat.
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Affiliation(s)
- Mei Zheng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Jingchen Lin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Xingbei Liu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Wei Chu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Jinpeng Li
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yujiao Gao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Kexin An
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- Author for communication:
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Righetti L, Bhandari DR, Rolli E, Tortorella S, Bruni R, Dall’Asta C, Spengler B. Mycotoxin Uptake in Wheat - Eavesdropping Fusarium Presence for Priming Plant Defenses or a Trojan Horse to Weaken Them? FRONTIERS IN PLANT SCIENCE 2021; 12:711389. [PMID: 34381485 PMCID: PMC8350570 DOI: 10.3389/fpls.2021.711389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Fusarium mycotoxins represent a major threat for cereal crops and food safety. While previous investigations have described plant biotransforming properties on mycotoxins or metabolic relapses of fungal infections in plants, so far, the potential consequences of radical exposure in healthy crops are mostly unknown. Therefore, we aimed at evaluating whether the exposure to mycotoxins, deoxynivalenol (DON) and zearalenone (ZEN), at the plant-soil interface may be considered a form of biotic stress capable of inducing priming or a potential initiation of fungal attack. To address this, we used atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging to investigate the activation or the inhibition of specific biosynthetic pathways and in situ localization of primary and secondary metabolites in wheat. According to our untargeted metabolomics investigation, the translocation of plant defense metabolites (i.e., hydroxycinnamic acid amide and flavones) follows the mycotoxin accumulation organs, which is the root for ZEN-treated plantlet and culm for DON-treated sample, suggesting a local "defense-on-demand response." Therefore, it can be hypothesized that DON and ZEN are involved in the eavesdropping of Fusarium presence in soil and that wheat response based on secondary metabolites may operate on multiple organs with a potential interplay that involves masked mycotoxins.
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Affiliation(s)
- Laura Righetti
- Department of Food and Drug, University of Parma, Parma, Italy
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Dhaka Ram Bhandari
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Enrico Rolli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Renato Bruni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
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35
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Ye X, Hu H, Zhou H, Jiang Y, Gao S, Yuan Z, Stiller J, Li C, Chen G, Liu Y, Wei Y, Zheng YL, Wang YG, Liu C. Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids. Genome 2021; 64:847-856. [PMID: 33661713 DOI: 10.1139/gen-2020-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.
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Affiliation(s)
- Xueling Ye
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Haiyan Hu
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Hong Zhou
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yunfeng Jiang
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Shang Gao
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Zhongwei Yuan
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiri Stiller
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Chengwei Li
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Gan Wang
- Science and Engineering Facility, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
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Lu Y, Zhao P, Zhang A, Ma L, Xu S, Wang X. Alternative Splicing Diversified the Heat Response and Evolutionary Strategy of Conserved Heat Shock Protein 90s in Hexaploid Wheat ( Triticum aestivum L.). Front Genet 2020; 11:577897. [PMID: 33329715 PMCID: PMC7729002 DOI: 10.3389/fgene.2020.577897] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/29/2020] [Indexed: 11/13/2022] Open
Abstract
Crops are challenged by the increasing high temperature. Heat shock protein 90 (HSP90), a molecular chaperone, plays a critical role in the heat response in plants. However, the evolutionary conservation and divergence of HSP90s homeologs in polyploidy crops are largely unknown. Using the newly released hexaploid wheat reference sequence, we identified 18 TaHSP90s that are evenly distributed as homeologous genes among three wheat subgenomes, and were highly conserved in terms of sequence identity and gene structure among homeologs. Intensive time-course transcriptomes showed uniform expression and transcriptional response profiles among the three TaHSP90 homeologs. Based on the comprehensive isoforms generated by combining full-length single-molecule sequencing and Illumina short read sequencing, 126 isoforms, including 90 newly identified isoforms of TaHSP90s, were identified, and each TaHSP90 generated one to three major isoforms. Intriguingly, the numbers and the splicing modes of the major isoforms generated by three TaHSP90 homeologs were obviously different. Furthermore, the quantified expression profiles of the major isoforms generated by three TaHSP90 homeologs are also distinctly varied, exhibiting differential alternative splicing (AS) responses of homeologs. Our results showed that the AS diversified the heat response of the conserved TaHSP90s and provided a new perspective for understanding about functional conservation and divergence of homologous genes.
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Affiliation(s)
- Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Aihua Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lingjian Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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Lee JS, Adams KL. Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress. THE PLANT GENOME 2020; 13:e20057. [PMID: 33043636 DOI: 10.1002/tpg2.20057] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/26/2020] [Accepted: 08/20/2020] [Indexed: 05/21/2023]
Abstract
Polyploidy has been a prevalent process during plant evolution and it has made a major impact on the structure and evolution of plant genomes. Many important crop plants are polyploid. There is considerable interest in expression patterns of duplicated genes in polyploids. Alternative splicing (AS) is a fundamental aspect of gene expression that produces multiple final transcript types from a single type of mRNAs. The effects of abiotic stress conditions on AS in polyploids has received little attention. We conducted a global transcriptome analysis of Brassica napus, an allotetraploid derived from B. rapa (AT ) and B. oleracea (CT ), by RNA-Seq of plants subjected to cold, heat, and drought stress treatments. Analyses of 27,360 pairs of duplicated genes revealed overall AT subgenome biases in gene expression and CT subgenome biases in the extent of alternative splicing under all three stress treatments. More genes increased in expression than decreased in response to the stresses. Negative correlations were found between expression levels and AS frequency for each type of AS. Cold stress produced the greatest changes in gene expression and AS. Cold-induced AS changes were more likely to be shared with those generated by drought than by heat stress. We used homeologs of FLC and CCA1 as case studies to show the dynamics of how duplicates in a polyploid respond to cold stress. Our results suggest that divergence in gene expression and AS patterns between duplicated genes may increase the flexibility of polyploids when responding to abiotic stressors.
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Affiliation(s)
- Joon Seon Lee
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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Wang M, Gong J, Bhullar NK. Iron deficiency triggered transcriptome changes in bread wheat. Comput Struct Biotechnol J 2020; 18:2709-2722. [PMID: 33101609 PMCID: PMC7550799 DOI: 10.1016/j.csbj.2020.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022] Open
Abstract
A series of complex transport, storage and regulation mechanisms control iron metabolism and thereby maintain iron homeostasis in plants. Despite several studies on iron deficiency responses in different plant species, these mechanisms remain unclear in the allohexaploid wheat, which is the most widely cultivated commercial crop. We used RNA sequencing to reveal transcriptomic changes in the wheat flag leaves and roots, when subjected to iron limited conditions. We identified 5969 and 2591 differentially expressed genes (DEGs) in the flag leaves and roots, respectively. Genes involved in the synthesis of iron ligands i.e., nicotianamine (NA) and deoxymugineic acid (DMA) were significantly up-regulated during iron deficiency. In total, 337 and 635 genes encoding transporters exhibited altered expression in roots and flag leaves, respectively. Several genes related to MAJOR FACILITATOR SUPERFAMILY (MFS), ATP-BINDING CASSETTE (ABC) transporter superfamily, NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN (NRAMP) family and OLIGOPEPTIDE TRANSPORTER (OPT) family were regulated, indicating their important roles in combating iron deficiency stress. Among the regulatory factors, the genes encoding for transcription factors of BASIC HELIX-LOOP-HELIX (bHLH) family were highly up-regulated in both roots and the flag leaves. The jasmonate biosynthesis pathway was significantly altered but with notable expression differences between roots and flag leaves. Homoeologs expression and induction bias analysis revealed subgenome specific differential expression. Our findings provide an integrated overview on regulated molecular processes in response to iron deficiency stress in wheat. This information could potentially serve as a guideline for breeding iron deficiency stress tolerant crops as well as for designing appropriate wheat iron biofortification strategies.
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Key Words
- 3-HMA, 3-hydroxymugineic acid
- ABC, ATP-BINDING CASSETTE
- ACC, 1-aminocyclopropane-1-carboxylate
- AEC, AUXIN EFFLUX CARRIER
- AOC, ALLENE OXIDE CYCLASE
- AOS, ALLENE OXIDE SYNTHASE
- AQP, AQUAPORIN
- AVA, avenic acid
- DEGs, differentially expressed genes
- DMA, deoxymugineic acid
- DMAS, DEOXYMUGINEIC ACID SYNTHASE
- DPA, days post anthesis
- ERF, ETHYLENE-RESPONSIVE FACTOR
- FAD, FATTY ACID DESATURASE
- FDR, false discovery rate
- FIT, FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
- FRO, FERRIC REDUCTASE OXIDASE
- GCN, gene co-expression network
- GO, Gene ontology
- GSH, GLUTATHIONE
- HC, high confidence
- HMA, HEAVY METAL-ASSOCIATED
- IDE, iron deficiency-responsive cis-acting element
- IDEF, IDE BINDING FACTOR
- IHW, independent hypothesis weighting
- ILR3, IAA‐LEUCINE RESISTANT3
- IREG/FPN, IRON REGULATED PROTEIN/FERROPORTIN
- IRT1, IRON-REGULATED TRANSPORTER
- Iron deficiency
- Iron, Fe
- JAs, jasmonates
- JMT, JASMONATE O-METHYLTRANSFERASE
- KAT, 3-KETOACYL-COA THIOLASE
- LOX, LIPOXYGENASE
- MA, mugineic acid
- MATE, MULTI ANTIMICROBIAL EXTRUSION PROTEIN
- MFS, MAJOR FACILITATOR SUPERFAMILY
- MRP, MULTIDRUG RESISTANCE PROTEIN
- MT, METALLOTHIONEIN
- NA, nicotianamine
- NAAT, NICOTIANAMINE AMINOTRANSFERASE
- NAC, NO APICAL MERISTEM (NAM)/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF)/CUP-SHAPED COTYLEDON (CUC)
- NAS, NICOTIANAMINE SYNTHASE
- NRAMP, NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN
- NRT1/PTR, NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER
- OPCL, 4-COUMARATE COA LIGASE
- OPR, 12-OXOPHYTODIENOATE REDUCTASE
- OPT, OLIGOPEPTIDE TRANSPORTER
- PDR, PLEIOTROPIC DRUG RESISTANCE
- PLA, PHOSPHOLIPASE A1
- PRI, POSITIVE REGULATOR OF IRON DEFICIENCY RESPONSE
- PSs, phytosiderophores
- PT, peptide transport
- PYE, POPEYE
- RNA sequencing
- SAM, S-adenosyl-L-methionine
- SAMS, S-ADENOSYL-L-METHIONINE SYNTHETASE
- SLC40A1, SOLUTE CARRIER FAMILY 40 MEMBER 1
- SWEET, SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS
- TOM, TRANSPORTER OF MUGINEIC ACID
- Transcriptomic profiles
- VIT, VACUOLAR IRON TRANSPORTER
- Wheat
- YSL, YELLOW STRIPE LIKE
- ZIFL, ZINC INDUCED FACILITATOR-LIKE
- ZIP, ZINC/IRON PERMEASE
- bHLH, BASIC HELIX-LOOP-HELIX
- bZIP, BASIC LEUCINE ZIPPER
- epiHDMA, 3-epihydroxy-2′-deoxymugineic acid
- epiHMA, 3-epihydroxymugineic acid
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Affiliation(s)
- Meng Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland
| | - Jiazhen Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Navreet K. Bhullar
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland
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Benbow HR, Brennan CJ, Zhou B, Christodoulou T, Berry S, Uauy C, Mullins E, Doohan FM. Insights into the resistance of a synthetically-derived wheat to Septoria tritici blotch disease: less is more. BMC PLANT BIOLOGY 2020; 20:407. [PMID: 32883202 PMCID: PMC7469286 DOI: 10.1186/s12870-020-02612-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Little is known about the initial, symptomless (latent) phase of the devastating wheat disease Septoria tritici blotch. However, speculations as to its impact on fungal success and disease severity in the field have suggested that a long latent phase is beneficial to the host and can reduce inoculum build up in the field over a growing season. The winter wheat cultivar Stigg is derived from a synthetic hexaploid wheat and contains introgressions from wild tetraploid wheat Triticum turgidum subsp. dicoccoides, which contribute to cv. Stigg's exceptional STB resistance, hallmarked by a long latent phase. We compared the early transcriptomic response to Zymoseptoria tritici of cv. Stigg to a susceptible wheat cultivar, to elucidate the mechanisms of and differences in pathogen recognition and disease response in these two hosts. RESULTS The STB-susceptible cultivar Longbow responds to Z. tritici infection with a stress response, including activation of hormone-responsive transcription factors, post translational modifications, and response to oxidative stress. The activation of key genes associated with these pathways in cv. Longbow was independently observed in a second susceptible wheat cultivar based on an independent gene expression study. By comparison, cv. Stigg is apathetic in response to STB, and appears to fail to activate a range of defence pathways that cv. Longbow employs. Stigg also displays some evidence of sub-genome bias in its response to Z. tritici infection, whereas the susceptible cv. Longbow shows even distribution of Z. tritici responsive genes across the three wheat sub-genomes. CONCLUSIONS We identify a suite of disease response genes that are involved in early pathogen response in susceptible wheat cultivars that may ultimately lead to susceptibility. In comparison, we hypothesise that rather than an active defence response to stave off disease progression, cv. Stigg's defence strategy is molecular lethargy, or a lower-amplitude of pathogen recognition that may stem from cv. Stigg's wild wheat-derived ancestry. Overall, we present insights into cv. Stigg's exceptional resistance to STB, and present key biological processes for further characterisation in this pathosystem.
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Affiliation(s)
- Harriet R Benbow
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Ciarán J Brennan
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Thalia Christodoulou
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Simon Berry
- Limagrain UK Ltd, Windmill Avenue, Woolpit, Suffolk, IP30 9UP, UK
| | | | - Ewen Mullins
- Teagasc Crops Research, Oak Park, Co. Carlow, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland.
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland.
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland.
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40
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Inoue K, Takahagi K, Kouzai Y, Koda S, Shimizu M, Uehara-Yamaguchi Y, Nakayama R, Kita T, Onda Y, Nomura T, Matsui H, Nagaki K, Nishii R, Mochida K. Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy. NAR Genom Bioinform 2020; 2:lqaa067. [PMID: 33575616 PMCID: PMC7671347 DOI: 10.1093/nargab/lqaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/15/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative Brachypodium cytotypes, including the allotetraploid Brachypodium hybridum and its diploid progenitors Brachypodium distachyon and Brachypodium stacei. We also artificially induced an autotetraploid B. distachyon. We identified patterns of homoeolog expression bias (HEB) across Brachypodium cytotypes and time-dependent gain and loss of HEB in B. hybridum. Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in B. hybridum relative to B. distachyon and B. stacei, suggesting diurnal synchronization of homoeolog expression in B. hybridum. Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in Brachypodium, and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy.
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Affiliation(s)
- Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yusuke Kouzai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Risa Nakayama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshie Kita
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hidetoshi Matsui
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
| | - Ryuei Nishii
- School of Information and Data Science, Nagasaki University, Nagasaki, 852-8131, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
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41
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Gholizadeh F, Mirzaghaderi G. Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response. PLoS One 2020; 15:e0236226. [PMID: 32866160 PMCID: PMC7458318 DOI: 10.1371/journal.pone.0236226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/08/2020] [Indexed: 11/18/2022] Open
Abstract
Amine oxidases (AOs) including copper containing amine oxidases (CuAOs) and FAD-dependent polyamine oxidases (PAOs) are associated with polyamine catabolism in the peroxisome, apoplast and cytoplasm and play an essential role in growth and developmental processes and response to biotic and abiotic stresses. Here, we identified PAO genes in common wheat (Triticum aestivum), T. urartu and Aegilops tauschii and reported the genome organization, evolutionary features and expression profiles of the wheat PAO genes (TaPAO). Expression analysis using publicly available RNASeq data showed that TaPAO genes are expressed redundantly in various tissues and developmental stages. A large percentage of TaPAOs respond significantly to abiotic stresses, especially temperature (i.e. heat and cold stress). Some TaPAOs were also involved in response to other stresses such as powdery mildew, stripe rust and Fusarium infection. Overall, TaPAOs may have various functions in stress tolerances responses, and play vital roles in different tissues and developmental stages. Our results provided a reference for further functional investigation of TaPAO proteins.
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Affiliation(s)
- Fatemeh Gholizadeh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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42
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Li M, Wang R, Wu X, Wang J. Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus. BMC Genomics 2020; 21:330. [PMID: 32349676 PMCID: PMC7191788 DOI: 10.1186/s12864-020-6747-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/21/2020] [Indexed: 01/01/2023] Open
Abstract
Background Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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43
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Batyrshina ZS, Yaakov B, Shavit R, Singh A, Tzin V. Comparative transcriptomic and metabolic analysis of wild and domesticated wheat genotypes reveals differences in chemical and physical defense responses against aphids. BMC PLANT BIOLOGY 2020; 20:19. [PMID: 31931716 PMCID: PMC6958765 DOI: 10.1186/s12870-019-2214-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/22/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Young wheat plants are continuously exposed to herbivorous insect attack. To reduce insect damage and maintain their growth, plants evolved different defense mechanisms, including the biosynthesis of deterrent compounds named benzoxazinoids, and/or trichome formation that provides physical barriers. It is unclear whether both of these mechanisms are equally critical in providing an efficient defense for wheat seedlings against aphids-an economically costly pest in cereal production. RESULTS In this study, we compared the transcriptome, metabolome, benzoxazinoids, and trichome density of three selected wheat genotypes, with a focus on differences related to defense mechanisms. We chose diverse wheat genotypes: two tetraploid wheat genotypes, domesticated durum 'Svevo' and wild emmer 'Zavitan,' and one hexaploid bread wheat, 'Chinese Spring.' The full transcriptomic analysis revealed a major difference between the three genotypes, while the clustering of significantly different genes suggested a higher similarity between the two domesticated wheats than between either and the wild wheat. A pathway enrichment analysis indicated that the genes associated with primary metabolism, as well as the pathways associated with defense such as phytohormones and specialized metabolites, were different between the three genotypes. Measurement of benzoxazinoid levels at the three time points (11, 15, and 18 days after germination) revealed high levels in the two domesticated genotypes, while in wild emmer wheat, they were below detection level. In contrast to the benzoxazinoid levels, the trichome density was dramatically higher in the wild emmer than in the domesticated wheat. Lastly, we tested the bird cherry-oat aphid's (Rhopalosiphum padi) performance and found that Chinese Spring is more resistant than the tetraploid genotypes. CONCLUSIONS Our results show that benzoxazinoids play a more significant defensive role than trichomes. Differences between the abundance of defense mechanisms in the wild and domesticated plants were observed in which wild emmer possesses high physical defenses while the domesticated wheat genotypes have high chemical defenses. These findings provide new insights into the defense adaptations of wheat plants against aphids.
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Affiliation(s)
- Zhaniya S Batyrshina
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreseht Ben Gurion, Beer-Sheva, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreseht Ben Gurion, Beer-Sheva, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreseht Ben Gurion, Beer-Sheva, Israel
| | - Anuradha Singh
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreseht Ben Gurion, Beer-Sheva, Israel
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreseht Ben Gurion, Beer-Sheva, Israel.
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Sub-Genome Polyploidization Effects on Metabolomic Signatures in Triploid Hybrids of Populus. FORESTS 2019. [DOI: 10.3390/f10121091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Allopolyploids are known to have superior advantages such as high growth speed. Triploids have even greater heterozygosity, explaining more phenotypic variance than 2n hybrid F1 and have therefore become new resources in breeding. To date, the metabolomic basis underlying polyploidization vigor remains unclear. Here, we identified and compared 235 metabolites in the shoot apical buds between multiple allo-triploid populations and parental 2n hybrid F1 in Populus via metabolome profiling using liquid chromatography–mass spectrometry (LC–MS) assays. Associations with growth vigor in three types of allo-triploid populations, namely first division restitution (FDR), second division restitution (SDR) and postmeiotic restitution (PMR) generated from doubled 2n female gametes and male gametes of 2n hybrid, were also investigated. Each allo-triploid population has different sub-genome duplicated. Major metabolomes were amino acids, secondary metabolism associated, and carbohydrates. We mapped 181 metabolites into known metabolism pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Ten compounds, i.e., fructose 1,6-diphosphate and xylulose, were more abundant in all allo-triploids than the 2n hybrid. Principal component analysis revealed the abundance of metabolites fell into distinct clusters corresponding to ploidy composition. Heterozygosity in triploids mainly effected the contents of carbohydrates and secondary metabolites rather than lipids. Comparisons between subgroups with different growth rates revealed some carbohydrates and secondary metabolites of flavonoids were positively associated with gene expression and the high growth vigor. The results provided an informative metabolomic basis for factors conferring growth vigor in polyploid Populus.
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Kaur G, Shukla V, Kumar A, Kaur M, Goel P, Singh P, Shukla A, Meena V, Kaur J, Singh J, Mantri S, Rouached H, Pandey AK. Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6141-6161. [PMID: 31738431 PMCID: PMC6859736 DOI: 10.1093/jxb/erz358] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/24/2019] [Indexed: 05/05/2023]
Abstract
Iron (Fe) is an essential micronutrient for all organisms. In crop plants, Fe deficiency can decrease crop yield significantly; however, our current understanding of how major crops respond to Fe deficiency remains limited. Herein, the effect of Fe deprivation at both the transcriptomic and metabolic level in hexaploid wheat was investigated. Genome-wide gene expression reprogramming was observed in wheat roots subjected to Fe starvation, with a total of 5854 genes differentially expressed. Homoeologue and subgenome-specific analysis unveiled the induction-biased contribution from the A and B genomes. In general, the predominance of genes coding for nicotianamine synthase, yellow stripe-like transporters, metal transporters, ABC transporters, and zinc-induced facilitator-like protein was noted. Expression of genes related to the Strategy II mode of Fe uptake was also predominant. Our transcriptomic data were in agreement with the GC-MS analysis that showed the enhanced accumulation of various metabolites such as fumarate, malonate, succinate, and xylofuranose, which could be contributing to Fe mobilization. Interestingly, Fe starvation leads to a significant temporal increase of glutathione S-transferase at both the transcriptional level and enzymatic activity level, which indicates the involvement of glutathione in response to Fe stress in wheat roots. Taken together, our result provides new insight into the wheat response to Fe starvation at the molecular level and lays the foundation to design new strategies for the improvement of Fe nutrition in crops.
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Affiliation(s)
- Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vishnu Shukla
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
- University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Anil Kumar
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Mandeep Kaur
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Parul Goel
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
| | - Palvinder Singh
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
| | - Anuj Shukla
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
| | - Varsha Meena
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
| | - Jaspreet Kaur
- University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Jagtar Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Shrikant Mantri
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
| | - Hatem Rouached
- BPMP, Université de Montpellier, INRA, CNRS, Montpellier SupAgro, Montpellier, France
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Mohali, Punjab, India
- Correspondence: or
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Baldwin T, Baldwin S, Klos K, Bregitzer P, Marshall J. Deletion of the benzoxazinoid detoxification gene NAT1 in Fusarium graminearum reduces deoxynivalenol in spring wheat. PLoS One 2019; 14:e0214230. [PMID: 31299046 PMCID: PMC6625701 DOI: 10.1371/journal.pone.0214230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 03/08/2019] [Indexed: 12/25/2022] Open
Abstract
Benzoxazinoid (Bx) metabolites produced by wheat and other members of the Poaceae have activity against Fusarium sp. that cause cereal diseases including Fusarium head blight (FHB) on wheat and barley. Certain Bx metabolites can be detoxified by Fusarium sp. with the arylamine N-acetyltransferase NAT1. Investigation of this pathway may reveal strategies for increasing FHB resistance, such as selection for higher levels of Bx metabolites within existing germplasm and/or engineering fungal susceptibility via host induced silencing of NAT1. We assessed the reactions of fifteen wheat cultivars or breeding lines adapted to the Northwestern United States to infection with F. graminearum Δnat1 mutants that should be sensitive to Bx metabolites. Significant differences were noted in disease severity and deoxynivalenol (DON) among the cultivars 21 d after inoculation with either mutant or wildtype (PH1) strains. Mutant vs. wildtype strains did not result in significant variation for infection severity (as measured by % infected florets), but inoculation with Δnat1 mutants vs. wildtype resulted in significantly lower DON concentrations in mature kernels (p < 0.0001). Of the cultivars tested, HRS3419 was the most resistant cultivar to PH1 (severity = 62%, DON = 45 ppm) and Δnat1 mutants (severity = 61%, DON = 30 ppm). The cultivar most susceptible to infection was Kelse with PH1 (severity = 100%, DON = 292 ppm) and Δnat1 mutants (severity = 100%, DON = 158 ppm). We hypothesized that sub-lethal Bx metabolite levels may suppress DON production in F. graminearum Δnat1 mutants. In vitro assays of Bx metabolites BOA, MBOA, and DIMBOA at 30 μM did not affect growth, but did reduce DON production by Δnat1 and PH1. Although the levels of Bx metabolites are likely too low in the wheat cultivars we tested to suppress FHB, higher levels of Bx metabolites may contribute towards reductions in DON and FHB.
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Affiliation(s)
- Thomas Baldwin
- National Small Grains Germplasm Research Facility, USDA-ARS, Aberdeen, Idaho, United States of America
- * E-mail: (TB); (JM)
| | - Suzette Baldwin
- Department of Plant, Soil, and Entomological Sciences University of Idaho Research and Extension, Idaho Falls, ID, United States of America
| | - Kathy Klos
- National Small Grains Germplasm Research Facility, USDA-ARS, Aberdeen, Idaho, United States of America
| | - Phil Bregitzer
- National Small Grains Germplasm Research Facility, USDA-ARS, Aberdeen, Idaho, United States of America
| | - Juliet Marshall
- Department of Plant, Soil, and Entomological Sciences University of Idaho Research and Extension, Idaho Falls, ID, United States of America
- * E-mail: (TB); (JM)
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Wang X, Chen S, Shi X, Liu D, Zhao P, Lu Y, Cheng Y, Liu Z, Nie X, Song W, Sun Q, Xu S, Ma C. Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1015-1032. [PMID: 30891832 PMCID: PMC6850178 DOI: 10.1111/tpj.14299] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/17/2019] [Accepted: 02/19/2019] [Indexed: 05/19/2023]
Abstract
Wheat (Triticum aestivum L.), a globally important crop, is challenged by increasing temperatures (heat stress, HS). However its polyploid nature, the incompleteness of its genome sequences and annotation, the lack of comprehensive HS-responsive transcriptomes and the unexplored heat sensing and signaling of wheat hinder our full understanding of its adaptations to HS. The recently released genome sequences of wheat, as well as emerging single-molecular sequencing technologies, provide an opportunity to thoroughly investigate the molecular mechanisms of the wheat response to HS. We generated a high-resolution spatio-temporal transcriptome map of wheat flag leaves and filling grain under HS at 0 min, 5 min, 10 min, 30 min, 1 h and 4 h by combining full-length single-molecular sequencing and Illumina short reads sequencing. This hybrid sequencing newly discovered 4947 loci and 70 285 transcripts, generating the comprehensive and dynamic list of HS-responsive full-length transcripts and complementing the recently released wheat reference genome. Large-scale analysis revealed a global landscape of heat adaptations, uncovering unexpected rapid heat sensing and signaling, significant changes of more than half of HS-responsive genes within 30 min, heat shock factor-dependent and -independent heat signaling, and metabolic alterations in early HS-responses. Integrated analysis also demonstrated the differential responses and partitioned functions between organs and subgenomes, and suggested a differential pattern of transcriptional and alternative splicing regulation in the HS response. This study provided comprehensive data for dissecting molecular mechanisms of early HS responses in wheat and highlighted the genomic plasticity and evolutionary divergence of polyploidy wheat.
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Affiliation(s)
- Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Siyuan Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Life SciencesNorthwest A&F UniversityYangling712100ShaanxiChina
- Center of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Danni Liu
- FrasergenWuhan East Lake High‐tech ZoneWuhan430075China
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Yanbing Cheng
- FrasergenWuhan East Lake High‐tech ZoneWuhan430075China
| | - Zhenshan Liu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Weining Song
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Qixin Sun
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
- Department of Plant Genetics & BreedingChina Agricultural UniversityYuanmingyuan Xi Road No. 2, Haidian DistrictBeijing100193China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Life SciencesNorthwest A&F UniversityYangling712100ShaanxiChina
- Center of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYangling712100ShaanxiChina
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48
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Cenci A, Hueber Y, Zorrilla-Fontanesi Y, van Wesemael J, Kissel E, Gislard M, Sardos J, Swennen R, Roux N, Carpentier SC, Rouard M. Effect of paleopolyploidy and allopolyploidy on gene expression in banana. BMC Genomics 2019; 20:244. [PMID: 30917780 PMCID: PMC6438041 DOI: 10.1186/s12864-019-5618-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
Background Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B genome, respectively). Unresolved hybridizations finally led to banana diversification into several autotriploid (AAA) and allotriploid cultivars (AAB and ABB). Using transcriptomic data, we investigated the impact of the genome structure on gene expression patterns in roots of 12 different triploid genotypes covering AAA, AAB and ABB subgenome constitutions. Results We demonstrate that (i) there are different genome structures, (ii) expression patterns go beyond the predicted genomic groups, and (iii) the proportion of the B genome influences the gene expression. The presence of the B genome is associated with a higher expression of genes involved in flavonoid biosynthesis, fatty acid metabolism, amino sugar and nucleotide sugar metabolism and oxidative phosphorylation. There are cultivar-specific chromosome regions with biased B:A gene expression ratios that demonstrate homoeologous exchanges (HE) between A and B sub-genomes. In two cultivars, aneuploidy was detected. We identified 3674 genes with a different expression level between allotriploid and autotriploid with ~ 57% having recently duplicated copies (paralogous). We propose a Paralog Inclusive Expression (PIE) analysis that appears to be suitable for genomes still in a downsizing and fractionation process following whole genome duplications. Our approach allows highlighting the genes with a maximum likelihood to affect the plant phenotype. Conclusions This study on banana is a good case to investigate the effects of alloploidy in crops. We conclude that allopolyploidy triggered changes in the genome structure of a crop and it clearly influences the gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5618-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France.
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Yasmin Zorrilla-Fontanesi
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Jelle van Wesemael
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Ewaut Kissel
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
| | - Marie Gislard
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, F-34396, Montpellier, France
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium.,Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium.,International Institute of Tropical Agriculture. c/o The Nelson Mandela African Institution for Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France
| | - Sebastien Christian Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium.,Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 05, France.
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49
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Pigolev AV, Miroshnichenko DN, Pushin AS, Terentyev VV, Boutanayev AM, Dolgov SV, Savchenko TV. Overexpression of Arabidopsis OPR3 in Hexaploid Wheat ( Triticum aestivum L.) Alters Plant Development and Freezing Tolerance. Int J Mol Sci 2018; 19:E3989. [PMID: 30544968 PMCID: PMC6320827 DOI: 10.3390/ijms19123989] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 01/09/2023] Open
Abstract
Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid (JA) in wheat growth, development, and responses to environmental stresses, we have generated transgenic bread wheat plants overexpressing Arabidopsis 12-OXOPHYTODIENOATE REDUCTASE 3 (AtOPR3), one of the key genes of the JA biosynthesis pathway. Analysis of transgenic plants showed that AtOPR3 overexpression affects wheat development, including germination, growth, flowering time, senescence, and alters tolerance to environmental stresses. Transgenic wheat plants with high AtOPR3 expression levels have increased basal levels of JA, and up-regulated expression of ALLENE OXIDE SYNTHASE, a jasmonate biosynthesis pathway gene that is known to be regulated by a positive feedback loop that maintains and boosts JA levels. Transgenic wheat plants with high AtOPR3 expression levels are characterized by delayed germination, slower growth, late flowering and senescence, and improved tolerance to short-term freezing. The work demonstrates that genetic modification of the jasmonate pathway is a suitable tool for the modulation of developmental traits and stress responses in wheat.
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Affiliation(s)
- Alexey V Pigolev
- Institute of Basic Biological Problems RAS, Pushchino 142290, Russia.
| | - Dmitry N Miroshnichenko
- Institute of Basic Biological Problems RAS, Pushchino 142290, Russia.
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino 142290, Russia.
| | - Alexander S Pushin
- Institute of Basic Biological Problems RAS, Pushchino 142290, Russia.
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino 142290, Russia.
| | | | | | - Sergey V Dolgov
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino 142290, Russia.
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50
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Blischak PD, Mabry ME, Conant GC, Pires JC. Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-121415-032302] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene and network dosage, and changes in gene expression. In this review, we discuss the prevalence of polyploidy across the tree of life, followed by an overview of studies investigating genome evolution and gene expression. We then provide an overview of methods in network biology, phylogenomics, and population genomics that are critical for advancing our understanding of evolution post-WGD, highlighting the need for models that can accommodate polyploids. Finally, we close with a brief note on the importance of random processes in the evolution of polyploids with respect to neutral versus selective forces, ancestral polymorphisms, and the formation of autopolyploids versus allopolyploids.
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Affiliation(s)
- Paul D. Blischak
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Makenzie E. Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Gavin C. Conant
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Current affiliation: Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA
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